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Chandrasegaran S, Klose JW, Pukala TL. Unraveling DNA Triplex Assembly: Mass Spectrometric Investigation of Modified Triplex Forming Oligonucleotides for Enhanced Gene Targeting. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024. [PMID: 39088835 DOI: 10.1021/jasms.4c00070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/03/2024]
Abstract
Deoxyribonucleic acid triplexes have potential roles in a range of biological processes involving gene and transcriptional regulation. A major challenge in exploiting the formation of these higher-order structures to target genes in vivo is their low stability, which is dependent on many factors including the length and composition of bases in the sequence. Here, different DNA base modifications have been explored, primarily using native mass spectrometry, in efforts to enable stronger binding between the triplex forming oligonucleotide (TFO) and duplex target sites. These modifications can also be used to overcome pyrimidine interruptions in the duplex sequence in promoter regions of genomes, to expand triplex target sequences for antigene therapies. Using model sequences with a single pyrimidine interruption, triplex forming oligonucleotides containing locked nucleic acid base modifications were shown to have a higher triplex binding propensity than DNA-only and dSpacer-containing TFOs. However, the triplex forming ability of these systems was limited by the competitive formation of multiple higher order assemblies. Triplex forming sequences that correspond to specific gene targets from the Pseudomonas aeruginosa genome were also investigated, with LNA-containing TFOs the only variant able to form triplex using these sequences. This work indicates the advantages of utilizing synthetically modified TFOs to form triplex assemblies in vivo for potential therapeutic applications and highlights the advantages of native mass spectrometry for the study of their formation.
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Affiliation(s)
| | - Jack W Klose
- Discipline of Chemistry, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Tara L Pukala
- Discipline of Chemistry, The University of Adelaide, Adelaide, South Australia 5005, Australia
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Koralewska N, Corradi E, Milewski MC, Masante L, Szczepanska A, Kierzek R, Figlerowicz M, Baudet ML, Kurzynska-Kokorniak A. Short 2'-O-methyl/LNA oligomers as highly-selective inhibitors of miRNA production in vitro and in vivo. Nucleic Acids Res 2024; 52:5804-5824. [PMID: 38676942 PMCID: PMC11162791 DOI: 10.1093/nar/gkae284] [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: 08/04/2023] [Revised: 03/27/2024] [Accepted: 04/04/2024] [Indexed: 04/29/2024] Open
Abstract
MicroRNAs (miRNAs) that share identical or near-identical sequences constitute miRNA families and are predicted to act redundantly. Yet recent evidence suggests that members of the same miRNA family with high sequence similarity might have different roles and that this functional divergence might be rooted in their precursors' sequence. Current knock-down strategies such as antisense oligonucleotides (ASOs) or miRNA sponges cannot distinguish between identical or near identical miRNAs originating from different precursors to allow exploring unique functions of these miRNAs. We here develop a novel strategy based on short 2'-OMe/LNA-modified oligonucleotides to selectively target specific precursor molecules and ablate the production of individual members of miRNA families in vitro and in vivo. Leveraging the highly conserved Xenopus miR-181a family as proof-of-concept, we demonstrate that 2'-OMe/LNA-ASOs targeting the apical region of pre-miRNAs achieve precursor-selective inhibition of mature miRNA-5p production. Furthermore, we extend the applicability of our approach to the human miR-16 family, illustrating its universality in targeting precursors generating identical miRNAs. Overall, our strategy enables efficient manipulation of miRNA expression, offering a powerful tool to dissect the functions of identical or highly similar miRNAs derived from different precursors within miRNA families.
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Affiliation(s)
- Natalia Koralewska
- Department of Molecular and Systems Biology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland
| | - Eloina Corradi
- Department of Cellular, Computational and Integrative Biology – CIBIO, University of Trento, Trento 38123, Italy
| | - Marek C Milewski
- Department of Molecular and Systems Biology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland
| | - Linda Masante
- Department of Cellular, Computational and Integrative Biology – CIBIO, University of Trento, Trento 38123, Italy
| | - Agnieszka Szczepanska
- Department of Ribonucleoprotein Biochemistry, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland
| | - Ryszard Kierzek
- Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland
| | - Marek Figlerowicz
- Department of Molecular and Systems Biology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland
| | - Marie-Laure Baudet
- Department of Cellular, Computational and Integrative Biology – CIBIO, University of Trento, Trento 38123, Italy
| | - Anna Kurzynska-Kokorniak
- Department of Ribonucleoprotein Biochemistry, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland
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Devyatkin VA, Shklyar AA, Fursova AZ, Rumyantseva YV, Kozhevnikova OS. Allele-specific PCR with fluorescently labeled probes: criteria for selecting primers for genotyping. Vavilovskii Zhurnal Genet Selektsii 2024; 28:351-359. [PMID: 38946890 PMCID: PMC11211992 DOI: 10.18699/vjgb-24-40] [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: 08/30/2023] [Revised: 10/04/2023] [Accepted: 10/12/2023] [Indexed: 07/02/2024] Open
Abstract
Single-nucleotide polymorphisms (SNPs) can serve as reliable markers in genetic engineering, selection, screening examinations, and other fields of science, medicine, and manufacturing. Whole-genome sequencing and genotyping by sequencing can detect SNPs with high specificity and identify novel variants. Nonetheless, in situations where the interest of researchers is individual specific loci, these methods become redundant, and their cost, the proportion of false positive and false negative results, and labor costs for sample preparation and analysis do not justify their use. Accordingly, accurate and rapid methods for genotyping individual alleles are still in demand, especially for verification of candidate polymorphisms in analyses of association with a given phenotype. One of these techniques is genotyping using TaqMan allele-specific probes (TaqMan dual labeled probes). The method consists of real-time PCR with a pair of primers and two oligonucleotide probes that are complementary to a sequence near a given locus in such a way that one probe is complementary to the wild-type allele, and the other to a mutant one. Advantages of this approach are its specificity, sensitivity, low cost, and quick results. It makes it possible to distinguish alleles in a genome with high accuracy without additional manipulations with DNA samples or PCR products; hence the popularity of this method in genetic association studies in molecular genetics and medicine. Due to advancements in technologies for the synthesis of oligonucleotides and improvements in techniques for designing primers and probes, we can expect expansion of the possibilities of this approach in terms of the diagnosis of hereditary diseases. In this article, we discuss in detail basic principles of the method, the processes that influence the result of genotyping, criteria for selecting optimal primers and probes, and the use of locked nucleic acid modifications in oligonucleotides as well as provide a protocol for the selection of primers and probes and for PCR by means of rs11121704 as an example. We hope that the presented protocol will allow research groups to independently design their own effective assays for testing for polymorphisms of interest.
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Affiliation(s)
- V A Devyatkin
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A A Shklyar
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A Zh Fursova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Yu V Rumyantseva
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - O S Kozhevnikova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Lewis JD, Salipante SJ. Development of advanced control material for reverse transcription-mediated bacterial nucleic acid amplification tests. J Clin Microbiol 2024; 62:e0024324. [PMID: 38629844 PMCID: PMC11237385 DOI: 10.1128/jcm.00243-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 03/28/2024] [Indexed: 05/09/2024] Open
Abstract
Detection of bacterial RNA by nucleic acid amplification tests (NAATs), such as reverse transcription PCR (RT-PCR) and reverse transcription loop-mediated isothermal amplification (RT-LAMP), offers distinct advantages over DNA-based methods. However, such assays also present challenges in ascertaining positive and internal control material that can reliably monitor success over all phases of testing (bacterial lysis, nucleic acid recovery, reverse transcription, amplification, and signal detection): since they are unable to distinguish between amplification of bacterial RNA transcripts and the DNA templates that encode them, using intact organisms as controls can inform cell lysis but not successful detection of RNA. We developed a control strategy for RNA-based bacterial NAATs that allows ready discrimination of RNA from DNA templates using self-splicing bacterial introns, such that those nucleic acids ultimately encode different sequences. We engineered two vectors encoding synthetic transgenes based on this principle, one that is active in the Gram-negative bacterium Escherichia coli and one that functions in both E. coli and the Gram-positive organism Staphylococcus aureus. We subsequently designed RT-LAMP assays that either target RNA and DNA from transgenic organisms or target RNA exclusively and demonstrated the specificity of amplification using purified nucleic acids. Using multiplex fluorescent RT-LAMP of heat-lysed specimens, we showed the practicality of deploying such transgenic organisms as an internal control to ascertain sample integrity and assay performance during clinical diagnostic testing. Our approach has broad utility for RNA-based bacterial NAATs, especially point-of-care assays and other applications where nucleic acids are nonspecifically liberated for testing.
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Affiliation(s)
- Janessa D. Lewis
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Stephen J. Salipante
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
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Grochowski CM, Gibbs RA, Doddapaneni H. Validation of Single-Nucleotide Mosaic Variants Through Droplet Digital PCR. Curr Protoc 2024; 4:e1041. [PMID: 38774978 PMCID: PMC11115377 DOI: 10.1002/cpz1.1041] [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] [Indexed: 05/25/2024]
Abstract
The detection, validation, and subsequent interpretation of potentially mosaic single-nucleotide variants (SNV) within next-generation sequencing data remains a challenge in both research and clinical laboratory settings. The ability to identify mosaic variants in high genome coverage sequencing data at levels of ≤1% underscores the necessity for developing guidelines and best practices to verify these variants orthogonally. Droplet digital PCR (ddPCR) has proven to be a powerful and precise method that allows for the determination of low-level variant fractions within a given sample. Herein we describe two precise ddPCR methods using either a fluorescent TaqMan hydrolysis probe approach or an EvaGreen fluorescent dye protocol. The TaqMan approach relies on two different fluorescent probes (FAM and HEX/VIC), each designed to amplify selectively only in the presence of a single nucleotide change denoting the variant or reference position. The fractional abundance is then calculated to determine the relative quantities of both alleles in the final sample. The EvaGreen protocol relies on two independent reactions with oligonucleotide primers designed with the single nucleotide change denoting the variant at the penultimate position of the primer. The relative amplification efficiency of both primer sets (reference and variant) can be compared to determine the mosaic level of a given variant. As the cost of high-coverage sequencing continues to decrease, the identification of potentially mosaic variants will also increase. The approaches outlined will allow clinicians and researchers a more precise determination of the true mosaic level of a given variant allowing them to better assess not only its potential pathogenicity but also its possible recurrence risk when offering genetic counseling to families. © 2024 Wiley Periodicals LLC. Basic Protocol: Droplet digital PCR (ddPCR) with TaqMan hydrolysis probes Alternate Protocol: EvaGreen oligonucleotide-specific ddPCR.
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Affiliation(s)
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine,
Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College
of Medicine, Houston, TX 77030, USA
| | - Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine,
Houston, TX 77030, USA
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Knight NL, Adhikari KC, Dodhia KN, Mair WJ, Lopez-Ruiz FJ. Workflows for detecting fungicide resistance in net form and spot form net blotch pathogens. PEST MANAGEMENT SCIENCE 2024; 80:2131-2140. [PMID: 38145910 DOI: 10.1002/ps.7951] [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: 06/28/2023] [Revised: 12/19/2023] [Accepted: 12/26/2023] [Indexed: 12/27/2023]
Abstract
BACKGROUND Fungicide resistance in Pyrenophora teres f. maculata and P. teres f. teres has become an important disease management issue. Control of the associated barley foliar diseases, spot form and net form net blotch, respectively, relies on three major groups of fungicides, demethylation inhibitors (DMIs), succinate dehydrogenase inhibitors (SDHIs) and quinone outside inhibitors (QoIs). However, resistance has been reported for the DMI and SDHI fungicides in Australia. To enhance detection of different resistance levels, phenotyping and genotyping workflows were designed. RESULTS The phenotyping workflow generated cultures directly from lesions and compared growth on discriminatory doses of tebuconazole (DMI) and fluxapyroxad (SDHI). Genotyping real-time polymerase chain reaction (PCR) assays were based on alleles associated with sensitivity or resistance to the DMI and SDHI fungicides. These workflows were applied to spot form and net form net blotch collections from 2019 consisting predominantly of P. teres f. teres from South Australia and P. teres f. maculata from Western Australia. For South Australia the Cyp51A L489-3 and SdhC-R134 alleles, associated with resistance to tebuconazole and fluxapyroxad, respectively, were the most prevalent. These alleles were frequently found in single isolates with dual resistance. This study also reports the first detection of a 134 base pair insertion located at position-66 (PtTi-6) in the Cyp51A promoter of P. teres f. maculata from South Australia. For Western Australia, the PtTi-1 insertion was the most common allele associated with resistance to tebuconazole. CONCLUSION The workflow and PCR assays designed in this study have been demonstrated to efficiently screen P. teres collections for both phenotypic and genetic resistance to DMI and SDHI fungicides. The distribution of reduced sensitivity and resistance to DMI and SDHI fungicides varied between regions in south-western Australia, suggesting the emergence of resistance was impacted by both local pathogen populations and disease management programmes. The knowledge of fungicide resistance in regional P. teres collections will be important for informing appropriate management strategies. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Noel L Knight
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Australia
| | - Kul C Adhikari
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Australia
| | - Kejal N Dodhia
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Australia
| | - Wesley J Mair
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Australia
| | - Francisco J Lopez-Ruiz
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Australia
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7
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Van Poelvoorde LAE, Gobbo A, Nauwelaerts SJD, Verhaegen B, Lesenfants M, Janssens R, Hutse V, Fraiture MA, De Keersmaecker S, Herman P, Van Hoorde K, Roosens N. Development of a reverse transcriptase digital droplet polymerase chain reaction-based approach for SARS-CoV-2 variant surveillance in wastewater. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2024; 96:e10999. [PMID: 38414298 DOI: 10.1002/wer.10999] [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: 11/27/2023] [Revised: 01/16/2024] [Accepted: 01/27/2024] [Indexed: 02/29/2024]
Abstract
An urgent need for effective surveillance strategies arose due to the global emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although vaccines and antivirals are available, concerns persist about the evolution of new variants with potentially increased infectivity, transmissibility, and immune evasion. Therefore, variant monitoring is crucial for public health decision-making. Wastewater-based surveillance has proven to be an effective tool to monitor SARS-CoV-2 variants within populations. Specific SARS-CoV-2 variants are detected and quantified in wastewater in this study using a reverse transcriptase digital droplet polymerase chain reaction (RT-ddPCR) approach. The 11 designed assays were first validated in silico using a substantial dataset of high-quality SARS-CoV-2 genomes to ensure comprehensive variant coverage. The assessment of the sensitivity and specificity with reference material showed the capability of the developed assays to reliably identify target mutations while minimizing false positives and false negatives. The applicability of the assays was evaluated using wastewater samples from a wastewater treatment plant in Ghent, Belgium. The quantification of the specific mutations linked to the variants of concern present in these samples was calculated using these assays based on the detection of single mutations, which confirms their use for real-world variant surveillance. In conclusion, this study provides an adaptable protocol to monitor SARS-CoV-2 variants in wastewater with high sensitivity and specificity. Its potential for broader application in other viral surveillance contexts highlights its added value for rapid response to emerging infectious diseases. PRACTITIONER POINTS: Robust RT-ddPCR methodology for specific SARS-CoV-2 variants of concern detection in wastewater. Rigorous validation that demonstrates high sensitivity and specificity. Demonstration of real-world applicability using wastewater samples. Valuable tool for rapid response to emerging infectious diseases.
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Affiliation(s)
| | - Andrea Gobbo
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | | | | | - Marie Lesenfants
- Epidemiology of infectious diseases, Sciensano, Brussels, Belgium
| | - Raphael Janssens
- Epidemiology of infectious diseases, Sciensano, Brussels, Belgium
| | - Veronik Hutse
- Epidemiology of infectious diseases, Sciensano, Brussels, Belgium
| | | | | | | | | | - Nancy Roosens
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
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Laššáková S, Šenkyřík P, Pazourková E, Hořínek A, Calda P, Břešťák M, Světnicová K, Neužil P, Korabečná M. Rapid non-invasive prenatal screening test for trisomy 21 based on digital droplet PCR. Sci Rep 2023; 13:22948. [PMID: 38135736 PMCID: PMC10746715 DOI: 10.1038/s41598-023-50330-x] [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: 05/23/2023] [Accepted: 12/19/2023] [Indexed: 12/24/2023] Open
Abstract
Non-invasive prenatal tests for the detection of fetal aneuploidies are predominantly based on the analysis of cell-free DNA (cfDNA) from the plasma of pregnant women by next-generation sequencing. The development of alternative tests for routine genetic laboratories is therefore desirable. Multiplex digital droplet PCR was used to detect 16 amplicons from chromosome 21 and 16 amplicons from chromosome 18 as the reference. Two fluorescently labeled lock nucleic acid probes were used for the detection of reaction products. The required accuracy was achieved by examining 12 chips from each patient using Stilla technology. The plasma cfDNA of 26 pregnant women with euploid pregnancies and 16 plasma samples from pregnancies with trisomy 21 were analyzed to determine the cutoff value for sample classification. The test was validated in a blind study on 30 plasma samples from pregnant patients with a risk for trisomy 21 ranging from 1:4 to 1:801. The results were in complete agreement with the results of the invasive diagnostic procedure (sensitivity, specificity, PPV, and NPV of 100%). Low cost, and speed of analysis make it a potential screening method for implementation into the clinical workflow to support the combined biochemical and ultrasound results indicating a high risk for trisomy 21.
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Affiliation(s)
- Soňa Laššáková
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic
| | - Pavel Šenkyřík
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic
| | - Eva Pazourková
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic
- Department of Nephrology, First Faculty of Medicine, Charles University and General University Hospital in Prague, U Nemocnice 499/2, 128 08, Prague 2, Czech Republic
| | - Aleš Hořínek
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic
- 3rd Department of Internal Medicine, First Faculty of Medicine, Charles University and General University Hospital in Prague, U Nemocnice 1, 128 08, Prague 1, Czech Republic
| | - Pavel Calda
- Department of Gynaecology, Obstetrics and Neonatology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Apolinarska 18, 128 51, Prague, Czech Republic
| | - Miroslav Břešťák
- Department of Gynaecology, Obstetrics and Neonatology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Apolinarska 18, 128 51, Prague, Czech Republic
- Prenatal Diagnosis Center ProfiG2 S.R.O., Vajgarská, 1141, Prague, Czech Republic
| | | | - Pavel Neužil
- Department of Microsystem Engineering, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072, Shaanxi, People's Republic of China
| | - Marie Korabečná
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic.
- Department of Laboratory Medicine, Faculty of Health Care and Social Work, University of Trnava in Trnava, Universitne Namestie 1, 918 43, Trnava, Slovak Republic.
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Zeller-Péronnet V, Bretschneider N, Lausch J, Hanifi N, Pavlovic M, Zarske M, Luu HQ, Busch U, Stingl K, Huber I. Multiplex Real-Time PCR for the Detection of Tetracycline, Ciprofloxacin, and Erythromycin Resistance Determinants from Human and Foodborne Campylobacter jejuni and Campylobacter coli. Microorganisms 2023; 11:2927. [PMID: 38138071 PMCID: PMC10745765 DOI: 10.3390/microorganisms11122927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/28/2023] [Accepted: 11/30/2023] [Indexed: 12/24/2023] Open
Abstract
Campylobacter jejuni and Campylobacter coli are the predominant thermophilic species responsible for foodborne gastroenteritis worldwide. Elevated resistance to certain antibiotics was observed due to antimicrobial therapy in farm animals and humans, while reduced antimicrobial usage partially reduced antibiotic resistance. Monitoring the antimicrobial resistance demonstrated a substantial fraction of multi-resistant isolates, indicating the necessity of reliable tools for their detection. In this study, resistance determinants in 129 German and 21 Vietnamese isolates were selected to establish a novel multiplex real-time PCR (qPCR), facilitating the simultaneous detection of four resistance determinants. These comprised tet(O) gene variants associated with tetracycline resistance, point mutations GyrA_T86I and GyrA_T86V associated with ciprofloxacin resistance, and the erm(B) gene together with the point mutation A2075G in the 23S rRNA gene, associated with erythromycin resistance. Moreover, the performance of the qPCR assay was evaluated by comparing the results of qPCR to phenotypic antimicrobial resistance profiles, obtained with standardized EUCAMP3 microdilution panel, which showed 100% similarity (inclusivity and exclusivity). Variation in measurement methods, including qPCR machines and master mixes showed robustness, essential for laboratories. The assay can be used for the rapid detection of resistance determinants, and is beneficial for monitoring the spread of antibiotic resistance in C. jejuni and C. coli.
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Affiliation(s)
- Véronique Zeller-Péronnet
- Department for Food and Food Hygiene, Bavarian Health and Food Safety Authority (LGL), 85764 Oberschleissheim, Germany; (V.Z.-P.); (N.B.); (N.H.); (M.P.); (U.B.)
| | - Nancy Bretschneider
- Department for Food and Food Hygiene, Bavarian Health and Food Safety Authority (LGL), 85764 Oberschleissheim, Germany; (V.Z.-P.); (N.B.); (N.H.); (M.P.); (U.B.)
| | - Johanna Lausch
- Department for Food and Food Hygiene, Bavarian Health and Food Safety Authority (LGL), 85764 Oberschleissheim, Germany; (V.Z.-P.); (N.B.); (N.H.); (M.P.); (U.B.)
| | - Nadera Hanifi
- Department for Food and Food Hygiene, Bavarian Health and Food Safety Authority (LGL), 85764 Oberschleissheim, Germany; (V.Z.-P.); (N.B.); (N.H.); (M.P.); (U.B.)
| | - Melanie Pavlovic
- Department for Food and Food Hygiene, Bavarian Health and Food Safety Authority (LGL), 85764 Oberschleissheim, Germany; (V.Z.-P.); (N.B.); (N.H.); (M.P.); (U.B.)
| | - Michael Zarske
- National Reference Laboratory for Campylobacter, Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), 10589 Berlin, Germany; (M.Z.); (K.S.)
| | - Huong Quynh Luu
- National Institute of Veterinary Research (NIVR), Hanoi 100000, Vietnam;
| | - Ulrich Busch
- Department for Food and Food Hygiene, Bavarian Health and Food Safety Authority (LGL), 85764 Oberschleissheim, Germany; (V.Z.-P.); (N.B.); (N.H.); (M.P.); (U.B.)
| | - Kerstin Stingl
- National Reference Laboratory for Campylobacter, Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), 10589 Berlin, Germany; (M.Z.); (K.S.)
| | - Ingrid Huber
- Department for Food and Food Hygiene, Bavarian Health and Food Safety Authority (LGL), 85764 Oberschleissheim, Germany; (V.Z.-P.); (N.B.); (N.H.); (M.P.); (U.B.)
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10
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Leatham B, McNall K, Subramanian HKK, Jacky L, Alvarado J, Yurk D, Wang M, Green DC, Tsongalis GJ, Rajagopal A, Schwartz JJ. A rapid, multiplex digital PCR assay to detect gene variants and fusions in non-small cell lung cancer. Mol Oncol 2023; 17:2221-2234. [PMID: 37714814 PMCID: PMC10620117 DOI: 10.1002/1878-0261.13523] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/22/2023] [Accepted: 09/15/2023] [Indexed: 09/17/2023] Open
Abstract
Digital PCR (dPCR) is emerging as an ideal platform for the detection and tracking of genomic variants in cancer due to its high sensitivity and simple workflow. The growing number of clinically actionable cancer biomarkers creates a need for fast, accessible methods that allow for dense information content and high accuracy. Here, we describe a proof-of-concept amplitude modulation-based multiplex dPCR assay capable of detecting 12 single-nucleotide and insertion/deletion (indel) variants in EGFR, KRAS, BRAF, and ERBB2, 14 gene fusions in ALK, RET, ROS1, and NTRK1, and MET exon 14 skipping present in non-small cell lung cancer (NSCLC). We also demonstrate the use of multi-spectral target-signal encoding to improve the specificity of variant detection by reducing background noise by up to an order of magnitude. The assay reported an overall 100% positive percent agreement (PPA) and 98.5% negative percent agreement (NPA) compared with a sequencing-based assay in a cohort of 62 human formalin-fixed paraffin-embedded (FFPE) samples. In addition, the dPCR assay rescued actionable information in 10 samples that failed to sequence, highlighting the utility of a multiplexed dPCR assay as a potential reflex solution for challenging NSCLC samples.
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Affiliation(s)
| | | | | | | | | | - Dominic Yurk
- ChromaCode IncCarlsbadCAUSA
- Department of Electrical EngineeringCalifornia Institute of TechnologyPasadenaCAUSA
| | - Mimi Wang
- ChromaCode IncCarlsbadCAUSA
- Slack TechnologiesSan FranciscoCAUSA
| | - Donald C. Green
- Department of Pathology and Laboratory MedicineDartmouth Hitchcock Medical CenterLebanonNHUSA
| | - Gregory J. Tsongalis
- Department of Pathology and Laboratory MedicineDartmouth Hitchcock Medical CenterLebanonNHUSA
| | - Aditya Rajagopal
- ChromaCode IncCarlsbadCAUSA
- Department of Electrical EngineeringCalifornia Institute of TechnologyPasadenaCAUSA
- Department of Biomedical EngineeringUniversity of Southern CaliforniaLos AngelesCAUSA
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11
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Zhong Y, Huang LX, Lin MT, Zhang ZY, Liu AL, Lei Y. A Y-shape-structured electrochemiluminescence biosensor based on carbon quantum dots and locked nucleic acid probe for microRNA determination with single-base resolution. Biosens Bioelectron 2023; 238:115583. [PMID: 37573643 DOI: 10.1016/j.bios.2023.115583] [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: 05/26/2023] [Revised: 07/24/2023] [Accepted: 08/07/2023] [Indexed: 08/15/2023]
Abstract
Since microRNAs (miRNAs) are predictors of tumorigenesis, accurate identification and quantification of miRNAs with highly similar sequences are expected to reflect tumor diagnosis and treatment. In this study, a highly selective and sensitive electrochemiluminescence (ECL) biosensor was constructed for miRNAs determination based on Y-shaped junction structure equipped with locked nucleic acids (LNA), graphene oxide-based nanocomposite to enrich luminophores, and conductive matrix. Specifically, two LNA-modified probes were designed for specific miRNA recognition, that is, a dual-amine functionalized hairpin capture probe and a signal probe. A Y-shaped DNA junction structure was generated on the electrode surface upon miRNA hybridizing across the two branches, so as to enhance the selectivity. Carbon quantum dots-polyethylene imine-graphene oxide (CQDs-PEI-GO) nanocomposites were developed to enrich luminophores CQDs, and thus enhancing the ECL intensity. For indirect signal amplification, an electrochemically activated poly(2-aminoterephthalic acid) (ATA) film decorated with gold nanoparticles was prepared on electrode as an effective matrix to accelerate the electron transfer. The fabricated ECL biosensor achieved sensitive determination of miRNA-222 with a limit-of-detection (LOD) as low as 1.95 fM (S/N = 3). Notably, Y-shaped junction structures equipped with LNA probes endowed ECL biosensor with salient single-base discrimination ability and anti-interference capacity. Overall, the proposed Y-shaped ECL biosensor has considerable promise for clinical biomarker determination.
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Affiliation(s)
- Yu Zhong
- Department of Pharmaceutical Analysis, Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, Faculty of Pharmacy, Fujian Medical University, Fuzhou, 350122, China
| | - Lin-Xiao Huang
- Department of Pharmaceutical Analysis, Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, Faculty of Pharmacy, Fujian Medical University, Fuzhou, 350122, China
| | - Mu-Tu Lin
- Department of Pharmaceutical Analysis, Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, Faculty of Pharmacy, Fujian Medical University, Fuzhou, 350122, China
| | - Zi-Yang Zhang
- Department of Pharmaceutical Analysis, Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, Faculty of Pharmacy, Fujian Medical University, Fuzhou, 350122, China
| | - Ai-Lin Liu
- Department of Pharmaceutical Analysis, Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, Faculty of Pharmacy, Fujian Medical University, Fuzhou, 350122, China.
| | - Yun Lei
- Department of Pharmaceutical Analysis, Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, Faculty of Pharmacy, Fujian Medical University, Fuzhou, 350122, China.
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12
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Vinokurov MA, Mironov KO, Domonova EA, Romanyuk TN, Popova AA, Akimkin VG. The genetic variant rs55986091 HLA-DQB1 is associated with a protective effect against cervical cancer. Front Oncol 2023; 13:1207935. [PMID: 37614503 PMCID: PMC10443639 DOI: 10.3389/fonc.2023.1207935] [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: 04/19/2023] [Accepted: 07/06/2023] [Indexed: 08/25/2023] Open
Abstract
Introduction Cervical cancer (CC) is a prevalent malignancy affecting women globally. The primary causative factor of CC is the high-risk oncogenic human papillomavirus (HR-HPV). However, it is noteworthy that not all women infected with HR-HPV develop cancer, indicating the potential involvement of genetic predisposition in the development of CC. This study aims to identify genetic risks and their distribution in groups of women with different epidemiological features of HR-HPV. Materials and methods A comparison was conducted among four groups of women, comprising 218 HPV-negative women, 120 HPV-positive women, 191 women diagnosed with cervical intraepithelial neoplasia (CIN) grade 2 or 3, and 124 women diagnosed with CC. The analysis focused on four single nucleotide polymorphisms (SNPs): rs55986091 in HLA-DQB1, rs138446575 in TTC34, rs1048943 in CYP1A1, and rs2910164 in miRNA-146a. Results The rs55986091-A allele exhibited a protective effect within the "CC" group when compared to the "HPV-Negative" group (OR = 0.4, 95% CI= 0.25-0.65) using a log-additive model. Additionally, similar protective effects were observed in the "CIN 2/3" group compared to the "HPV-Negative" group (OR = 0.47, 95% CI = 0.28-0.79). Conclusion The data obtained emphasize the importance of developing PCR-based diagnostic kits for the identification of SNP alleles, particularly for rs55986091, among HR-HPV-positive women within the Russian population.
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Affiliation(s)
- Michael A. Vinokurov
- Central Research Institute of Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Moscow, Russia
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13
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Chen FE, Wang J, Nambiar AH, Hardick J, Melendez J, Trick AY, Wang TH. Point-of-Care Amenable Detection of Mycoplasma genitalium and Its Antibiotic Resistance Mutations. ACS Sens 2023; 8:1550-1557. [PMID: 36961769 PMCID: PMC11257175 DOI: 10.1021/acssensors.2c02630] [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] [Indexed: 03/25/2023]
Abstract
Mycoplasma genitalium (MG) is an emerging sexually transmitted bacterium. Due to its fastidious and slow-growing nature, MG is difficult to detect through culture-based diagnostics. Like Neisseria gonorrheae, another bacterial pathogen linked to sexually transmitted infections (STIs), MG has developed resistance to macrolide and fluoroquinolone antibiotics used to treat STIs. The ability to detect MG and identify genomic mutations associated with antibiotic resistance simultaneously can enable antibiotic stewardship and mitigate the spread of antibiotic-resistant MG. Toward this end, we first developed a multiplexed probe-based PCR-melt assay that detects MG and the presence of macrolide resistance mutations in the 23S rRNA gene and fluoroquinolone resistance mutations in the parC gene. Each target was identified via its unique combination of fluorescence label and melting temperature. This approach allowed differentiation between the different types of mutations at the genes of interest. Following initial assay optimization, the assay was integrated into a droplet magnetofluidic cartridge used in a portable platform to integrate automated sample extraction, PCR amplification, and detection. Lastly, we demonstrated that the integrated assay and droplet magnetofluidic platform could detect MG and antibiotic resistance-associated mutations in clinical isolates spiked into urine samples in 40 min.
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Affiliation(s)
- Fan-En Chen
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Jonathan Wang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Anju Haridas Nambiar
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Justin Hardick
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland 21218, United States
| | - Johan Melendez
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland 21218, United States
| | - Alexander Y Trick
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Tza-Huei Wang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
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14
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Zhang R, Ou X, Sun X, Fan G, Zhao B, Tian F, Li F, Shen X, Zhao Y, Ma X. Multiplex LNA probe-based RAP assay for rapid and highly sensitive detection of rifampicin-resistant Mycobacterium tuberculosis. Front Microbiol 2023; 14:1141424. [PMID: 37180280 PMCID: PMC10172479 DOI: 10.3389/fmicb.2023.1141424] [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: 01/10/2023] [Accepted: 04/11/2023] [Indexed: 05/16/2023] Open
Abstract
Objectives The World Health Organization (WHO) Global tuberculosis Report 2021 stated that rifampicin-resistant tuberculosis (RR-TB) remains a major public health threat. However, the in-practice diagnostic techniques for RR-TB have a variety of limitations including longer time, lack of sensitivity, and undetectable low proportion of heterogeneous drug resistance. Methods Here we developed a multiplex LNA probe-based RAP method (MLP-RAP) for more sensitive detection of multiple point mutations of the RR-TB and its heteroresistance. A total of 126 clinical isolates and 78 sputum samples collected from the National Tuberculosis Reference Laboratory, China CDC, were tested by MLP-RAP assay. In parallel, qPCR and Sanger sequencing of nested PCR product assay were also performed for comparison. Results The sensitivity of the MLP-RAP assay could reach 5 copies/μl using recombinant plasmids, which is 20 times more sensitive than qPCR (100 copies/μl). In addition, the detection ability of rifampicin heteroresistance was 5%. The MLP-RAP assay had low requirements (boiling method) for nucleic acid extraction and the reaction could be completed within 1 h when placed in a fluorescent qPCR instrument. The result of the clinical evaluation showed that the MLP-RAP method could cover codons 516, 526, 531, and 533 with good specificity. 41 out of 78 boiled sputum samples were detected positive by MLP-RAP assay, which was further confirmed by Sanger sequencing of nested PCR product assay, on the contrary, qPCR was able to detect 32 samples only. Compared with Sanger sequencing of nested PCR product assay, both the specificity and sensitivity of the MLP-RAP assay were 100%. Conclusion MLP-RAP assay can detect RR-TB infection with high sensitivity and specificity, indicating that this assay has the prospect of being applied for rapid and sensitive RR-TB detection in general laboratories where fluorescent qPCR instrument is available.
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Affiliation(s)
- Ruiqing Zhang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xichao Ou
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiuli Sun
- Clinical Laboratory, North China University of Science and Technology, Tangshan, China
| | - Guohao Fan
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Bing Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Fengyu Tian
- Hebei Key Laboratory of Molecular Medicine, Hebei Medical University, Shijiazhuang, China
| | - Fengyu Li
- Hebei Key Laboratory of Molecular Medicine, Hebei Medical University, Shijiazhuang, China
| | - Xinxin Shen
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yanlin Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xuejun Ma
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
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15
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Prout J, Tian M, Palladino A, Wright J, Thompson JF. LNA blockers for improved amplification selectivity. Sci Rep 2023; 13:4858. [PMID: 36964235 PMCID: PMC10038989 DOI: 10.1038/s41598-023-31871-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 03/20/2023] [Indexed: 03/26/2023] Open
Abstract
LNA-containing oligonucleotides bind DNA more tightly than standard DNA, so they can interact with targeted sequences and affect multiple processes. When a desired DNA is present at low concentrations relative to nearly identical undesired DNAs, LNAs can block amplification of unwanted DNAs. Using a short rAAV and synthetic DNA sequence as a model, we studied the length, number, and positioning of LNA bases to improve blocker effectiveness. Oligonucleotides 18-24 bases long with LNAs at every other position were most effective. Highly degenerate targets were used to characterize the impact of mismatches on blocking. Mismatches at LNA ends had little impact on blocking activity. Single and double mismatches were tolerated with longer blockers, especially if the mismatches were near LNA ends. Shorter LNAs were more selective, with > 1 mismatch preventing effective blocking. Neither the strand to which a blocker bound nor the distance between the blocker and priming sites greatly impacted blocking efficiency. We used these findings to design blockers of wild-type DNA versus the single-base A1AT PiZ allele. Blockers are most specific when the mismatch is located away from the LNA 5' end. Pairs of partially overlapping blockers on opposite strands with a centrally-located mismatch have maximal activity and specificity.
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Affiliation(s)
- Jaime Prout
- Department of Genomics and Computational Biology, Homology Medicines, Inc., Bedford, MA, 01730, USA
| | - Michael Tian
- Department of Genomics and Computational Biology, Homology Medicines, Inc., Bedford, MA, 01730, USA
| | - Alicia Palladino
- Department of Genomics and Computational Biology, Homology Medicines, Inc., Bedford, MA, 01730, USA
| | - Jason Wright
- Department of Genomics and Computational Biology, Homology Medicines, Inc., Bedford, MA, 01730, USA
| | - John F Thompson
- Department of Genomics and Computational Biology, Homology Medicines, Inc., Bedford, MA, 01730, USA.
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16
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Kim K, Choi YM, Kim DH, Jang J, Choe WH, Kim BJ. Locked nucleic acid real-time polymerase chain reaction method identifying two polymorphisms of hepatitis B virus genotype C2 infections, rt269L and rt269I. World J Gastroenterol 2023; 29:1721-1734. [PMID: 37077521 PMCID: PMC10107212 DOI: 10.3748/wjg.v29.i11.1721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 01/13/2023] [Accepted: 02/27/2023] [Indexed: 03/17/2023] Open
Abstract
BACKGROUND The presence of two distinct hepatitis B virus (HBV) Pol RT polymorphisms, rt269L and rt269I, could contribute to the unique clinical or virological phenotype of HBV genotype C2. Therefore, a simple and sensitive method capable of identifying both types in chronic hepatitis B (CHB) patients infected with genotype C2 should be developed.
AIM To develop a novel simple and sensitive locked nucleic acid (LNA)-real time-polymerase chain reaction (RT-PCR) method capable of identifying two rt269 types in CHB genotype C2 patients.
METHODS We designed proper primer and probe sets for LNA-RT-PCR for the separation of rt269 types. Using synthesized DNAs of the wild type and variant forms, melting temperature analysis, detection sensitivity, and endpoint genotyping for LNA-RT-PCR were performed. The developed LNA-RT-PCR method was applied to a total of 94 CHB patients of genotype C2 for the identification of two rt269 polymorphisms, and these results were compared with those obtained by a direct sequencing protocol.
RESULTS The LNA-RT-PCR method could identify two rt269L and rt269I polymorphisms of three genotypes, two rt269L types [‘L1’ (WT) and ‘L2’] and one rt269I type (‘I’) in single (63 samples, 72.4%) or mixed forms (24 samples, 27.6%) in 87 (92.6% sensitivity) of 94 samples from Korean CHB patients. When the results were compared with those obtained by the direct sequencing protocol, the LNA-RT-PCR method showed the same results in all but one of 87 positive detected samples (98.9% specificity).
CONCLUSION The newly developed LNA-RT-PCR method could identify two rt269 polymorphisms, rt269L and rt269I, in CHB patients with genotype C2 infections. This method could be effectively used for the understanding of disease progression in genotype C2 endemic areas.
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Affiliation(s)
- Kijeong Kim
- Department of Microbiology, College of Medicine, Chung-Ang University, Seoul 06974, South Korea
| | - Yu-Min Choi
- Department of Microbiology and Immunology, College of Medicine, Seoul National University, Seoul 03080, South Korea
| | - Dong Hyun Kim
- Department of Microbiology and Immunology, College of Medicine, Seoul National University, Seoul 03080, South Korea
| | - Junghwa Jang
- Department of Microbiology and Immunology, College of Medicine, Seoul National University, Seoul 03080, South Korea
| | - Won Hyeok Choe
- Department of Internal Medicine, Konkuk University School of Medicine, Seoul 05030, South Korea
| | - Bum-Joon Kim
- Department of Microbiology and Immunology, College of Medicine, Seoul National University, Seoul 03080, South Korea
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, South Korea
- Liver Research Institute, College of Medicine, Seoul National University, Seoul 03080, South Korea
- Seoul National University Medical Research Center, Seoul 03080, South Korea
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17
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Van Poelvoorde LAE, Picalausa C, Gobbo A, Verhaegen B, Lesenfants M, Herman P, Van Hoorde K, Roosens NHC. Development of a Droplet Digital PCR to Monitor SARS-CoV-2 Omicron Variant BA.2 in Wastewater Samples. Microorganisms 2023; 11:microorganisms11030729. [PMID: 36985302 PMCID: PMC10059707 DOI: 10.3390/microorganisms11030729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/07/2023] [Accepted: 03/10/2023] [Indexed: 03/14/2023] Open
Abstract
Wastewater-based surveillance can be used as a complementary method to other SARS-CoV-2 surveillance systems. It allows the emergence and spread of infections and SARS-CoV-2 variants to be monitored in time and place. This study presents an RT-ddPCR method that targets the T19I amino acid mutation in the spike protein of the SARS-CoV-2 genomes, which is specific to the BA.2 variant (omicron). The T19I assay was evaluated both in silico and in vitro for its inclusivity, sensitivity, and specificity. Moreover, wastewater samples were used as a proof of concept to monitor and quantify the emergence of the BA.2 variant from January until May 2022 in the Brussels-Capital Region which covers a population of more than 1.2 million inhabitants. The in silico analysis showed that more than 99% of the BA.2 genomes could be characterized using the T19I assay. Subsequently, the sensitivity and specificity of the T19I assay were successfully experimentally evaluated. Thanks to our specific method design, the positive signal from the mutant probe and wild-type probe of the T19I assay was measured and the proportion of genomes with the T19I mutation, characteristic of the BA.2 mutant, compared to the entire SARS-CoV-2 population was calculated. The applicability of the proposed RT-ddPCR method was evaluated to monitor and quantify the emergence of the BA.2 variant over time. To validate this assay as a proof of concept, the measurement of the proportion of a specific circulating variant with genomes containing the T19I mutation in comparison to the total viral population was carried out in wastewater samples from wastewater treatment plants in the Brussels-Capital Region in the winter and spring of 2022. This emergence and proportional increase in BA.2 genomes correspond to what was observed in the surveillance using respiratory samples; however, the emergence was observed slightly earlier, which suggests that wastewater sampling could be an early warning system and could be an interesting alternative to extensive human testing.
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Affiliation(s)
| | - Corinne Picalausa
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium
| | - Andrea Gobbo
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium
| | | | - Marie Lesenfants
- Epidemiology of Infectious Diseases, Sciensano, 1050 Brussels, Belgium
| | | | | | - Nancy H. C. Roosens
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium
- Correspondence:
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18
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Abraham Punnoose J, Thomas KJ, Chandrasekaran AR, Vilcapoma J, Hayden A, Kilpatrick K, Vangaveti S, Chen A, Banco T, Halvorsen K. High-throughput single-molecule quantification of individual base stacking energies in nucleic acids. Nat Commun 2023; 14:631. [PMID: 36746949 PMCID: PMC9902561 DOI: 10.1038/s41467-023-36373-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 01/26/2023] [Indexed: 02/08/2023] Open
Abstract
Base stacking interactions between adjacent bases in DNA and RNA are important for many biological processes and in biotechnology applications. Previous work has estimated stacking energies between pairs of bases, but contributions of individual bases has remained unknown. Here, we use a Centrifuge Force Microscope for high-throughput single molecule experiments to measure stacking energies between adjacent bases. We found stacking energies strongest between purines (G|A at -2.3 ± 0.2 kcal/mol) and weakest between pyrimidines (C|T at -0.5 ± 0.1 kcal/mol). Hybrid stacking with phosphorylated, methylated, and RNA nucleotides had no measurable effect, but a fluorophore modification reduced stacking energy. We experimentally show that base stacking can influence stability of a DNA nanostructure, modulate kinetics of enzymatic ligation, and assess accuracy of force fields in molecular dynamics simulations. Our results provide insights into fundamental DNA interactions that are critical in biology and can inform design in biotechnology applications.
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Affiliation(s)
- Jibin Abraham Punnoose
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Kevin J Thomas
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | | | - Javier Vilcapoma
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Andrew Hayden
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Kacey Kilpatrick
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA.,Department of Chemistry, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Sweta Vangaveti
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Alan Chen
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA.,Department of Chemistry, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Thomas Banco
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA.
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19
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Ivanov GS, Tribulovich VG, Pestov NB, David TI, Amoah AS, Korneenko TV, Barlev NA. Artificial genetic polymers against human pathologies. Biol Direct 2022; 17:39. [PMID: 36474260 PMCID: PMC9727881 DOI: 10.1186/s13062-022-00353-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
Originally discovered by Nielsen in 1991, peptide nucleic acids and other artificial genetic polymers have gained a lot of interest from the scientific community. Due to their unique biophysical features these artificial hybrid polymers are now being employed in various areas of theranostics (therapy and diagnostics). The current review provides an overview of their structure, principles of rational design, and biophysical features as well as highlights the areas of their successful implementation in biology and biomedicine. Finally, the review discusses the areas of improvement that would allow their use as a new class of therapeutics in the future.
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Affiliation(s)
- Gleb S Ivanov
- Institute of Cytology, Tikhoretsky Ave 4, Saint Petersburg, Russia, 194064
- St. Petersburg State Technological Institute (Technical University), Saint Petersburg, Russia, 190013
| | - Vyacheslav G Tribulovich
- St. Petersburg State Technological Institute (Technical University), Saint Petersburg, Russia, 190013
| | - Nikolay B Pestov
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products, Moscow, Russia, 108819
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia, 141701
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia, 117997
- Institute of Biomedical Chemistry, Moscow, Russia, 119121б
| | - Temitope I David
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia, 141701
| | - Abdul-Saleem Amoah
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia, 141701
| | - Tatyana V Korneenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia, 117997
| | - Nikolai A Barlev
- Institute of Cytology, Tikhoretsky Ave 4, Saint Petersburg, Russia, 194064.
- Institute of Biomedical Chemistry, Moscow, Russia, 119121б.
- School of Medicine, Nazarbayev University, 010000, Astana, Kazakhstan.
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20
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Efficient multiplexing and variant discrimination in reverse-transcription loop-mediated isothermal amplification with sequence-specific hybridization probes. Biotechniques 2022; 73:247-255. [DOI: 10.2144/btn-2022-0096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Loop-mediated isothermal amplification (LAMP) has proven a robust and reliable nucleic acid amplification method that is well suited for simplified and rapid molecular diagnostics. Various approaches have emerged for sequence-specific detection of LAMP products, but with limitations to their widespread utility or applicability for single-nucleotide polymorphism detection and multiplexing. Here we demonstrate the use of simple hybridization probes (as used for qPCR) that enable simple multiplexing and SARS-CoV-2 variant typing in reverse-transcription LAMP. This approach requires no modification to the LAMP primers and is amenable to the detection of single-nucleotide polymorphisms and small sequence changes, which is usually difficult in LAMP. By extending LAMP’s ability to be utilized for multitarget and single-base change detection, we hope to increase its potential to enable more and better molecular diagnostic testing.
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21
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Chassalevris T, Chaintoutis SC, Koureas M, Petala M, Moutou E, Beta C, Kyritsi M, Hadjichristodoulou C, Kostoglou M, Karapantsios T, Papadopoulos A, Papaioannou N, Dovas CI. SARS-CoV-2 wastewater monitoring using a novel PCR-based method rapidly captured the Delta-to-Omicron ΒΑ.1 transition patterns in the absence of conventional surveillance evidence. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022. [PMID: 35753493 DOI: 10.1101/2022.01.28.21268186] [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: 05/09/2023]
Abstract
Conventional SARS-CoV-2 surveillance based on genotyping of clinical samples is characterized by challenges related to the available sequencing capacity, population sampling methodologies, and is time, labor, and resource-demanding. Wastewater-based variant surveillance constitutes a valuable supplementary practice, since it does not require extensive sampling, and provides information on virus prevalence in a timely and cost-effective manner. Consequently, we developed a sensitive real-time RT-PCR-based approach that exclusively amplifies and quantifies SARS-CoV-2 genomic regions carrying the S:Δ69/70 deletion, indicative of the Omicron BA.1 variant, in wastewater. The method was incorporated in the analysis of composite daily samples taken from the main Wastewater Treatment Plant of Thessaloniki, Greece, from 1 December 2021. The applicability of the methodology is dependent on the epidemiological situation. During Omicron BA.1 global emergence, Thessaloniki was experiencing a massive epidemic wave attributed solely to the Delta variant, according to genomic surveillance data. Since Delta does not possess the S:Δ69/70, the emergence of Omicron BA.1 could be monitored via the described methodology. Omicron BA.1 was detected in sewage samples on 19 December 2021 and a rapid increase of its viral load was observed in the following 10-day period, with an estimated early doubling time of 1.86 days. The proportion of the total SARS-CoV-2 load attributed to BA.1 reached 91.09 % on 7 January, revealing a fast Delta-to-Omicron transition pattern. The detection of Omicron BA.1 subclade in wastewater preceded the outburst of reported (presumable) Omicron cases in the city by approximately 7 days. The proposed wastewater surveillance approach based on selective PCR amplification of a genomic region carrying a deletion signature enabled rapid, real-time data acquisition on Omicron BA.1 prevalence and dynamics during the slow remission of the Delta wave. Timely provision of these results to State authorities readily influences the decision-making process for targeted public health interventions, including control measures, awareness, and preparedness.
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Affiliation(s)
- Taxiarchis Chassalevris
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece
| | - Serafeim C Chaintoutis
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece
| | - Michalis Koureas
- Department of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 22 Papakyriazi str., 41222 Larissa, Greece
| | - Maria Petala
- Laboratory of Environmental Engineering & Planning, Department of Civil Engineering, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Evangelia Moutou
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece
| | - Christina Beta
- Laboratory of Environmental Engineering & Planning, Department of Civil Engineering, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Maria Kyritsi
- Department of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 22 Papakyriazi str., 41222 Larissa, Greece
| | - Christos Hadjichristodoulou
- Department of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 22 Papakyriazi str., 41222 Larissa, Greece
| | - Margaritis Kostoglou
- Laboratory of Chemical and Environmental Technology, School of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Thodoris Karapantsios
- Laboratory of Chemical and Environmental Technology, School of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Agis Papadopoulos
- EYATH S.A., Thessaloniki Water Supply and Sewerage Company S.A., 54636 Thessaloniki, Greece
| | - Nikolaos Papaioannou
- Laboratory of Pathology, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Chrysostomos I Dovas
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece.
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22
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Chassalevris T, Chaintoutis SC, Koureas M, Petala M, Moutou E, Beta C, Kyritsi M, Hadjichristodoulou C, Kostoglou M, Karapantsios T, Papadopoulos A, Papaioannou N, Dovas CI. SARS-CoV-2 wastewater monitoring using a novel PCR-based method rapidly captured the Delta-to-Omicron ΒΑ.1 transition patterns in the absence of conventional surveillance evidence. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 844:156932. [PMID: 35753493 PMCID: PMC9225927 DOI: 10.1016/j.scitotenv.2022.156932] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 05/09/2022] [Accepted: 06/20/2022] [Indexed: 05/21/2023]
Abstract
Conventional SARS-CoV-2 surveillance based on genotyping of clinical samples is characterized by challenges related to the available sequencing capacity, population sampling methodologies, and is time, labor, and resource-demanding. Wastewater-based variant surveillance constitutes a valuable supplementary practice, since it does not require extensive sampling, and provides information on virus prevalence in a timely and cost-effective manner. Consequently, we developed a sensitive real-time RT-PCR-based approach that exclusively amplifies and quantifies SARS-CoV-2 genomic regions carrying the S:Δ69/70 deletion, indicative of the Omicron BA.1 variant, in wastewater. The method was incorporated in the analysis of composite daily samples taken from the main Wastewater Treatment Plant of Thessaloniki, Greece, from 1 December 2021. The applicability of the methodology is dependent on the epidemiological situation. During Omicron BA.1 global emergence, Thessaloniki was experiencing a massive epidemic wave attributed solely to the Delta variant, according to genomic surveillance data. Since Delta does not possess the S:Δ69/70, the emergence of Omicron BA.1 could be monitored via the described methodology. Omicron BA.1 was detected in sewage samples on 19 December 2021 and a rapid increase of its viral load was observed in the following 10-day period, with an estimated early doubling time of 1.86 days. The proportion of the total SARS-CoV-2 load attributed to BA.1 reached 91.09 % on 7 January, revealing a fast Delta-to-Omicron transition pattern. The detection of Omicron BA.1 subclade in wastewater preceded the outburst of reported (presumable) Omicron cases in the city by approximately 7 days. The proposed wastewater surveillance approach based on selective PCR amplification of a genomic region carrying a deletion signature enabled rapid, real-time data acquisition on Omicron BA.1 prevalence and dynamics during the slow remission of the Delta wave. Timely provision of these results to State authorities readily influences the decision-making process for targeted public health interventions, including control measures, awareness, and preparedness.
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Affiliation(s)
- Taxiarchis Chassalevris
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece
| | - Serafeim C Chaintoutis
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece
| | - Michalis Koureas
- Department of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 22 Papakyriazi str., 41222 Larissa, Greece
| | - Maria Petala
- Laboratory of Environmental Engineering & Planning, Department of Civil Engineering, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Evangelia Moutou
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece
| | - Christina Beta
- Laboratory of Environmental Engineering & Planning, Department of Civil Engineering, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Maria Kyritsi
- Department of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 22 Papakyriazi str., 41222 Larissa, Greece
| | - Christos Hadjichristodoulou
- Department of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 22 Papakyriazi str., 41222 Larissa, Greece
| | - Margaritis Kostoglou
- Laboratory of Chemical and Environmental Technology, School of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Thodoris Karapantsios
- Laboratory of Chemical and Environmental Technology, School of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Agis Papadopoulos
- EYATH S.A., Thessaloniki Water Supply and Sewerage Company S.A., 54636 Thessaloniki, Greece
| | - Nikolaos Papaioannou
- Laboratory of Pathology, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Chrysostomos I Dovas
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece.
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23
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Nedorezova DD, Dubovichenko MV, Belyaeva EP, Grigorieva ED, Peresadina AV, Kolpashchikov DM. Specificity of oligonucleotide gene therapy (OGT) agents. Theranostics 2022; 12:7132-7157. [PMID: 36276652 PMCID: PMC9576606 DOI: 10.7150/thno.77830] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/11/2022] [Indexed: 11/24/2022] Open
Abstract
Oligonucleotide gene therapy (OGT) agents (e. g. antisense, deoxyribozymes, siRNA and CRISPR/Cas) are promising therapeutic tools. Despite extensive efforts, only few OGT drugs have been approved for clinical use. Besides the problem of efficient delivery to targeted cells, hybridization specificity is a potential limitation of OGT agents. To ensure tight binding, a typical OGT agent hybridizes to the stretch of 15-25 nucleotides of a unique targeted sequence. However, hybrids of such lengths tolerate one or more mismatches under physiological conditions, the problem known as the affinity/specificity dilemma. Here, we assess the scale of this problem by analyzing OGT hybridization-dependent off-target effects (HD OTE) in vitro, in animal models and clinical studies. All OGT agents except deoxyribozymes exhibit HD OTE in vitro, with most thorough evidence of poor specificity reported for siRNA and CRISPR/Cas9. Notably, siRNA suppress non-targeted genes due to (1) the partial complementarity to mRNA 3'-untranslated regions (3'-UTR), and (2) the antisense activity of the sense strand. CRISPR/Cas9 system can cause hundreds of non-intended dsDNA breaks due to low specificity of the guide RNA, which can limit therapeutic applications of CRISPR/Cas9 by ex-vivo formats. Contribution of this effects to the observed in vivo toxicity of OGT agents is unclear and requires further investigation. Locked or peptide nucleic acids improve OGT nuclease resistance but not specificity. Approaches that use RNA marker dependent (conditional) activation of OGT agents may improve specificity but require additional validation in cell culture and in vivo.
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Affiliation(s)
- Daria D. Nedorezova
- Laboratory of Molecular Robotics and Biosensor Materials, International Institute SCAMT, ITMO University, 9 Lomonosov Str., St. Petersburg, 191002, Russian Federation
| | - Mikhail V. Dubovichenko
- Laboratory of Molecular Robotics and Biosensor Materials, International Institute SCAMT, ITMO University, 9 Lomonosov Str., St. Petersburg, 191002, Russian Federation
| | - Ekaterina P. Belyaeva
- Laboratory of Molecular Robotics and Biosensor Materials, International Institute SCAMT, ITMO University, 9 Lomonosov Str., St. Petersburg, 191002, Russian Federation
| | - Ekaterina D. Grigorieva
- Laboratory of Molecular Robotics and Biosensor Materials, International Institute SCAMT, ITMO University, 9 Lomonosov Str., St. Petersburg, 191002, Russian Federation
| | - Arina V. Peresadina
- Laboratory of Molecular Robotics and Biosensor Materials, International Institute SCAMT, ITMO University, 9 Lomonosov Str., St. Petersburg, 191002, Russian Federation
| | - Dmitry M. Kolpashchikov
- Laboratory of Molecular Robotics and Biosensor Materials, International Institute SCAMT, ITMO University, 9 Lomonosov Str., St. Petersburg, 191002, Russian Federation
- Chemistry Department, University of Central Florida, Orlando, FL 32816-2366, USA
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32816, USA
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24
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Jiménez-Montenegro L, Mendizabal JA, Alfonso L, Azparren L, Urrutia O. Development of a duplex qPCR assay with locked nucleic acid probes for A, B and E kappa-casein variants detection. Sci Rep 2022; 12:16387. [PMID: 36180500 PMCID: PMC9525573 DOI: 10.1038/s41598-022-20586-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 09/15/2022] [Indexed: 11/09/2022] Open
Abstract
Milk proteins determine important milk technological characteristics. Among caseins, Ƙ-casein has been correlated with fat and protein content and cheese yield. Fourteen Ƙ-caseins variants have been described but the alleles A, B and E are the most important ones due to their frequency and/or influence on the technological aptitudes of milk. Therefore, in the present study two different duplex qPCR assays with locked nucleic acid probes (for positions 13104 and 13124 of the Ƙ-casein gene) were developed for the detection of A, B and E variants. Firstly, DNA isolation method from milk somatic cells and hair was optimised. The developed 13124-qPCR assay showed an increased sensitivity reaching up to 6.7 copies DNA copies/reaction at a 95% confidence level with A, B and E alleles reference samples. The 13104-qPCR assay reached up to 6.7 DNA copies/reaction for A allele reference sample and 67 DNA copies/reaction for B and E samples. Intra-assay variation results were below 6%. Applicability was determined using DNA samples from animals with known genotype for Ƙ-casein (AA, AB, BB, BE, AE, EE) and both assays were able to discriminate among the six genotypes with 100% accuracy. Thus, this qPCR method represents a sensitive and rapid option for the detection of Ƙ-casein alleles in both hair and milk samples.
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Affiliation(s)
- L Jiménez-Montenegro
- IS-FOOD, School of Agricultural Engineering and Biosciences, Public University of Navarre (UPNA), Campus de Arrosadia, 31006, Pamplona, Spain
| | - J A Mendizabal
- IS-FOOD, School of Agricultural Engineering and Biosciences, Public University of Navarre (UPNA), Campus de Arrosadia, 31006, Pamplona, Spain
| | - L Alfonso
- IS-FOOD, School of Agricultural Engineering and Biosciences, Public University of Navarre (UPNA), Campus de Arrosadia, 31006, Pamplona, Spain
| | - L Azparren
- IS-FOOD, School of Agricultural Engineering and Biosciences, Public University of Navarre (UPNA), Campus de Arrosadia, 31006, Pamplona, Spain
| | - O Urrutia
- IS-FOOD, School of Agricultural Engineering and Biosciences, Public University of Navarre (UPNA), Campus de Arrosadia, 31006, Pamplona, Spain.
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25
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Targeting non-coding RNA family members with artificial endonuclease XNAzymes. Commun Biol 2022; 5:1010. [PMID: 36153384 PMCID: PMC9509326 DOI: 10.1038/s42003-022-03987-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 09/13/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractNon-coding RNAs (ncRNAs) offer a wealth of therapeutic targets for a range of diseases. However, secondary structures and high similarity within sequence families make specific knockdown challenging. Here, we engineer a series of artificial oligonucleotide enzymes (XNAzymes) composed of 2’-deoxy-2’-fluoro-β-D-arabino nucleic acid (FANA) that specifically or preferentially cleave individual ncRNA family members under quasi-physiological conditions, including members of the classic microRNA cluster miR-17~92 (oncomiR-1) and the Y RNA hY5. We demonstrate self-assembly of three anti-miR XNAzymes into a biostable catalytic XNA nanostructure, which targets the cancer-associated microRNAs miR-17, miR-20a and miR-21. Our results provide a starting point for the development of XNAzymes as a platform technology for precision knockdown of specific non-coding RNAs, with the potential to reduce off-target effects compared with other nucleic acid technologies.
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26
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Kongta R, Panyasit N, Jansaento W, Duangmano S. Development of E-ice-COLD-PCR assay combined with HRM analysis for Nucleophosmin1 gene mutation detection in acute myelogenous leukemia. PLoS One 2022; 17:e0274034. [PMID: 36103476 PMCID: PMC9473412 DOI: 10.1371/journal.pone.0274034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 08/21/2022] [Indexed: 12/08/2022] Open
Abstract
Mutations of the nucleophosmin1 (NPM1) gene represent the most frequent molecular alteration in acute myelogenous leukemia (AML), especially in patients with AML who have a normal karyotype. These alterations have been shown to carry favorable prognostic significance in patients with AML. Several methods have been developed for detection of NPM1 gene mutations. However, their ability to detect low levels of mutations in a wild-type background is limited. In this study, the Enhance improved and complete enrichment Co-amplification at Lower Denaturation temperature Polymerase Chain Reaction (E-ice-COLD-PCR) assay combined with High Resolution Melting (HRM) analysis was developed and validated for highly specific and sensitive screening for NPM1 gene mutations. A total of 83 blood samples from patients with AML were collected, and their DNA was extracted. For mutational analysis, the E-ice-COLD-PCR assay for the detection of NPM1 gene mutations was developed. PCR products were analyzed by HRM analysis. All positive samples were confirmed by direct sequencing. This assay enabled detection specificity and sensitivity of NPM1 mutations in 9/83 patients with AML. Direct sequencing results were 100% concordant with this method. In addition, the limit of detection was 12.5% mutant in the final concentration of 5 ng genomic DNA. The E-ice-COLD-PCR assay with HRM analysis is a highly specific and sensitive screening method for enrichment of detecting NPM1 gene mutations. This method has both a short turn around time and easier interpretation compared to those of other methods.
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Affiliation(s)
- Rattana Kongta
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Noppamas Panyasit
- Division of Hematology, Department of Internal Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | | | - Suwit Duangmano
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
- Cancer Research Unit of Associated Medical Sciences (AMS-CRU), Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
- * E-mail:
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27
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Chowdhury S, Wang J, Nuccio SP, Mao H, Di Antonio M. Short LNA-modified oligonucleotide probes as efficient disruptors of DNA G-quadruplexes. Nucleic Acids Res 2022; 50:7247-7259. [PMID: 35801856 PMCID: PMC9303293 DOI: 10.1093/nar/gkac569] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 06/09/2022] [Accepted: 06/18/2022] [Indexed: 12/20/2022] Open
Abstract
G-quadruplexes (G4s) are well known non-canonical DNA secondary structures that can form in human cells. Most of the tools available to investigate G4-biology rely on small molecule ligands that stabilise these structures. However, the development of probes that disrupt G4s is equally important to study their biology. In this study, we investigated the disruption of G4s using Locked Nucleic Acids (LNA) as invader probes. We demonstrated that strategic positioning of LNA-modifications within short oligonucleotides (10 nts.) can significantly accelerate the rate of G4-disruption. Single-molecule experiments revealed that short LNA-probes can promote disruption of G4s with mechanical stability sufficient to stall polymerases. We corroborated this using a single-step extension assay, revealing that short LNA-probes can relieve replication dependent polymerase-stalling at G4 sites. We further demonstrated the potential of such LNA-based probes to study G4-biology in cells. By using a dual-luciferase assay, we found that short LNA probes can enhance the expression of c-KIT to levels similar to those observed when the c-KIT promoter is mutated to prevent the formation of the c-KIT1 G4. Collectively, our data suggest a potential use of rationally designed LNA-modified oligonucleotides as an accessible chemical-biology tool for disrupting individual G4s and interrogating their biological functions in cells.
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Affiliation(s)
- Souroprobho Chowdhury
- Imperial College London, Chemistry Department, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK.,Institute of Chemical Biology, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK
| | - Jiayi Wang
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Sabrina Pia Nuccio
- Imperial College London, Chemistry Department, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK.,Institute of Chemical Biology, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK.,The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Hanbin Mao
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Marco Di Antonio
- Imperial College London, Chemistry Department, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK.,Institute of Chemical Biology, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK.,The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
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28
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Yang K, Schuder DN, Ngor AK, Chaput JC. REVEALR-Based Genotyping of SARS-CoV-2 Variants of Concern in Clinical Samples. J Am Chem Soc 2022; 144:11685-11692. [PMID: 35729726 PMCID: PMC9236216 DOI: 10.1021/jacs.2c03420] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Indexed: 11/29/2022]
Abstract
The SARS-CoV-2 virus has evolved into new strains that increase viral transmissibility and reduce vaccine protection. The rapid circulation of these more harmful strains across the globe has created a pressing need for alternative public health screening tools. REVEALR (RNA-encoded viral nucleic acid analytic reporter), a rapid and highly sensitive DNAzyme-based detection system, functions with perfect accuracy against patient-derived clinical samples. Here, we design REVEALR into a novel genotyping assay that detects single-base mismatches corresponding to each of the major SARS-CoV-2 strains found in the United States. Of 34 sequence-verified patient samples collected in early, mid, and late 2021 at the UCI Medical Center in Orange, California, REVEALR identified the correct variant [Wuhan-Hu-1, alpha (B.1.1.7), gamma (P.1), epsilon (B.1.427/9), delta (B.1.617.2), and omicron (B.1.1.529)] with 100% accuracy. The assay, which is programmable and amenable to multiplexing, offers an important new approach to personalized diagnostics.
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Affiliation(s)
- Kefan Yang
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA 92697-3958, United States
| | - Daniel N. Schuder
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3958, United States
| | - Arlene K. Ngor
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697-3958, United States
| | - John C. Chaput
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697-3958, United States
- Department of Chemistry, University of California, Irvine, CA 92697-3958, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3958, United States
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA 92697-3958, United States
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29
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Jiménez-Montenegro L, Mendizabal J, Alfonso L, Urrutia O. DNA extraction procedures and validation parameters of a real time PCR method to control milk containing only A2 β-casein. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.109259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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30
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Assessment of the Real-Time PCR Method Claiming to be Specific for Detection and Quantification of the First Commercialised Genome-Edited Plant. FOOD ANAL METHOD 2022. [DOI: 10.1007/s12161-022-02237-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Abstract
A real-time PCR method was recently published with a claim to be specific for the detection and identification of some genome-edited oilseed rape (OSR) lines commercialised in North America. The method was designed to detect a single base mutation in the AHAS1C gene, which confers herbicide tolerance. The authors claim that the method is event-specific for the genome-edited OSR line 5715 and fulfils all requirements for GMO analytical methods according to EU regulations. We have thoroughly assessed the method in relation to the minimum performance requirements (MPR) established by the European Network of GMO Laboratories (ENGL). The method was found to be sufficiently sensitive and robust when tested with pure genomic DNA of the OSR line 40 K. However, our results show that the method is not event-specific and detects also OSR lines carrying the same point mutation caused by somaclonal variation. Moreover, impaired robustness was observed using non-modified genomic DNA at the amount specified in the original protocol. Significant non-specific PCR amplifications with PCR products as non-target template DNA and with genomic DNA from numerous OSR varieties as well as from wild radish were found by three ISO/IEC 17025 accredited reference laboratories in tests using different master mixes and PCR cycler models. The assessment shows that the method does not meet the MPR for qualitative PCR methods and therefore is not fit-for-purpose for official controls of genetically modified products in the EU. Suggestions are provided for conditions under which analytical methods for genome-edited organisms should be validated.
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31
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Djebbi K, Xing J, Weng T, Bahri M, Elaguech MA, Du C, Shi B, Hu L, He S, Liao P, Tlili C, Wang D. Highly sensitive fluorescence multiplexed miRNAs biosensors for accurate clinically diagnosis lung cancer disease using LNA-modified DNA probe and DSN enzyme. Anal Chim Acta 2022; 1208:339778. [DOI: 10.1016/j.aca.2022.339778] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/21/2022] [Accepted: 03/25/2022] [Indexed: 12/26/2022]
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32
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Nörz D, Grunwald M, Tang HT, Weinschenk C, Günther T, Robitaille A, Giersch K, Fischer N, Grundhoff A, Aepfelbacher M, Pfefferle S, Lütgehetmann M. Clinical Evaluation of a Fully-Automated High-Throughput Multiplex Screening-Assay to Detect and Differentiate the SARS-CoV-2 B.1.1.529 (Omicron) and B.1.617.2 (Delta) Lineage Variants. Viruses 2022; 14:608. [PMID: 35337015 PMCID: PMC8950896 DOI: 10.3390/v14030608] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 03/01/2022] [Accepted: 03/12/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The recently emerged SARS-CoV-2 B.1.1.529 lineage and its sublineages (Omicron variant) pose a new challenge to healthcare systems worldwide due to its ability to efficiently spread in immunized populations and its resistance to currently available monoclonal antibody therapies. RT-PCR-based variant tests can be used to screen large sample-sets rapidly and accurately for relevant variants of concern (VOC). The aim of this study was to establish and validate a multiplex assay on the cobas 6800/8800 systems to allow discrimination between the two currently circulating VOCs, Omicron and Delta, in clinical samples. METHODS Primers and probes were evaluated for multiplex compatibility. Analytic performance was assessed using cell culture supernatant of an Omicron variant isolate and a clinical Delta variant sample, normalized to WHO-Standard. Clinical performance of the multiplex assay was benchmarked against NGS results. RESULTS In silico testing of all oligos showed no interactions with a high risk of primer-dimer formation or amplification of human DNA/RNA. Over 99.9% of all currently available Omicron variant sequences are a perfect match for at least one of the three Omicron targets included in the multiplex. Analytic sensitivity was determined as 19.0 IU/mL (CI95%: 12.9-132.2 IU/mL) for the A67V + del-HV69-70 target, 193.9 IU/mL (CI95%: 144.7-334.7 IU/mL) for the E484A target, 35.5 IU/mL (CI95%: 23.3-158.0 IU/mL) for the N679K + P681H target and 105.0 IU/mL (CI95%: 80.7-129.3 IU/mL) for the P681R target. All sequence variances were correctly detected in the clinical sample set (225/225 Targets). CONCLUSION RT-PCR-based variant screening compared to whole genome sequencing is both rapid and reliable in detecting relevant sequence variations in SARS-CoV-2 positive samples to exclude or verify relevant VOCs. This allows short-term decision-making, e.g., for patient treatment or public health measures.
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Affiliation(s)
- Dominik Nörz
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (D.N.); (M.G.); (H.T.T.); (C.W.); (K.G.); (N.F.); (M.A.); (S.P.)
| | - Moritz Grunwald
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (D.N.); (M.G.); (H.T.T.); (C.W.); (K.G.); (N.F.); (M.A.); (S.P.)
| | - Hui Ting Tang
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (D.N.); (M.G.); (H.T.T.); (C.W.); (K.G.); (N.F.); (M.A.); (S.P.)
| | - Celine Weinschenk
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (D.N.); (M.G.); (H.T.T.); (C.W.); (K.G.); (N.F.); (M.A.); (S.P.)
| | - Thomas Günther
- Leibniz Institute for Experimental Virology (HPI), Virus Genomics, 20251 Hamburg, Germany; (T.G.); (A.R.); (A.G.)
| | - Alexis Robitaille
- Leibniz Institute for Experimental Virology (HPI), Virus Genomics, 20251 Hamburg, Germany; (T.G.); (A.R.); (A.G.)
| | - Katja Giersch
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (D.N.); (M.G.); (H.T.T.); (C.W.); (K.G.); (N.F.); (M.A.); (S.P.)
| | - Nicole Fischer
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (D.N.); (M.G.); (H.T.T.); (C.W.); (K.G.); (N.F.); (M.A.); (S.P.)
| | - Adam Grundhoff
- Leibniz Institute for Experimental Virology (HPI), Virus Genomics, 20251 Hamburg, Germany; (T.G.); (A.R.); (A.G.)
| | - Martin Aepfelbacher
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (D.N.); (M.G.); (H.T.T.); (C.W.); (K.G.); (N.F.); (M.A.); (S.P.)
| | - Susanne Pfefferle
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (D.N.); (M.G.); (H.T.T.); (C.W.); (K.G.); (N.F.); (M.A.); (S.P.)
| | - Marc Lütgehetmann
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (D.N.); (M.G.); (H.T.T.); (C.W.); (K.G.); (N.F.); (M.A.); (S.P.)
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Xu J, Pu Y, Lin R, Xiao S, Fu Y, Wang T. PEAC: An Ultrasensitive and Cost-Effective MRD Detection System in Non-small Cell Lung Cancer Using Plasma Specimen. Front Med (Lausanne) 2022; 9:822200. [PMID: 35308511 PMCID: PMC8928926 DOI: 10.3389/fmed.2022.822200] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/14/2022] [Indexed: 12/25/2022] Open
Abstract
Circulating tumor DNA (ctDNA), a tumor-derived fraction of cell-free DNA (cfDNA), has emerged as a promising marker in targeted therapy, immunotherapy, and minimal residual disease (MRD) monitoring in postsurgical patients. However, ctDNA level in early-stage cancers and postsurgical patients is very low, which posed many technical challenges to improve the detection rate and sensitivity, especially in the clinical practice of MRD detection. These challenges usually include insufficient DNA input amount, limit of detection (LOD), and high experimental costs. To resolve these challenges, we developed an ultrasensitive ctDNA MRD detection system in this study, namely PErsonalized Analysis of Cancer (PEAC), to simultaneously detect up to 37 mutations, which account for 70–80% non-small cell lung cancer (NSCLC) driver mutations from low plasma sample volume and enables LOD of 0.01% at a single-site level. We demonstrated the high performance achieved by PEAC on both cfDNA reference standards and clinical plasma samples from three NSCLC patient cohorts. For cfDNA reference standards, PEAC achieved a specificity of 99% and a sensitivity of 87% for the mutations at 0.01% allele fraction. In the second cohort, PEAC showed 100% concordance rate between ddPCR and Next-generation sequencing (NGS) among 29 samples. In the third cohort, 22 of 59 patients received EGFR TKI treatment. Among them, three in four patients identified low level actionable gene mutations only by PEAC had partial responses after targeted therapy, demonstrating high ctDNA detection ability of PEAC. Overall, the developed PEAC system can detect the majority of NSCLC driver mutations using 8–10 ml plasma samples, and has the advantages of high detection sensitivity and lower costs compared with the existing technologies such as ddPCR and NGS. These advantages make the PEAC system quite appropriate for ctDNA and MRD detection in early-stage NSCLC and postsurgical recurrence monitoring.
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Affiliation(s)
- Jianping Xu
- Department of Medical Oncology, Cancer Hospital, Chinese Academy of Medical Sciences, Beijing, China
- Peking Union Medical College, Beijing, China
- *Correspondence: Jianping Xu
| | - Yue Pu
- Department of Research and Development, Hangzhou Repugene Technology Co., Ltd., Hangzhou, China
| | - Rui Lin
- Department of Research and Development, Hangzhou Repugene Technology Co., Ltd., Hangzhou, China
| | - Shanshan Xiao
- Department of Research and Development, Hangzhou Repugene Technology Co., Ltd., Hangzhou, China
| | - Yingxue Fu
- Department of Research and Development, Hangzhou Repugene Technology Co., Ltd., Hangzhou, China
| | - Tao Wang
- Department of Research and Development, Hangzhou Repugene Technology Co., Ltd., Hangzhou, China
- Tao Wang
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Tan C, Yan Y, Guo N, Wang F, Wang S, Zhu L, Wang Y, Ma Y, Guo Y. Single-Tube Multiplex Digital Polymerase Chain Reaction Assay for Molecular Diagnosis and Prediction of Severity of Spinal Muscular Atrophy. Anal Chem 2022; 94:3517-3525. [PMID: 35137581 DOI: 10.1021/acs.analchem.1c04403] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disease characterized by the degeneration of motor neurons and progressive muscle atrophy. Accurate detection of SMN1 and SMN2 copy numbers is essential for SMA diagnosis, carrier screening, disease severity prediction, therapy, and prognosis. However, a method for SMN1 and SMN2 copy number determination that is simultaneously accurate, simple, rapid, multitargeted, and applicable to various samples has not previously been reported. Here, we developed a single-tube multiplex digital polymerase chain reaction (dPCR) assay for simultaneous determination of the copy numbers of SMN1 exons 7 and 8 and SMN2 exons 7 and 8. A total of 317 clinical samples, including peripheral blood, amniotic fluid, chorionic villus, buccal swabs, and dried blood spots, were collected to evaluate the performance of this dPCR-based assay. The test results were accurate for all the clinical samples. Our assay is accurate, rapid, easy to handle, and applicable to many types of samples and uses a small amount of DNA; it is a powerful tool for SMA molecular diagnosis, large-scale screening, and disease severity assessment.
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Affiliation(s)
- Chianru Tan
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yousheng Yan
- Prenatal Diagnostic Center, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing 100026, China
| | - Na Guo
- TargetingOne Corporation, Beijing 100190, China
| | - Fang Wang
- TargetingOne Corporation, Beijing 100190, China
| | - Songtao Wang
- Department of Central Laboratory, Peking University First Hospital, Beijing 100034, China
| | | | - Yipeng Wang
- Prenatal Diagnostic Center, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing 100026, China
| | - Yinan Ma
- Department of Central Laboratory, Peking University First Hospital, Beijing 100034, China
| | - Yong Guo
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
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Single-Amplicon Multiplex Real-Time Reverse Transcription-PCR with Tiled Probes To Detect SARS-CoV-2 spike Mutations Associated with Variants of Concern. J Clin Microbiol 2021; 59:e0144621. [PMID: 34432488 PMCID: PMC8601233 DOI: 10.1128/jcm.01446-21] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
To provide an accessible and inexpensive method to surveil for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mutations, we developed a multiplex real-time reverse transcription-PCR (rRT-PCR) assay, the Spike single-nucleotide polymorphism (SNP) assay, to detect specific mutations in the spike receptor binding domain. A single primer pair was designed to amplify a 348-bp region of spike, and probes were initially designed to detect K417, E484K, and N501Y. The assay was evaluated using characterized variant sample pools and residual nasopharyngeal samples. Variant calls were confirmed by SARS-CoV-2 genome sequencing in a subset of samples. Subsequently, a fourth probe was designed to detect L452R. The lower limit of 95% detection was 2.46 to 2.48 log10 genome equivalents (GE)/ml for the three initial targets (∼1 to 2 GE/reaction). Among 253 residual nasopharyngeal swabs with detectable SARS-CoV-2 RNA, the Spike SNP assay was positive in 238 (94.1%) samples. All 220 samples with threshold cycle (CT) values of <30 for the SARS-CoV-2 N2 target were detected, whereas 18/33 samples with N2 CT values of ≥30 were detected. Spike SNP results were confirmed by sequencing in 50/50 samples (100%). Addition of the 452R probe did not affect performance for the original targets. The Spike SNP assay accurately identifies SARS-CoV-2 mutations in the receptor binding domain, and it can be quickly modified to detect new mutations that emerge.
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Adhikari SP, Vukelich P, Guenther DC, Karmakar S, Hrdlicka PJ. Recognition of double-stranded DNA using LNA-modified toehold Invader probes. Org Biomol Chem 2021; 19:9276-9290. [PMID: 34657934 PMCID: PMC8625219 DOI: 10.1039/d1ob01888d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Development of molecules capable of binding to specific sequences of double-stranded (ds) DNA continues to attract considerable interest, as this may yield useful tools for applications in life science, biotechnology, and medicine. We have previously demonstrated sequence-unrestricted of dsDNA using Invader probes, i.e., DNA duplexes that are energetically activated through incorporation of +1 interstrand zipper arrangements of O2'-intercalator-functionalized RNA monomers. Nonetheless, recognition of extended dsDNA target regions remains challenging due to the high stability of the corresponding probes. To address this, we introduce toehold Invader probes, i.e., Invader probes with 5'-single-stranded overhangs. This design provides access to probes with shortened double-stranded segments, which facilitates probe denaturation. The single-stranded overhangs can, furthermore, be modified with affinity-enhancing modifications like LNA (locked nucleic acid) monomers to additionally increase target affinity. Herein, we report the biophysical and dsDNA-targeting properties of different toehold Invader designs and compare them to conventional Invader probes. LNA-modified toehold Invader probes display promising recognition characteristics, including greatly improved affinity to dsDNA, excellent binding specificity, and fast recognition kinetics, which enabled recognition of chromosomal DNA targets that have proven refractory to recognition by conventional Invader probes. Thus, toehold Invader probes represent another step toward a robust, oligonucleotide-based approach for sequence-unrestricted dsDNA-recognition.
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Affiliation(s)
- Shiva P Adhikari
- Department of Chemistry, University of Idaho, Moscow, ID-83844, USA.
| | - Philip Vukelich
- Department of Chemistry, University of Idaho, Moscow, ID-83844, USA.
| | - Dale C Guenther
- Department of Chemistry, University of Idaho, Moscow, ID-83844, USA.
| | - Saswata Karmakar
- Department of Chemistry, University of Idaho, Moscow, ID-83844, USA.
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Fu G, Chazen RS, MacMillan C, Witterick IJ. Development of a Molecular Assay for Detection and Quantification of the BRAF Variation in Residual Tissue From Thyroid Nodule Fine-Needle Aspiration Biopsy Specimens. JAMA Netw Open 2021; 4:e2127243. [PMID: 34613404 PMCID: PMC8495535 DOI: 10.1001/jamanetworkopen.2021.27243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 07/09/2021] [Indexed: 12/14/2022] Open
Abstract
Importance Thyroid cancer, predominantly papillary thyroid carcinoma (PTC), is common, but an estimated 30% of ultrasonography-guided fine-needle aspiration (FNA) biopsies of thyroid nodules are indeterminate. BRAF variation, associated with poor clinicopathological characteristics, is a useful molecular marker for diagnostics. Objective To develop a sensitive molecular assay for BRAF V600E detection in remaining tissue of thyroid FNA biopsies to identify patients with cancer carrying a BRAF variation. Design, Setting, and Participants This diagnostic study used tumor tissue from surgical formalin-fixed, paraffin-embedded (FFPE) specimens and residual tissue from thyroid FNA biopsies for genomic DNA extraction. FFPE specimens served as the validation set, and residual tissue from FNA biopsies served as the test set. A molecular assay was developed for accurate detection of BRAF V600E variation using locked nucleic acid (LNA) probe-based droplet digital polymerase chain reaction (dPCR), and the assay was validated by BRAF V600E immunohistochemical staining (IHC). The study was conducted between February 2019 and May 2021. Results A total of 271 specimens, including 77 FFPE specimens (with a follow-up of 48 matched surgical specimens) and 146 residual FNA samples, were collected from 223 patients (mean [SD] age, 53.8 [15.3] years; 174 [78.0%] women; 49 [22.0%] men). The molecular assay by dPCR was first established to specifically and accurately detect and quantify wild-type BRAF and variant BRAF in DNA from human follicular thyroid carcinoma-derived FTC-133 and papillary thyroid carcinoma-derived BCPAP cells. The linearity of quantification of BRAF V600E was calculated (y = 0.7339x; R2 = 0.9996) with sensitivity at 0.02 copies/μL and reproducibility in detecting variant DNA at various dilutions(coefficient of variance in 0.3% DNA, 9.63%; coefficient of variance in 1.0% DNA, 7.41%). In validation testing, the dPCR assay and IHC staining exhibited 100% specificity in concordantly identifying BRAF V600E in PTCs (κ = 0.873; P < .001) and sensitivity of 32.0% (95% CI, 19.1% to 44.9%) in dPCR and 26.0% (95% CI, 13.1% to 38.9%) in IHC staining, with an improvement by 23.08% in dPCR compared with the IHC staining. The dPCR assay further detected BRAF V600E in 39 of 146 residual FNA specimens (26.7%). At short-term follow-up, 48 patients, including 14 of 39 patients with BRAF variation and 34 of 107 patients without BRAF variation on residual FNA specimens, underwent resection. The dPCR assay of BRAF status in the matched surgical specimens showed BRAF V600E variations in 12 patients and wild-type BRAF in 36 patients, with a high agreement to that in residual tissue of FNA specimens (κ = 0.789; P < .001). Among 14 patients with BRAF variations on residual FNA, 13 were diagnosed with PTC and 1 was diagnosed with anaplastic thyroid cancer at the thyroidectomy. Conclusions and Relevance This diagnostic study developed a sensitive molecular assay for detection and quantification of BRAF V600E variation in residual tissue from thyroid FNA biopsies to identify patients with cancer harboring BRAF V600E in a cost-effective manner, highlighting the clinical value of molecular assay of the remaining FNA tissue in the management of thyroid nodules.
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Affiliation(s)
- Guodong Fu
- Alex and Simona Shnaider Research Laboratory in Molecular Oncology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Mount Sinai Hospital, Toronto, Canada
| | - Ronald S. Chazen
- Alex and Simona Shnaider Research Laboratory in Molecular Oncology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Mount Sinai Hospital, Toronto, Canada
| | - Christina MacMillan
- Alex and Simona Shnaider Research Laboratory in Molecular Oncology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Mount Sinai Hospital, Toronto, Canada
- Department of Pathology and Laboratory Medicine, Sinai Health System, Mount Sinai Hospital, University of Toronto, Toronto, Canada
| | - Ian J. Witterick
- Alex and Simona Shnaider Research Laboratory in Molecular Oncology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Mount Sinai Hospital, Toronto, Canada
- Joseph and Mildred Sonshine Family Centre for Head and Neck Diseases, Sinai Health System, Mount Sinai Hospital, Toronto, Canada
- Department of Otolaryngology-Head and Neck Surgery, Sinai Health System, Mount Sinai Hospital, University of Toronto, Toronto, Canada
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Nörz D, Grunwald M, Tang HT, Olearo F, Günther T, Robitaille A, Fischer N, Grundhoff A, Aepfelbacher M, Pfefferle S, Lütgehetmann M. Rapid Automated Screening for SARS-CoV-2 B.1.617 Lineage Variants (Delta/Kappa) through a Versatile Toolset of qPCR-Based SNP Detection. Diagnostics (Basel) 2021; 11:1818. [PMID: 34679517 PMCID: PMC8534837 DOI: 10.3390/diagnostics11101818] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/23/2021] [Accepted: 09/25/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The recent emergence of distinct and highly successful SARS-CoV-2 lineages has substantial implications for individual patients and public health measures. While next-generation-sequencing is routinely performed for surveillance purposes, RT-qPCR can be used to rapidly rule-in or rule-out relevant variants, e.g., in outbreak scenarios. The objective of this study was to create an adaptable and comprehensive toolset for multiplexed Spike-gene SNP detection, which was applied to screen for SARS-CoV-2 B.1.617 lineage variants. METHODS We created a broad set of single nucleotide polymorphism (SNP)-assays including del-Y144/145, E484K, E484Q, P681H, P681R, L452R, and V1176F based on a highly specific multi-LNA (locked nucleic acid)-probe design to maximize mismatch discrimination. As proof-of-concept, a multiplex-test was compiled and validated (SCOV2-617VOC-UCT) including SNP-detection for L452R, P681R, E484K, and E484Q to provide rapid screening capabilities for the novel B.1.617 lineages. RESULTS For the multiplex-test (SCOV2-617VOC-UCT), the analytic lower limit of detection was determined as 182 IU/mL for L452R, 144 IU/mL for P681R, and 79 IU/mL for E484Q. A total of 233 clinical samples were tested with the assay, including various on-target and off-target sequences. All SNPs (179/179 positive) were correctly identified as determined by SARS-CoV-2 whole genome sequencing. CONCLUSION The recurrence of SNP locations and flexibility of methodology presented in this study allows for rapid adaptation to current and future variants. Furthermore, the ability to multiplex various SNP-assays into screening panels improves speed and efficiency for variant testing. We show 100% concordance with whole genome sequencing for a B.1.617.2 screening assay on the cobas6800 high-throughput system.
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Affiliation(s)
- Dominik Nörz
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (D.N.); (M.G.); (H.T.T.); (F.O.); (N.F.); (M.A.); (S.P.)
| | - Moritz Grunwald
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (D.N.); (M.G.); (H.T.T.); (F.O.); (N.F.); (M.A.); (S.P.)
| | - Hui Ting Tang
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (D.N.); (M.G.); (H.T.T.); (F.O.); (N.F.); (M.A.); (S.P.)
| | - Flaminia Olearo
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (D.N.); (M.G.); (H.T.T.); (F.O.); (N.F.); (M.A.); (S.P.)
| | - Thomas Günther
- Virus Genomics, Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (T.G.); (A.R.); (A.G.)
| | - Alexis Robitaille
- Virus Genomics, Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (T.G.); (A.R.); (A.G.)
| | - Nicole Fischer
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (D.N.); (M.G.); (H.T.T.); (F.O.); (N.F.); (M.A.); (S.P.)
| | - Adam Grundhoff
- Virus Genomics, Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (T.G.); (A.R.); (A.G.)
| | - Martin Aepfelbacher
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (D.N.); (M.G.); (H.T.T.); (F.O.); (N.F.); (M.A.); (S.P.)
| | - Susanne Pfefferle
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (D.N.); (M.G.); (H.T.T.); (F.O.); (N.F.); (M.A.); (S.P.)
| | - Marc Lütgehetmann
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (D.N.); (M.G.); (H.T.T.); (F.O.); (N.F.); (M.A.); (S.P.)
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Dimzas D, Chassalevris T, Ozolina Z, Dovas CI, Diakou A. Investigation of the Food-Transmitted Parasites Trichinella spp. and Alaria spp. in Wild Boars in Greece by Classical and Molecular Methods and Development of a Novel Real-Time PCR for Alaria spp. Detection. Animals (Basel) 2021; 11:ani11102803. [PMID: 34679826 PMCID: PMC8532891 DOI: 10.3390/ani11102803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/21/2021] [Accepted: 09/23/2021] [Indexed: 11/29/2022] Open
Abstract
Simple Summary There are many parasites that may be transmitted to humans via food, and meat is a major source of such infections. Trichinella spp. is one of the most important meat-transmitted parasites, while Alaria spp. may be considered an emerging pathogen, albeit to date rarely reported in humans. Raw and undercooked wild boar meat has been proven as a major source of human infection by both parasites. In the present study, an investigation of the presence of these parasites in wild boar meat was conducted for the first time in Greece. Classical parasitological methods and molecular techniques were implemented for the examination of samples collected from 128 hunted wild boars, and none of them were found positive for Trichinella spp. or Alaria spp. For the detection of Alaria spp., a novel molecular method was developed, offering a powerful complementary diagnostic tool that may be useful for the epizootiological surveillance of the parasite. The epizootiology/epidemiology, clinical implications, and importance of monitoring of these parasitic infections are briefly discussed. Abstract Foodborne parasitic diseases represent a major threat to public health. Trichinellosis, caused by the nematode parasite Trichinella spp., is one of the most important foodborne diseases, while alariosis, caused by the trematode parasite Alaria spp., is less common in humans, and rare cases have been reported only in the USA and Canada. Both parasites can infect humans via the consumption of raw or undercooked wild boar meat. In order to investigate the prevalence of these parasites in wild boar meat in Greece, samples from the diaphragm pillars and the region of the mandibular angle from 128 wild boars, hunted in Greece, were collected. The samples were examined by classical parasitological (compression, artificial digestion, and Alaria spp. migration) and by molecular (real-time PCR) methods. For Trichinella spp. an existent real-time PCR detecting all species likely to be present in Greece was applied, while for Alaria spp. a real-time PCR was developed, employing an LNA TaqMan probe targeting the large subunit ribosomal RNA gene. All examined wild boar samples from Greece resulted negative for Trichinella and Alaria species, indicating a low prevalence of infection in the examined population. The novel real-time PCR for Alaria spp. has 81.5% amplification efficiency and is able to detect 0.12 larvae per 50 g of tissue and could be utilized as a complementary to AMT diagnostic tool in surveillance.
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Affiliation(s)
- Dimitris Dimzas
- Laboratory of Parasitology and Parasitic Diseases, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Taxiarchis Chassalevris
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra Str., 54627 Thessaloniki, Greece; (T.C.); (C.I.D.)
| | - Zanda Ozolina
- Institute of Food Safety, Animal Health and Environment “BIOR”, Lejupes Str. 3, 1076 Riga, Latvia;
| | - Chrysostomos I. Dovas
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra Str., 54627 Thessaloniki, Greece; (T.C.); (C.I.D.)
| | - Anastasia Diakou
- Laboratory of Parasitology and Parasitic Diseases, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
- Correspondence:
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Chu SV, Vu ST, Nguyen HM, Le NT, Truong PT, Vu VTT, Phung TTB, Nguyen ATV. Fast and Sensitive Real-Time PCR Detection of Major Antiviral-Drug Resistance Mutations in Chronic Hepatitis B Patients by Use of a Predesigned Panel of Locked-Nucleic-Acid TaqMan Probes. J Clin Microbiol 2021; 59:e0093621. [PMID: 34319801 PMCID: PMC8451437 DOI: 10.1128/jcm.00936-21] [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: 04/20/2021] [Accepted: 07/19/2021] [Indexed: 11/20/2022] Open
Abstract
We developed a novel real-time PCR assay that simultaneously evaluates 11 major nucleos(t)ide antiviral (NA) drug resistance mutations (mt) in chronic hepatitis B patients (CHB), including L180M, M204I/V, and V207M (lamivudine [LMV] resistance), N/H238A/T (adefovir [ADF] resistance), which are circulating in Vietnam; and T184G/L, S202I, and M250V (entecavir [ETV] resistance) and A194T (tenofovir resistance), which have been recently reported in several studies across the globe. We detected drug-resistant mt in hepatitis B virus (HBV) samples using our predesigned panel of allele-specific locked-nucleic acid (LNA) probes. Our assay had a high sensitivity of 5% in a low-HBV DNA population of ≥5 × 103 IU/ml and was validated in a cohort of 130 treatment-naive children and 98 NA-experienced adults with CHB. Single-point mt for LMV and ADF resistance were detected in 57.7% and 54.1% of the child and adult samples, respectively, with rtV207M (children, 42.3%; adults, 36.7%) and rtN238T/A (children, 15.4%; adults, 16.3%) being the most frequent mt in these populations. Multiple-point mt, including rtL180M-rtM204V- rtN238A and rtL180M-rtM204I, were identified in only two children, resulting in LMV-ADF resistance and reduced ETV susceptibility. In conclusion, this assay accurately identified the mt profile of children (98.4%) and adults (91.2%) with CHB, which is comparable to established methods. This fast and sensitive screening method can be used for the detection of major NA-resistant mt circulating in developing countries, as well as providing a model for the development of similar mt-detection assays, especially for use in nonhospitalized patients who need their results within half a day, before starting treatment.
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Affiliation(s)
- Son V. Chu
- Key Laboratory of Enzyme and Protein Technology, VNU University of Science, Vietnam National University, Hanoi, Hanoi, Vietnam
| | - Son T. Vu
- Key Laboratory of Enzyme and Protein Technology, VNU University of Science, Vietnam National University, Hanoi, Hanoi, Vietnam
| | - Hang M. Nguyen
- Department of Research in Molecular Biology for Infectious Diseases, National Children’s Hospital, Hanoi, Vietnam
| | - Ngan T. Le
- Department of Microbiology, Bach Mai Hospital, Hanoi, Vietnam
| | | | - Van T. T. Vu
- Department of Microbiology, Bach Mai Hospital, Hanoi, Vietnam
| | - Thuy T. B. Phung
- Department of Research in Molecular Biology for Infectious Diseases, National Children’s Hospital, Hanoi, Vietnam
| | - Anh T. V. Nguyen
- Key Laboratory of Enzyme and Protein Technology, VNU University of Science, Vietnam National University, Hanoi, Hanoi, Vietnam
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Deneault E, Chaineau M, Nicouleau M, Castellanos Montiel MJ, Franco Flores AK, Haghi G, Chen CXQ, Abdian N, Shlaifer I, Beitel LK, Durcan TM. A streamlined CRISPR workflow to introduce mutations and generate isogenic iPSCs for modeling amyotrophic lateral sclerosis. Methods 2021; 203:297-310. [PMID: 34500068 DOI: 10.1016/j.ymeth.2021.09.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/28/2021] [Accepted: 09/03/2021] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) represents a complex neurodegenerative disorder with significant genetic heterogeneity. To date, both the genetic etiology and the underlying molecular mechanisms driving this disease remain poorly understood, although in recent years several studies have highlighted a number of genetic mutations causative for ALS. With these mutations pointing to potential pathways that may be affected within individuals with ALS, having the ability to generate human neurons and other disease relevant cells containing these mutations becomes even more critical if new therapies are to emerge. Recent developments with the advent of induced pluripotent stem cells (iPSCs) and clustered regularly interspaced short palindromic repeats (CRISPR) gene editing fields gave us the tools to introduce or correct a specific mutation at any site within the genome of an iPSC, and thus model the specific contribution of risk mutations. In this study we describe a rapid and efficient way to either introduce a mutation into a control line, or to correct an allele-specific mutation, generating an isogenic control line from patient-derived iPSCs with a given mutation. The mutations introduced were the G94A (also known as G93A) mutation into SOD1 or H517Q into FUS, and the mutation corrected was a patient iPSC line with I114T mutation in SOD1. A combination of small molecules and growth factors were used to guide a stepwise differentiation of the edited cells into motor neurons in order to demonstrate that disease-relevant cells could be generated for downstream applications. Through a combination of iPSCs and CRISPR editing, the cells generated here will provide fundamental insights into the molecular mechanisms underlying neuron degeneration in ALS.
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Affiliation(s)
- Eric Deneault
- The Neuro's Early Drug Discovery Unit (EDDU), McGill University, 3801 University Street, Montreal, Quebec H3A 2B4, Canada
| | - Mathilde Chaineau
- The Neuro's Early Drug Discovery Unit (EDDU), McGill University, 3801 University Street, Montreal, Quebec H3A 2B4, Canada
| | - Michael Nicouleau
- The Neuro's Early Drug Discovery Unit (EDDU), McGill University, 3801 University Street, Montreal, Quebec H3A 2B4, Canada
| | - Maria José Castellanos Montiel
- The Neuro's Early Drug Discovery Unit (EDDU), McGill University, 3801 University Street, Montreal, Quebec H3A 2B4, Canada
| | - Anna Kristyna Franco Flores
- The Neuro's Early Drug Discovery Unit (EDDU), McGill University, 3801 University Street, Montreal, Quebec H3A 2B4, Canada
| | - Ghazal Haghi
- The Neuro's Early Drug Discovery Unit (EDDU), McGill University, 3801 University Street, Montreal, Quebec H3A 2B4, Canada
| | - Carol X-Q Chen
- The Neuro's Early Drug Discovery Unit (EDDU), McGill University, 3801 University Street, Montreal, Quebec H3A 2B4, Canada
| | - Narges Abdian
- The Neuro's Early Drug Discovery Unit (EDDU), McGill University, 3801 University Street, Montreal, Quebec H3A 2B4, Canada
| | - Irina Shlaifer
- The Neuro's Early Drug Discovery Unit (EDDU), McGill University, 3801 University Street, Montreal, Quebec H3A 2B4, Canada
| | - Lenore K Beitel
- The Neuro's Early Drug Discovery Unit (EDDU), McGill University, 3801 University Street, Montreal, Quebec H3A 2B4, Canada
| | - Thomas M Durcan
- The Neuro's Early Drug Discovery Unit (EDDU), McGill University, 3801 University Street, Montreal, Quebec H3A 2B4, Canada.
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Kabza AM, Kundu N, Zhong W, Sczepanski JT. Integration of chemically modified nucleotides with DNA strand displacement reactions for applications in living systems. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2021; 14:e1743. [PMID: 34328690 DOI: 10.1002/wnan.1743] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/26/2021] [Accepted: 07/06/2021] [Indexed: 01/21/2023]
Abstract
Watson-Crick base pairing rules provide a powerful approach for engineering DNA-based nanodevices with programmable and predictable behaviors. In particular, DNA strand displacement reactions have enabled the development of an impressive repertoire of molecular devices with complex functionalities. By relying on DNA to function, dynamic strand displacement devices represent powerful tools for the interrogation and manipulation of biological systems. Yet, implementation in living systems has been a slow process due to several persistent challenges, including nuclease degradation. To circumvent these issues, researchers are increasingly turning to chemically modified nucleotides as a means to increase device performance and reliability within harsh biological environments. In this review, we summarize recent progress toward the integration of chemically modified nucleotides with DNA strand displacement reactions, highlighting key successes in the development of robust systems and devices that operate in living cells and in vivo. We discuss the advantages and disadvantages of commonly employed modifications as they pertain to DNA strand displacement, as well as considerations that must be taken into account when applying modified oligonucleotide to living cells. Finally, we explore how chemically modified nucleotides fit into the broader goal of bringing dynamic DNA nanotechnology into the cell, and the challenges that remain. This article is categorized under: Diagnostic Tools > In Vivo Nanodiagnostics and Imaging Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Diagnostic Tools > Biosensing.
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Affiliation(s)
- Adam M Kabza
- Department of Chemistry, Texas A&M University, College Station, Texas, USA
| | - Nandini Kundu
- Department of Chemistry, Texas A&M University, College Station, Texas, USA
| | - Wenrui Zhong
- Department of Chemistry, Texas A&M University, College Station, Texas, USA
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43
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Chaintoutis SC, Chassalevris T, Tsiolas G, Balaska S, Vlatakis I, Mouchtaropoulou E, Siarkou VI, Tychala A, Koutsioulis D, Skoura L, Argiriou A, Dovas CI. A one-step real-time RT-PCR assay for simultaneous typing of SARS-CoV-2 mutations associated with the E484K and N501Y spike protein amino-acid substitutions. J Virol Methods 2021; 296:114242. [PMID: 34274369 PMCID: PMC8282437 DOI: 10.1016/j.jviromet.2021.114242] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/14/2021] [Accepted: 07/14/2021] [Indexed: 11/18/2022]
Abstract
The emergence of SARS-CoV-2 mutations resulting in the S protein amino-acid substitutions N501Y and E484K, which have been associated with enhanced transmissibility and immune escape, respectively, necessitates immediate actions, for which their rapid identification is crucial. For the simultaneous typing of both of these mutations of concern (MOCs), a one-step real-time RT-PCR assay employing four locked nucleic acid (LNA) modified TaqMan probes was developed. The assay is highly sensitive with a LOD of 117 copies/reaction, amplification efficiencies >94 % and a linear range of over 5 log10 copies/reaction. Validation of the assay using known SARS-CoV-2-positive and negative samples from human and animals revealed its ability to correctly identify wild type strains, and strains possessing either one or both targeted amino-acid substitutions, thus comprising a useful pre-screening tool for rapid MOC identification. The basic principles of the methodology for the development of the assay are explained in order to facilitate the rapid design of similar assays able to detect emerging MOCs.
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Affiliation(s)
- Serafeim C Chaintoutis
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece
| | - Taxiarchis Chassalevris
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece
| | - George Tsiolas
- Institute of Applied Biosciences, Centre of Research and Technology Hellas, Thermi, 57001, Thessaloniki, Greece
| | - Sofia Balaska
- Department of Microbiology, AHEPA University Hospital, Medical School, Faculty of Health Sciences, Aristotle University of Thessaloniki, 1 Stilponos Kyriakidi str., 54636, Thessaloniki, Greece
| | - Ioannis Vlatakis
- EnzyQuest PC, Science and Technology Park of Crete, 100 Nikolaou Plastira str., Vassilika Vouton, 70013, Heraklion, Greece
| | - Evangelia Mouchtaropoulou
- Institute of Applied Biosciences, Centre of Research and Technology Hellas, Thermi, 57001, Thessaloniki, Greece
| | - Victoria I Siarkou
- Laboratory of Microbiology and Infectious Diseases, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, University Campus, 54134, Thessaloniki, Greece
| | - Areti Tychala
- Department of Microbiology, AHEPA University Hospital, Medical School, Faculty of Health Sciences, Aristotle University of Thessaloniki, 1 Stilponos Kyriakidi str., 54636, Thessaloniki, Greece
| | - Dimitris Koutsioulis
- EnzyQuest PC, Science and Technology Park of Crete, 100 Nikolaou Plastira str., Vassilika Vouton, 70013, Heraklion, Greece
| | - Lemonia Skoura
- Department of Microbiology, AHEPA University Hospital, Medical School, Faculty of Health Sciences, Aristotle University of Thessaloniki, 1 Stilponos Kyriakidi str., 54636, Thessaloniki, Greece
| | - Anagnostis Argiriou
- Institute of Applied Biosciences, Centre of Research and Technology Hellas, Thermi, 57001, Thessaloniki, Greece; Department of Food Science and Nutrition, University of the Aegean, 81400, Myrina, Lemnos, Greece
| | - Chrysostomos I Dovas
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece.
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Ferreira I, Slott S, Astakhova K, Weber G. Complete Mesoscopic Parameterization of Single LNA Modifications in DNA Applied to Oncogene Probe Design. J Chem Inf Model 2021; 61:3615-3624. [PMID: 34251211 DOI: 10.1021/acs.jcim.1c00470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The use of mesoscopic models to describe the thermodynamic properties of locked nucleic acid (LNA)-modified nucleotides can provide useful insights into their properties, such as hydrogen-bonding and stacking interactions. In addition, the mesoscopic parameters can be used to optimize LNA insertion in probes, to achieve accurate melting temperature predictions, and to obtain duplex opening profiles at the base-pair level. Here, we applied this type of model to parameterize a large set of melting temperatures for LNA-modified sequences, from published sources, covering all possible nearest-neighbor configurations. We have found a very large increase in Morse potentials, which indicates very strong hydrogen bonding as the main cause of improved LNA thermodynamic stability. LNA-modified adenine-thymine (AT) was found to have similar hydrogen bonding to unmodified cytosine-guanine (CG) base pairs, while for LNA CG, we found exceptionally large hydrogen bonding. In contrast, stacking interactions, which were thought to be behind the stability of LNA, were similar to unmodified DNA in most cases. We applied the new LNA parameters to the design of BRAF, KRAS, and EGFR oncogene variants by testing all possible LNA modifications. Selected sequences were then synthesized and had their hybridization temperatures measured, achieving a prediction accuracy within 1 °C. We performed a detailed base-pair opening analysis to discuss specific aspects of these probe hybridizations that may be relevant for probe design.
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Affiliation(s)
- Izabela Ferreira
- Departamento de Física, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, MG, Brazil.,Programa Interunidades de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, MG, Brazil
| | - Sofie Slott
- Department of Chemistry, Technical University of Denmark, Kemitorvet, Bygning 207, 2800 Kgs. Lyngby, Denmark
| | - Kira Astakhova
- Department of Chemistry, Technical University of Denmark, Kemitorvet, Bygning 207, 2800 Kgs. Lyngby, Denmark
| | - Gerald Weber
- Departamento de Física, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, MG, Brazil
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Novel High-Throughput Multiplex qPCRs for the Detection of Canine Vector-Borne Pathogens in the Asia-Pacific. Microorganisms 2021; 9:microorganisms9051092. [PMID: 34069665 PMCID: PMC8161336 DOI: 10.3390/microorganisms9051092] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 05/18/2021] [Accepted: 05/18/2021] [Indexed: 01/10/2023] Open
Abstract
The Asia-Pacific hosts a large diversity of canine vector-borne pathogens (VBPs) with some of the most common and most pathogenic, generating significant mortality as well as a spectrum of health impacts on local dog populations. The VBPs Anaplasma platys, Babesia gibsoni, Babesia vogeli, Ehrlichia canis, Hepatozoon canis and haemotropic Mycoplasma spp. are all endemic throughout the region, with many exhibiting shifting geographical distributions that warrant urgent attention. Moreover, many of these species cause similar clinical signs when parasitising canine hosts, whilst knowledge of the exact pathogen is critical to ensure treatment is effective. This is complicated by frequent coinfection that can exacerbate pathology. Here, we describe the development, optimisation and validation of two novel quadruplex Taq-Man based real-time PCRs (qPCRs) for the specific and sensitive detection of the aforementioned VBPs. To ensure accurate evaluation of diagnostic performance, results of our qPCRs were evaluated on field samples from Thai dogs and compared with both conventional PCR (cPCR) results and next-generation sequencing (NGS) metabarcoding. Our qPCRs were found to be more sensitive at detecting canine VBP than cPCR and generated results similar to those achieved by NGS. These qPCRs will provide a valuable high-throughput diagnostic tool available to epidemiologists, researchers and clinicians for the diagnosis of key canine VBPs in the Asia-Pacific and further afield.
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46
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Zhang M, Yang C, Tasan I, Zhao H. Expanding the Potential of Mammalian Genome Engineering via Targeted DNA Integration. ACS Synth Biol 2021; 10:429-446. [PMID: 33596056 DOI: 10.1021/acssynbio.0c00576] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Inserting custom designed DNA sequences into the mammalian genome plays an essential role in synthetic biology. In particular, the ability to introduce foreign DNA in a site-specific manner offers numerous advantages over random DNA integration. In this review, we focus on two mechanistically distinct systems that have been widely adopted for targeted DNA insertion in mammalian cells, the CRISPR/Cas9 system and site-specific recombinases. The CRISPR/Cas9 system has revolutionized the genome engineering field thanks to its high programmability and ease of use. However, due to its dependence on linearized DNA donor and endogenous cellular pathways to repair the induced double-strand break, CRISPR/Cas9-mediated DNA insertion still faces limitations such as small insert size, and undesired editing outcomes via error-prone repair pathways. In contrast, site-specific recombinases, in particular the Serine integrases, demonstrate large-cargo capability and no dependence on cellular repair pathways for DNA integration. Here we first describe recent advances in improving the overall efficacy of CRISPR/Cas9-based methods for DNA insertion. Moreover, we highlight the advantages of site-specific recombinases over CRISPR/Cas9 in the context of targeted DNA integration, with a special focus on the recent development of programmable recombinases. We conclude by discussing the importance of protein engineering to further expand the current toolkit for targeted DNA insertion in mammalian cells.
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Affiliation(s)
- Meng Zhang
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Che Yang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ipek Tasan
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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47
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Zhang Y, Wang Q, Wang J, Tang X. Chemical Modification and Transformation Strategies of Guide RNAs in CRISPR-Cas9 Gene Editing Systems. Chempluschem 2021; 86:587-600. [PMID: 33830675 DOI: 10.1002/cplu.202000785] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 03/13/2021] [Indexed: 12/19/2022]
Abstract
The CRISPR (clustered regularly interspaced short palindromic repeat)-Cas9 (CRISPR-associated protein 9) is a most powerful tool and has been widely used in gene editing and gene regulation since its discovery. However, wild-type CRISPR-Cas9 suffers from off-target effects and low editing efficiency. To overcome these limitations, engineered Cas9 proteins have been extensively investigated. In addition to Cas9 protein engineering, chemically synthesized guide RNAs have been developed to improve the efficiency and specificity of genome editing as well as spatiotemporal controllability, which broadens the biological applications of CRISPR-Cas9 gene editing system and increases their potentials as therapeutics. In this review, we summarize the latest research advances in remodeling guide RNAs through length optimization, chemical modifications, and conditional control, as well as their powerful applications in gene editing tools and promising therapeutic agents.
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Affiliation(s)
- Yu Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38, Xueyuan Rd., Beijing, 100191, P. R. China
| | - Qian Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38, Xueyuan Rd., Beijing, 100191, P. R. China
| | - Jing Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38, Xueyuan Rd., Beijing, 100191, P. R. China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38, Xueyuan Rd., Beijing, 100191, P. R. China
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48
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Puente-Lelievre C, Eischeid AC. Development and validation of a duplex real-time PCR assay with locked nucleic acid (LNA) probes for the specific detection of allergenic walnut in complex food matrices. Food Control 2021. [DOI: 10.1016/j.foodcont.2020.107644] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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49
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Emaus MN, Anderson JL. Selective extraction of low-abundance BRAF V600E mutation from plasma, urine, and sputum using ion-tagged oligonucleotides and magnetic ionic liquids. Anal Bioanal Chem 2021; 414:277-286. [PMID: 33644840 DOI: 10.1007/s00216-021-03216-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/31/2021] [Accepted: 02/03/2021] [Indexed: 10/22/2022]
Abstract
Sequence-specific DNA extractions have the potential to improve the detection of low-abundance mutations from complex matrices, making them ideal for circulating tumor DNA analysis during the early stages of cancer. Ion-tagged oligonucleotides (ITOs) are oligonucleotides modified with an allylimidazolium salt via thiolene click chemistry. The allylimidazolium-based tag allows the ITO-DNA duplex to be selectively captured by a hydrophobic magnetic ionic liquid (MIL). In this study, the selectivity of the ITO-MIL method was examined by extracting low abundance of the BRAF V600E mutation-a common single-nucleotide polymorphism associated with several different cancers-from diluted human plasma, artificial urine, and diluted artificial sputum. Quantitative polymerase chain reaction (qPCR) was not able to distinguish a 9% BRAF V600E standard (50 fg·μL-1 BRAF V600E, 500 fg·μL-1 wild-type BRAF) from the 100% wild-type BRAF (50 fg·μL-1) standard. However, introducing the ITO-MIL extraction prior to qPCR allowed for samples consisting of 0.1% BRAF V600E (50 fg·μL-1 V600E BRAF, 50,000 fg·μL-1 wild-type BRAF) to be distinguished from the 100% wild-type BRAF standard. Ion-tagged oligonucleotides (ITOs) are combined with magnetic ionic liquids (MILs) to extract low-abundance BRAF V600E mutation from diluted human plasma, artificial urine, and diluted artificial sputum. The ITO-MIL extraction prior to qPCR allowed for samples consisting of 0.1% BRAF V600E to be distinguished from the 100% wild-type BRAF standard.
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Affiliation(s)
- Miranda N Emaus
- Department of Chemistry, Iowa State University, 1605 Gilman Hall, Ames, IA, 50011, USA
| | - Jared L Anderson
- Department of Chemistry, Iowa State University, 1605 Gilman Hall, Ames, IA, 50011, USA.
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50
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Simultaneous absolute quantification and sequencing of fish environmental DNA in a mesocosm by quantitative sequencing technique. Sci Rep 2021; 11:4372. [PMID: 33623060 PMCID: PMC7902826 DOI: 10.1038/s41598-021-83318-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 02/02/2021] [Indexed: 11/08/2022] Open
Abstract
The combination of high-throughput sequencing technology and environmental DNA (eDNA) analysis has the potential to be a powerful tool for comprehensive, non-invasive monitoring of species in the environment. To understand the correlation between the abundance of eDNA and that of species in natural environments, we have to obtain quantitative eDNA data, usually via individual assays for each species. The recently developed quantitative sequencing (qSeq) technique enables simultaneous phylogenetic identification and quantification of individual species by counting random tags added to the 5′ end of the target sequence during the first DNA synthesis. Here, we applied qSeq to eDNA analysis to test its effectiveness in biodiversity monitoring. eDNA was extracted from water samples taken over 4 days from aquaria containing five fish species (Hemigrammocypris neglectus, Candidia temminckii, Oryzias latipes, Rhinogobius flumineus, and Misgurnus anguillicaudatus), and quantified by qSeq and microfluidic digital PCR (dPCR) using a TaqMan probe. The eDNA abundance quantified by qSeq was consistent with that quantified by dPCR for each fish species at each sampling time. The correlation coefficients between qSeq and dPCR were 0.643, 0.859, and 0.786 for H. neglectus, O. latipes, and M. anguillicaudatus, respectively, indicating that qSeq accurately quantifies fish eDNA.
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