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Kofanova O, Paul S, Pexaras A, Bellora C, Petersons A, Schmitt M, Baker Berjaoui M, Qaoud Y, Kenk M, Wagner H, Fleshner N, Betsou F. Biospecimen Qualification in a Clinical Biobank of Urological Diseases. Biopreserv Biobank 2024; 22:257-267. [PMID: 37878356 DOI: 10.1089/bio.2022.0190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023] Open
Abstract
Development of novel biomarkers for diagnosis of disease and assessment of treatment efficacy utilizes a wide range of biospecimens for discovery research. The fitness of biospecimens for the purpose of biomarker development depends on the clinical characteristics of the donor and on a number of critical and potentially uncontrolled pre-analytical variables. Pre-analytical factors influence the reliability of the biomarkers to be analyzed and can seriously impact analytic outcomes. Sample quality stratification assays and tools can be utilized by biorepositories to minimize bias resulting from samples' inconsistent quality. In this study, we evaluated the quality of biobanked specimens by comparing analytical outcomes at 1, 5, and 10 years after collection. Our results demonstrate that currently available assays and tools can be used by biobank laboratories to support objective biospecimen qualification. We have established a workflow to monitor the quality of different types of biospecimens and, in this study, present the results of a qualification exercise applied to fluid samples and their derivatives in the context of urological diseases.
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Affiliation(s)
- Olga Kofanova
- Integrated Biobank of Luxembourg (IBBL), Luxembourg Institute of Health (LIH), Dudelange, Luxembourg
| | - Sangita Paul
- McCain GU BioBank (MGB), University Health Network-Princess Margaret Cancer Centre, Toronto, Canada
| | - Achilleas Pexaras
- Integrated Biobank of Luxembourg (IBBL), Luxembourg Institute of Health (LIH), Dudelange, Luxembourg
| | - Camille Bellora
- Integrated Biobank of Luxembourg (IBBL), Luxembourg Institute of Health (LIH), Dudelange, Luxembourg
| | - Ala Petersons
- Integrated Biobank of Luxembourg (IBBL), Luxembourg Institute of Health (LIH), Dudelange, Luxembourg
| | - Margaux Schmitt
- Integrated Biobank of Luxembourg (IBBL), Luxembourg Institute of Health (LIH), Dudelange, Luxembourg
| | - Mohamad Baker Berjaoui
- McCain GU BioBank (MGB), University Health Network-Princess Margaret Cancer Centre, Toronto, Canada
| | - Yazan Qaoud
- McCain GU BioBank (MGB), University Health Network-Princess Margaret Cancer Centre, Toronto, Canada
| | - Miran Kenk
- McCain GU BioBank (MGB), University Health Network-Princess Margaret Cancer Centre, Toronto, Canada
| | - Heidi Wagner
- McCain GU BioBank (MGB), University Health Network-Princess Margaret Cancer Centre, Toronto, Canada
| | - Neil Fleshner
- McCain GU BioBank (MGB), University Health Network-Princess Margaret Cancer Centre, Toronto, Canada
| | - Fay Betsou
- Integrated Biobank of Luxembourg (IBBL), Luxembourg Institute of Health (LIH), Dudelange, Luxembourg
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Wilkinson AF, Barra MJ, Novak EN, Bond M, Richards-Kortum R. Point-of-care isothermal nucleic acid amplification tests: progress and bottlenecks for extraction-free sample collection and preparation. Expert Rev Mol Diagn 2024; 24:509-524. [PMID: 38973430 DOI: 10.1080/14737159.2024.2375233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 06/28/2024] [Indexed: 07/09/2024]
Abstract
INTRODUCTION Suitable sample collection and preparation methods are essential to enable nucleic acid amplification testing at the point of care (POC). Strategies that allow direct isothermal nucleic acid amplification testing (iNAAT) of crude sample lysate without the need for nucleic acid extraction minimize time to result as well as the need for operator expertise and costly infrastructure. AREAS COVERED The authors review research to understand how sample matrix and preparation affect the design and performance of POC iNAATs. They focus on approaches where samples are directly combined with liquid reagents for preparation and amplification via iNAAT strategies. They review factors related to the type and method of sample collection, storage buffers, and lysis strategies. Finally, they discuss RNA targets and relevant regulatory considerations. EXPERT OPINION Limitations in sample preparation methods are a significant technical barrier preventing implementation of nucleic acid testing at the POC. The authors propose a framework for co-designing sample preparation and amplification steps for optimal performance with an extraction-free paradigm by considering a sample matrix and lytic strategy prior to an amplification assay and readout. In the next 5 years, the authors anticipate increasing priority on the co-design of sample preparation and iNAATs.
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Affiliation(s)
| | - Maria J Barra
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Emilie N Novak
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Meaghan Bond
- Rice360 Institute for Global Health Technologies, Rice University, Houston, TX, USA
| | - Rebecca Richards-Kortum
- Department of Bioengineering, Rice University, Houston, TX, USA
- Rice360 Institute for Global Health Technologies, Rice University, Houston, TX, USA
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3
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Sbruzzi RC, Feira MF, Cadore NA, Giudicelli GC, Kowalski TW, Gregianini TS, Chies JAB, Vianna FSL. An Efficient Extraction Method Allowing the Genetic Evaluation of Host DNA from Samples Collected for Virus Infection Diagnosis in Viral Transport Medium. Biopreserv Biobank 2024; 22:166-173. [PMID: 37579075 DOI: 10.1089/bio.2022.0188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2023] Open
Abstract
Introduction: During the COVID-19 pandemic, an extraordinary number of nasopharyngeal secretion samples inoculated in viral transport medium (VTM) were collected and analyzed to detect SARS-CoV-2 infection. In addition to viral detection, those samples can also be a source of host genomic material, providing excellent opportunities for biobanking and research. Objective: To describe a simple, in-house-developed DNA extraction method to obtain high yield and quality genomic DNA from VTM samples for host genetic analysis and assess its relative efficiency by comparing its yield and suitability to downstream applications to two different commercial DNA extraction kits. Methods: In this study, 13 VTM samples were processed by two commercial silica-based kits and compared with an in-House-developed protocol for host DNA extraction. An additional 452 samples were processed by the in-House method. The quantity and quality of the differentially extracted DNA samples were assessed by Qubit and spectrophotometric measurements. The suitability of extracted samples for downstream applications was tested by polymerase chain reaction (PCR) amplification followed by amplicon sequencing and allelic discrimination in real-time PCR. Results: The in-House method provided greater median DNA yield (0.81 μg), being significantly different from the PureLink® method (0.14 μg, p < 0.001), but not from the QIAamp® method (0.47 μg, p = 0.980). Overall satisfactory results in DNA concentrations and purity, in addition to cost, were observed using the in-House method, whose samples were able to produce clear amplification in PCR and sequencing reads, as well as effective allelic discrimination in real-time PCR TaqMan® assay. Conclusion: The described in-House method proved to be suitable and economically viable for genomic DNA extraction from VTM samples for biobanking purposes. These results are extremely valuable for the study of the COVID-19 pandemic and other emergent infectious diseases, allowing host genetic studies to be performed in samples initially collected for diagnosis.
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Affiliation(s)
- Renan C Sbruzzi
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Mariléa F Feira
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Nathan A Cadore
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Giovanna C Giudicelli
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Instituto Nacional de Ciência e Tecnologia de Genética Médica Populacional, Porto Alegre, Brazil
| | - Thayne W Kowalski
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Instituto Nacional de Ciência e Tecnologia de Genética Médica Populacional, Porto Alegre, Brazil
- Centro Universitário CESUCA, Cachoeirinha, Brazil
- Núcleo de Bioinformática, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | - Tatiana S Gregianini
- Laboratório Central de Saúde Pública, Centro Estadual de Vigilância em Saúde, Secretaria Estadual de Saúde do estado do Rio Grande do Sul (LACEN/CEVS/SES-RS), Porto Alegre, Brazil
| | - José A B Chies
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Fernanda S L Vianna
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Instituto Nacional de Ciência e Tecnologia de Genética Médica Populacional, Porto Alegre, Brazil
- Programa de Pós-Graduação em Ciências Médicas, Faculdade de Medicina, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
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Barau C, Maillé P, Sirab N, Ghaleh B, Allory Y. Automated DNA, RNA, and Protein Extraction from Urine for Biobanking. J Biomol Tech 2022; 33:3fc1f5fe.9e4e4f65. [PMID: 35836999 PMCID: PMC9258912 DOI: 10.7171/3fc1f5fe.9e4e4f65] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
INTRODUCTION/OBJECTIVE DNA, RNA, and proteins are unavoidable human biomarkers. Today, blood remains the commonly used source of biomarkers despite numerous limitations. Therefore, other sources of biomarkers such as urine could be more appropriate for research in the field of bladder cancer. The aim of this study was to set up a new automated procedure for urinary DNA, RNA, and protein extraction and to evaluate their quality and quantity. MATERIALS AND METHODS This study was conducted in the setting of the COBLAnCE cohort. Urinary DNA and RNA were extracted using the Maxwell 16 system, and urinary proteins were isolated by precipitation from the supernatant and the cell pellet. The concentration and purity of nucleic acids were determined by spectrophotometry. RNA integrity was determined by the Agilent Bioanalyzer. PCR assays were also used to ensure the quality of DNA and RNA samples. The quality of protein samples obtained was determined by Western blot analysis. RESULTS PCR experiments performed highlighted that it is possible to use the DNA and RNA samples for amplification, gene expression, or genotyping. However, DNA and RNA recovery from urine was highly variable among patients, with a significant impact of the patient's gender. The samples were highly degraded. Finally, our protocol of protein isolation was effective in extracting urinary supernatant proteins as well as pellet proteins. DISCUSSION Therefore, urine samples could constitute valuable resources for subsequent investigations in bladder cancer. These samples will allow identifying new easy-access biomarkers for the early detection of cancer, monitoring cancer progression, and assessing response to therapy.
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Affiliation(s)
- Caroline Barau
- APHP, Hôpital Henri Mondor,
Plateforme de Ressources BiologiquesCréteilF-94000France
| | - Pascale Maillé
- APHP, Hôpital Henri Mondor,
Département de PathologieCréteilF-94000France
| | - Nanor Sirab
- APHP, Hôpital Henri Mondor,
Département de PathologieCréteilF-94000France
| | - Bijan Ghaleh
- APHP, Hôpital Henri Mondor,
Plateforme de Ressources BiologiquesCréteilF-94000France
- ADDRESS CORRESPONDENCE TO: Bijan Ghaleh, Plateforme de Ressources
Biologiques, Hôpital Henri Mondor, 51 avenue du Maréchal de Lattre de
Tassigny, 94000 Créteil (Phone: 33-1-49813796; E-mail:
)
| | - Yves Allory
- Institut Curie,
CNRS, UMR 144Paris75248France
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Detection of Cancer Mutations by Urine Liquid Biopsy as a Potential Tool in the Clinical Management of Bladder Cancer Patients. Cancers (Basel) 2022; 14:cancers14040969. [PMID: 35205727 PMCID: PMC8870091 DOI: 10.3390/cancers14040969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/02/2022] [Accepted: 02/11/2022] [Indexed: 11/28/2022] Open
Abstract
Simple Summary The management of bladder cancer faces multiple challenges concerning the diagnostic and follow-up approaches. The standard diagnostic examination comprises invasive cystoscopy. Urine cytology and recently proposed urine-based biomarkers have been unable to replace cystoscopy, thus prompting calls for improvements. Here, we explore urine liquid biopsy to detect cancer mutations and subsequently evaluate the utility of urine as a suitable specimen for diagnosing bladder cancer. Our results show that the analysis of pre- and postoperative urine with a cost-effective 127-gene panel enables the characterization of tumor mutations. These findings provide cumulative evidence in support of the results of previous studies that testing urine for mutations is a useful strategy to complement the clinical management of bladder cancer patients. Abstract The standard diagnostic and follow-up examination for bladder cancer is diagnostic cystoscopy, an invasive test that requires compliance for a long period. Urine cytology and recent biomarkers come short of replacing cystoscopy. Urine liquid biopsy promises to solve this problem and potentially allows early detection, evaluation of treatment efficacy, and surveillance. A previous study reached 52–68% sensitivity using small-panel sequencing but could increase sensitivity to 68–83% by adding aneuploidy and promoter mutation detection. Here, we explore whether a large 127-gene panel alone is sufficient to detect tumor mutations in urine from bladder cancer patients. We recruited twelve bladder cancer patients, obtained preoperative and postoperative urine samples, and successfully analyzed samples from eleven patients. In ten patients, we found at least one mutation in bladder-cancer-associated genes, i.e., a promising sensitivity of 91%. In total, we identified 114 variants, of which 90 were predicted as nonbenign, 30% were associated with cancer, and 13% were actionable according to the CIViC database. Sanger sequencing of the patients’ formalin-fixed, paraffin-embedded (FFPE) tumor tissues confirmed the findings. We concluded that incorporating urine liquid biopsy is a promising strategy in the management of bladder cancer patients.
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6
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Masigol M, Radaha EL, Kannan AD, Salberg AG, Fattahi N, Parameswaran P, Hansen RR. Polymer Surface Dissection for Correlated Microscopic and Compositional Analysis of Bacterial Aggregates during Membrane Biofouling. ACS APPLIED BIO MATERIALS 2022; 5:134-145. [PMID: 35014824 DOI: 10.1021/acsabm.1c00971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Multispecies biofilms are a common limitation in membrane bioreactors, causing membrane clogging, degradation, and failure. There is a poor understanding of biological fouling mechanisms in these systems due to the limited number of experimental techniques useful for probing microbial interactions at the membrane interface. Here, we develop a new experimental method, termed polymer surface dissection (PSD), to investigate multispecies assembly processes over membrane surfaces. The PSD method uses photodegradable polyethylene glycol hydrogels functionalized with bioaffinity ligands to bind and detach microscale, microbial aggregates from the membrane for microscopic observation. Subsequent exposure of the hydrogel to high resolution, patterned UV light allows for controlled release of any selected aggregate of desired size at high purity for DNA extraction. Follow-up 16S community analysis reveals aggregate composition, correlating microscopic images with the bacterial community structure. The optimized approach can isolate aggregates with microscale spatial precision and yields genomic DNA at sufficient quantity and quality for sequencing from aggregates with areas as low as 2000 μm2, without the need of culturing for sample enrichment. To demonstrate the value of the approach, PSD was used to reveal the composition of microscale aggregates of different sizes during early-stage biofouling of aerobic wastewater communities over PVDF membranes. Larger aggregates exhibited lower diversity of bacterial communities, and a shift in the community structure was found as aggregate size increased to areas between 25,000 and 45,000 μm2, below which aggregates were more enriched in Bacteroidetes and above which aggregates were more enriched with Proteobacteria. The findings demonstrate that community succession can be observed within microscale aggregates and that the PSD method is useful for identification and characterization of early colonizing bacteria that drive biofouling on membrane surfaces.
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Affiliation(s)
- Mohammadali Masigol
- Tim Taylor Department of Chemical Engineering, Kansas State University, Manhattan, Kansas 66506, United States
| | - Esther L Radaha
- Tim Taylor Department of Chemical Engineering, Kansas State University, Manhattan, Kansas 66506, United States
| | - Arvind D Kannan
- Department of Civil Engineering, Kansas State University, Manhattan, Kansas 66506, United States
| | - Abigail G Salberg
- Tim Taylor Department of Chemical Engineering, Kansas State University, Manhattan, Kansas 66506, United States
| | - Niloufar Fattahi
- Tim Taylor Department of Chemical Engineering, Kansas State University, Manhattan, Kansas 66506, United States
| | - Prathap Parameswaran
- Department of Civil Engineering, Kansas State University, Manhattan, Kansas 66506, United States
| | - Ryan R Hansen
- Tim Taylor Department of Chemical Engineering, Kansas State University, Manhattan, Kansas 66506, United States
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7
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Hii KC, Robie ER, Saihidi I, Berita A, Alarja NA, Xiu L, Merchant JA, Binder RA, Goh JKT, Guernier-Cambert V, Galán D, Gregory MJ, Gray GC. Leptospirosis infections among hospital patients, Sarawak, Malaysia. TROPICAL DISEASES TRAVEL MEDICINE AND VACCINES 2021; 7:32. [PMID: 34719397 PMCID: PMC8559352 DOI: 10.1186/s40794-021-00154-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 09/07/2021] [Indexed: 11/23/2022]
Abstract
Background Leptospirosis diagnoses have increased in Sarawak, Malaysia in recent years. Methods To better understand the burden of disease and associated risk factors, we evaluated 147 patients presenting with clinical leptospirosis to local hospitals in Sarawak, Malaysia for the presence of Leptospira and associated antibodies. Sera and urine specimens collected during the acute illness phase were assessed via a commercially available rapid diagnostic test (Leptorapide, Linnodee Ltd., Antrim, Northern Ireland), an ELISA IgM assay (Leptospira IgM ELISA, PanBio, Queensland, Australia) and a pan-Leptospira real-time PCR (qPCR) assay to estimate disease prevalence and diagnostic accuracy of each method. Microagglutination testing was performed on a subset of samples. Results Overall, 45 out of 147 patients (30.6%) showed evidence of leptospires through qPCR in either one or both sera (20 patients) or urine (33 patients), and an additional ten (6.8%) were considered positive through serological testing, for an overall prevalence of 37.4% within the study population. However, each diagnostic method individually yielded disparate prevalence estimates: rapid test 42.2% for sera and 30.5% for urine, ELISA 15.0% for sera, qPCR 13.8% for sera and 23.4% for urine. Molecular characterization of a subset of positive samples by conventional PCR identified the bacterial species as Leptospira interrogans in 4 specimens. A multivariate risk factor analysis for the outcome of leptospirosis identified having completed primary school (OR = 2.5; 95 CI% 1.0–6.4) and weekly clothes-washing in local rivers (OR = 10.6; 95 CI% 1.4–214.8) with increased likelihood of leptospirosis when compared with those who had not. Conclusion Overall, the data suggest a relatively high prevalence of leptospirosis in the study population. The low sensitivities of the rapid diagnostic test and ELISA assay against qPCR highlight a need for better screening tools. Supplementary Information The online version contains supplementary material available at 10.1186/s40794-021-00154-2.
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Affiliation(s)
- King-Ching Hii
- Department of Pediatrics, Kapit Hospital, Ministry of Health Malaysia, Kapit, Sarawak, Malaysia
| | - Emily R Robie
- Duke Global Health Institute, Duke University, Durham, NC, USA.,Division of Infectious Diseases, Duke University School of Medicine, DUMC Box 102359, Durham, NC, 27710, USA
| | - Izreena Saihidi
- Department of Pediatrics, Kapit Hospital, Ministry of Health Malaysia, Kapit, Sarawak, Malaysia
| | - Antoinette Berita
- Department of Pediatrics, Kapit Hospital, Ministry of Health Malaysia, Kapit, Sarawak, Malaysia
| | - Natalie A Alarja
- Duke Global Health Institute, Duke University, Durham, NC, USA.,Division of Infectious Diseases, Duke University School of Medicine, DUMC Box 102359, Durham, NC, 27710, USA
| | - Leshan Xiu
- Duke Global Health Institute, Duke University, Durham, NC, USA.,Division of Infectious Diseases, Duke University School of Medicine, DUMC Box 102359, Durham, NC, 27710, USA.,National Health Commission Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - James A Merchant
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - Raquel A Binder
- Duke Global Health Institute, Duke University, Durham, NC, USA.,Division of Infectious Diseases, Duke University School of Medicine, DUMC Box 102359, Durham, NC, 27710, USA
| | - Johnny Keh-Tun Goh
- Department of Pediatrics, Kapit Hospital, Ministry of Health Malaysia, Kapit, Sarawak, Malaysia
| | - Vanina Guernier-Cambert
- Present address: Agricultural Research Service, National Animal Disease Center, United States Department of Agriculture, Ames, IA, USA
| | - Diego Galán
- Division of Infectious Diseases, Duke University School of Medicine, DUMC Box 102359, Durham, NC, 27710, USA
| | - Michael J Gregory
- United States Naval Medical Research Center- Asia, Singapore, Singapore
| | - Gregory C Gray
- Duke Global Health Institute, Duke University, Durham, NC, USA. .,Division of Infectious Diseases, Duke University School of Medicine, DUMC Box 102359, Durham, NC, 27710, USA. .,Emerging Infectious Disease Program, Duke-NUS Medical School, Singapore, Singapore. .,Global Health Center, Duke Kunshan University, Kunshan, China.
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8
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Mrofchak R, Madden C, Evans MV, Hale VL. Evaluating extraction methods to study canine urine microbiota. PLoS One 2021; 16:e0253989. [PMID: 34242284 PMCID: PMC8270191 DOI: 10.1371/journal.pone.0253989] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 06/16/2021] [Indexed: 12/19/2022] Open
Abstract
The urinary microbiota is the collection of microbes present in urine that may play a role in host health. Studies of urine microbiota have traditionally relied upon culturing methods aimed at identifying pathogens. However, recent culture-free sequencing studies of the urine microbiota have determined that a diverse array of microbes is present in health and disease. To study these microbes and their potential role in diseases like bladder cancer or interstitial cystitis, consistent extraction and detection of bacterial DNA from urine is critical. However, urine is a low biomass substrate, requiring sensitive methods to capture DNA and making the risk of contamination high. To address this challenge, we collected urine samples from ten healthy dogs and extracted DNA from each sample using five different commercially available extraction methods. Extraction methods were compared based on total and bacterial DNA concentrations and bacterial community composition and diversity assessed through 16S rRNA gene sequencing. Significant differences in the urinary microbiota were observed by dog and sex but not extraction method. The Bacteremia Kit yielded the highest total DNA concentrations (Kruskal-Wallis, p = 0.165, not significant) and the highest bacterial DNA concentrations (Kruskal-Wallis, p = 0.044). Bacteremia also extracted bacterial DNA from the greatest number of samples. Taken together, these results suggest that the Bacteremia kit is an effective option for studying the urine microbiota. This work lays the foundation to study the urine microbiome in a wide range of urogenital diseases in dogs and other species.
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Affiliation(s)
- Ryan Mrofchak
- Department of Veterinary Preventive Medicine, Ohio State University College of Veterinary Medicine, Columbus, Ohio, United States of America
| | - Christopher Madden
- Department of Veterinary Preventive Medicine, Ohio State University College of Veterinary Medicine, Columbus, Ohio, United States of America
| | - Morgan V. Evans
- Department of Veterinary Preventive Medicine, Ohio State University College of Veterinary Medicine, Columbus, Ohio, United States of America
- Division of Environmental Health Sciences, Ohio State University College of Public Health, Columbus, Ohio, United States of America
| | - Vanessa L. Hale
- Department of Veterinary Preventive Medicine, Ohio State University College of Veterinary Medicine, Columbus, Ohio, United States of America
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Nauwelaerts SJD, Van Geel D, Delvoye M, De Cremer K, Bernard A, Roosens NHC, De Keersmaecker SCJ. Selection of a Noninvasive Source of Human DNA Envisaging Genotyping Assays in Epidemiological Studies: Urine or Saliva? J Biomol Tech 2021; 31:27-35. [PMID: 32042275 DOI: 10.7171/jbt.20-3101-004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Genetic epidemiology requires an appropriate approach to measure genetic variation within the population. The aim of this study was to evaluate the characteristics and genotyping results of DNA extracted from 2 human DNA sources, selected for their rapid and noninvasive sampling, and the use of simple and standardized protocols that are essential for large-scale epidemiologic studies. Saliva and urine samples were collected at the same day from 20 subjects aged 9-10 yr. Genomic DNA was extracted using commercial kits. Quantitative and qualitative evaluation was done by assessing the yield, the purity, and integrity of the extracted DNA. As a proof-of-concept, genotyping was performed targeting CC16 A38G and uteroglobin-related protein 1 (UGRP1)-112G/A. Saliva was found to provide the highest yield and concentration of total DNA extracted. Salivary DNA showed higher purity and a significantly less degraded state compared to urinary DNA. Consequently, the salivary DNA gave better genotyping results than urinary DNA. Therefore, if the choice exists, saliva is the preferred noninvasive matrix for genotyping purposes in large-scale genetic epidemiologic studies. Only in particular cases using urine could nevertheless be considered useful, although specific limitations need to be taken into account.
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Affiliation(s)
- Sarah J D Nauwelaerts
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium.,Louvain Centre for Toxicology and Applied Pharmacology, Université Catholique de Louvain Woluwe, 1200 Brussels, Belgium
| | - Dirk Van Geel
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium
| | - Maud Delvoye
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium
| | - Koen De Cremer
- Platform Chromatography and Mass Spectrometry, Sciensano, 1050 Brussels, Belgium; and
| | - Alfred Bernard
- Louvain Centre for Toxicology and Applied Pharmacology, Université Catholique de Louvain Woluwe, 1200 Brussels, Belgium
| | - Nancy H C Roosens
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium
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10
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Genotyping of the Major SARS-CoV-2 Clade by Short-Amplicon High-Resolution Melting (SA-HRM) Analysis. Genes (Basel) 2021; 12:genes12040531. [PMID: 33916492 PMCID: PMC8067340 DOI: 10.3390/genes12040531] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/30/2021] [Accepted: 04/02/2021] [Indexed: 12/17/2022] Open
Abstract
The genome of the SARS-CoV-2 virus, the causal agent of the COVID-19 pandemic, has diverged due to multiple mutations since its emergence as a human pathogen in December 2019. Some mutations have defined several SARS-CoV-2 clades that seem to behave differently in terms of regional distribution and other biological features. Next-generation sequencing (NGS) approaches are used to classify the sequence variants in viruses from individual human patients. However, the cost and relative scarcity of NGS equipment and expertise in developing countries prevent studies aimed to associate specific clades and variants to clinical features and outcomes in such territories. As of March 2021, the GR clade and its derivatives, including the B.1.1.7 and B.1.1.28 variants, predominate worldwide. We implemented the post-PCR small-amplicon high-resolution melting analysis to genotype SARS-CoV-2 viruses isolated from the saliva of individual patients. This procedure was able to clearly distinguish two groups of samples of SARS-CoV-2-positive samples predicted, according to their melting profiles, to contain GR and non-GR viruses. This grouping of the samples was validated by means of amplification-refractory mutation system (ARMS) assay as well as Sanger sequencing.
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11
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Crego-Vicente B, Fernández-Soto P, Febrer-Sendra B, García-Bernalt Diego J, Boissier J, Angora EK, Oleaga A, Muro A. Application of a Genus-Specific LAMP Assay for Schistosome Species to Detect Schistosoma haematobium x Schistosoma bovis Hybrids. J Clin Med 2021; 10:jcm10061308. [PMID: 33810080 PMCID: PMC8004683 DOI: 10.3390/jcm10061308] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/08/2021] [Accepted: 03/18/2021] [Indexed: 02/07/2023] Open
Abstract
Schistosomiasis is a disease of great medical and veterinary importance in tropical and subtropical regions caused by different species of parasitic flatworms of the genus Schistosoma. The emergence of natural hybrids of schistosomes indicate the risk of possible infection to humans and their zoonotic potential, specifically for Schistosoma haematobium and S. bovis. Hybrid schistosomes have the potential to replace existing species, generate new resistances, pathologies and extending host ranges. Hybrids may also confuse the serological, molecular and parasitological diagnosis. Currently, LAMP technology based on detection of nucleic acids is used for detection of many agents, including schistosomes. Here, we evaluate our previously developed species-specific LAMP assays for S. haematobium, S. mansoni, S. bovis and also the genus-specific LAMP for the simultaneous detection of several Schistosoma species against both DNA from pure and, for the first time, S. haematobium x S. bovis hybrids. Proper operation was evaluated with DNA from hybrid schistosomes and with human urine samples artificially contaminated with parasites' DNA. LAMP was performed with and without prior DNA extraction. The genus-specific LAMP properly amplified pure Schistosoma species and different S. haematobium-S. bovis hybrids with different sensitivity. The Schistosoma spp.-LAMP method is potentially adaptable for field diagnosis and disease surveillance in schistosomiasis endemic areas where human infections by schistosome hybrids are increasingly common.
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Affiliation(s)
- Beatriz Crego-Vicente
- Infectious and Tropical Diseases Research Group (e-INTRO), Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Biomedical Research Institute of Salamanca, Faculty of Pharmacy, University of Salamanca, 37007 Salamanca, Spain; (B.C.-V.); (B.F.-S.); (J.G.-B.D.)
| | - Pedro Fernández-Soto
- Infectious and Tropical Diseases Research Group (e-INTRO), Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Biomedical Research Institute of Salamanca, Faculty of Pharmacy, University of Salamanca, 37007 Salamanca, Spain; (B.C.-V.); (B.F.-S.); (J.G.-B.D.)
- Correspondence: (P.F.-S.); (A.M.); Tel.: +34-677596173 (P.F.-S.); +34-677596155 (A.M.)
| | - Begoña Febrer-Sendra
- Infectious and Tropical Diseases Research Group (e-INTRO), Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Biomedical Research Institute of Salamanca, Faculty of Pharmacy, University of Salamanca, 37007 Salamanca, Spain; (B.C.-V.); (B.F.-S.); (J.G.-B.D.)
| | - Juan García-Bernalt Diego
- Infectious and Tropical Diseases Research Group (e-INTRO), Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Biomedical Research Institute of Salamanca, Faculty of Pharmacy, University of Salamanca, 37007 Salamanca, Spain; (B.C.-V.); (B.F.-S.); (J.G.-B.D.)
| | - Jérôme Boissier
- IHPE, Université Montpellier, CNRS, Ifremer, Université Perpignan Via Domitia, 66100 Perpignan, France;
| | - Etienne K. Angora
- Swiss Tropical and Public Health Institute, P.O. Box CH-4002 Basel, Switzerland;
- Department of Public Health, University of Basel, P.O. Box CH-4003 Basel, Switzerland
- Unité de Formation et de Recherche Sciences Pharmaceutiques et Biologiques, Université Félix Houphouët-Boigny, Abidjan BPV 34, Côte d’Ivoire
| | - Ana Oleaga
- Parasitology Laboratory, Institute of Natural Resources and Agrobiology (IRNASA, CSIC), Cordel de Merinas 40-52, 37008 Salamanca, Spain;
| | - Antonio Muro
- Infectious and Tropical Diseases Research Group (e-INTRO), Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Biomedical Research Institute of Salamanca, Faculty of Pharmacy, University of Salamanca, 37007 Salamanca, Spain; (B.C.-V.); (B.F.-S.); (J.G.-B.D.)
- Correspondence: (P.F.-S.); (A.M.); Tel.: +34-677596173 (P.F.-S.); +34-677596155 (A.M.)
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12
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Bundgaard-Nielsen C, Ammitzbøll N, Isse YA, Muqtar A, Jensen AM, Leutscher PDC, Arenholt LTS, Hagstrøm S, Sørensen S. Voided Urinary Microbiota Is Stable Over Time but Impacted by Post Void Storage. Front Cell Infect Microbiol 2020; 10:435. [PMID: 32984068 PMCID: PMC7477311 DOI: 10.3389/fcimb.2020.00435] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 07/16/2020] [Indexed: 12/18/2022] Open
Abstract
Background: New sensitive techniques have revealed a thriving bacterial community in the human urinary tract, challenging the perception that urine in healthy humans is sterile. While the functional role of this urinary microbiota is unknown, dysbiosis has been linked to urgency urinary incontinence and risk of urinary tract infections. When comparing studies, it is crucial to account for possible confounders introduced due to methodological differences. Here we investigated whether collection and storage conditions had any impact on the urinary microbial composition. Results: For comparison of different storage conditions, midstream urine was collected from five healthy adult female donors and analyzed by 16S rRNA gene sequencing. Samples stored at -80 and -20°C, but not 4°C, were found to be comparable to freshly handled voided urine. Using the same methods, the daily or day-to-day variation in urinary microbiota was investigated in 19 healthy donors, including four women, five men, five girls, and five boys. Apart from two male adult donors, none of the tested conditions gave rise to significant differences in alpha and beta diversities between individuals. Conclusion: The composition of voided urinary microbiota was found to be effectively maintained by freezing, but not storage at 4°C. In addition, we did not observe any intrapersonal daily or day-to-day variations in microbiota composition in women, girls or boys. Together our study supports present methodologies that can be used in future studies investigating the urinary microbiota.
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Affiliation(s)
- Caspar Bundgaard-Nielsen
- Centre for Clinical Research, North Denmark Regional Hospital, Hjørring, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Nadia Ammitzbøll
- Centre for Clinical Research, North Denmark Regional Hospital, Hjørring, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Yusuf Abdi Isse
- Centre for Clinical Research, North Denmark Regional Hospital, Hjørring, Denmark.,Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Abdisalam Muqtar
- Centre for Clinical Research, North Denmark Regional Hospital, Hjørring, Denmark.,Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Ann-Maria Jensen
- Centre for Clinical Research, North Denmark Regional Hospital, Hjørring, Denmark
| | - Peter D C Leutscher
- Centre for Clinical Research, North Denmark Regional Hospital, Hjørring, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.,Steno Diabetes Center North Jutland, Aalborg, Denmark
| | - Louise Thomsen Schmidt Arenholt
- Centre for Clinical Research, North Denmark Regional Hospital, Hjørring, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.,Department of Gynecology and Obstetrics, North Denmark Regional Hospital, Hjørring, Denmark
| | - Søren Hagstrøm
- Centre for Clinical Research, North Denmark Regional Hospital, Hjørring, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.,Steno Diabetes Center North Jutland, Aalborg, Denmark.,Department of Pediatrics, Aalborg University Hospital, Aalborg, Denmark
| | - Suzette Sørensen
- Centre for Clinical Research, North Denmark Regional Hospital, Hjørring, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.,Steno Diabetes Center North Jutland, Aalborg, Denmark
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13
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Lee EY, Lee EJ, Yoon H, Lee DH, Kim KH. Comparison of Four Commercial Kits for Isolation of Urinary Cell-Free DNA and Sample Storage Conditions. Diagnostics (Basel) 2020; 10:diagnostics10040234. [PMID: 32325682 PMCID: PMC7236016 DOI: 10.3390/diagnostics10040234] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/16/2020] [Accepted: 04/16/2020] [Indexed: 12/25/2022] Open
Abstract
Urinary cell-free DNA (cfDNA) is an attractive body fluid for liquid biopsy. In this study, we compared the efficiencies of four commercial kits for urinary cell-free DNA (cfDNA) isolation and of various sample storage conditions. Urinary cfDNA was isolated from 10 healthy individuals using four commercial kits: QIAamp Circulating Nucleic Acid Kit (QC; Qiagen), MagMAX™ Cell-Free DNA Isolation Kit (MM; Applied Biosystems), Urine Cell-Free Circulating DNA Purification Midi Kit (NU; Norgen Biotek), and Quick-DNA™ Urine Kit (ZQ; Zymo Research). To assess the isolation efficiency, an Agilent 2100 Bioanalyzer with High Sensitivity DNA chips was used, and cfDNA yield was defined as the amount of cfDNA obtained from 1 mL of urine. MM and QC provided the highest cfDNA yield in the 50–300 bp range, and MM and NU gave the highest cfDNA yield in the 50–100 bp range. In particular, the NU kit was efficient for isolation of more fragmented cfDNA in the range of 50–100 bp with the lowest cellular genomic DNA contamination. ZQ had the best cost-efficiency for isolating the same amount of urinary cfDNA. Samples stored at −70 °C with the addition of 10 mM EDTA resulted in the highest cfDNA yield 3 months after sample collection.
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Affiliation(s)
- Eun Young Lee
- Department of Urology, College of Medicine, Ewha Womans University, Seoul 07804, Korea; (E.Y.L.); (E.-J.L.); (H.Y.); (D.H.L.)
- Ewha Medical Research Institute, College of Medicine, Ewha Womans University, Seoul 07804, Korea
| | - Eun-Ju Lee
- Department of Urology, College of Medicine, Ewha Womans University, Seoul 07804, Korea; (E.Y.L.); (E.-J.L.); (H.Y.); (D.H.L.)
- Ewha Medical Research Institute, College of Medicine, Ewha Womans University, Seoul 07804, Korea
| | - Hana Yoon
- Department of Urology, College of Medicine, Ewha Womans University, Seoul 07804, Korea; (E.Y.L.); (E.-J.L.); (H.Y.); (D.H.L.)
| | - Dong Hyeon Lee
- Department of Urology, College of Medicine, Ewha Womans University, Seoul 07804, Korea; (E.Y.L.); (E.-J.L.); (H.Y.); (D.H.L.)
| | - Kwang Hyun Kim
- Department of Urology, College of Medicine, Ewha Womans University, Seoul 07804, Korea; (E.Y.L.); (E.-J.L.); (H.Y.); (D.H.L.)
- Correspondence: ; Tel.: +82-2-6986-1685; Fax: +82-2-6986-3258
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14
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Rajar P, Åsegg-Atneosen M, Saugstad OD, Solberg R, Baumbusch LO. Quantification of circulating cell-free DNA (cfDNA) in urine using a newborn piglet model of asphyxia. PLoS One 2020; 14:e0227066. [PMID: 31891615 PMCID: PMC6938324 DOI: 10.1371/journal.pone.0227066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 12/10/2019] [Indexed: 12/03/2022] Open
Abstract
Cell free DNA (cfDNA) in plasma has been described as a potential diagnostic indicator for a variety of clinical conditions, including neonatal hypoxia. Neonatal hypoxia or perinatal asphyxia is a severe medical condition caused by a temporary interruption in oxygen availability during birth. Previously, we have reported temporal changes of cfDNA detected in blood in a newborn piglet model of perinatal asphyxia. However, cfDNA can also be found in other body liquids, opening for a less invasive diagnostic prospective. The objective of this study was to test and establish a reliable method for the isolation and quantification of cfDNA from urine and to explore changes in the quantities of cfDNA using a newborn piglet model of asphyxia. Animals were exposed to hypoxia-reoxygenation (n = 6), hypoxia-reoxygenation + hypothermia (n = 6) or were part of the sham-operated control group (n = 6) and urine samples (n = 18) were collected at 570 minutes post-intervention. Two alternative applications of cfDNA measurement were tested, an indirect method comprising a centrifugation step together with DNA extraction with magnetic beads versus a direct assessment based on two centrifugation steps. CfDNA concentrations were determined by a fluorescent assay using PicoGreen and by qRT-PCR. Genomic (gDNA) and mitochondrial DNA (mtDNA) cfDNA were determined in parallel, taking into account potential differences in the rates of damages caused by oxidative stress. In contrast to previous publications, our results indicate that the direct method is insufficient. Application of the indirect method obtained with the fluorescence assay revealed mean cfDNA levels (SD) of 1.23 (1.76) ng/ml for the hypoxia samples, 4.47 (6.15) ng/ml for the samples exposed to hypoxia + hypothermia and 2.75 (3.62) ng/ml for the control animals. The mean cfDNA levels in piglets exposed to hypoxia + hypothermia revealed significantly higher cfDNA amounts compared to mean cfDNA levels in the samples purely exposed to hypoxia (p < 0.05); however, no significant difference could be determined when compared to the control group (p = 0.09). Application of the indirect method by qRT-PCR revealed mean cfDNA levels of mtDNA and gDNA at the detection limit of the technique and thus no reliable statistics could be performed between the observed cfDNA levels in the investigated groups. The methodology for detection and monitoring of cfDNA in urine has to be further optimized before it can be applied in a clinical setting in the future.
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Affiliation(s)
- Polona Rajar
- Department of Pediatric Research, Division of Pediatric and Adolescent Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway.,University of Oslo, Oslo, Norway
| | - Monica Åsegg-Atneosen
- Department of Pediatric Research, Division of Pediatric and Adolescent Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway.,University of Oslo, Oslo, Norway
| | - Ola Didrik Saugstad
- Department of Pediatric Research, Division of Pediatric and Adolescent Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway.,University of Oslo, Oslo, Norway
| | - Rønnaug Solberg
- Department of Pediatric Research, Division of Pediatric and Adolescent Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway.,Department of Pediatrics, Vestfold Hospital Trust, Tønsberg, Norway
| | - Lars Oliver Baumbusch
- Department of Pediatric Research, Division of Pediatric and Adolescent Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
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15
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Gorchakov R, Berry RM, Patel SM, El Sahly HM, Ronca SE, Murray KO. Optimizing PCR Detection of Zika Virus from Various Body Fluids. Am J Trop Med Hyg 2019; 100:427-433. [PMID: 30560770 PMCID: PMC6367632 DOI: 10.4269/ajtmh.18-0755] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Current diagnostic protocols of acute Zika virus (ZIKV) infection focus on detection of viral RNA in serum or urine using reverse transcription quantitative polymerase chain reaction (RT-qPCR); however, detecting infection can be a challenge, given that 80% of people with acute ZIKV infection are asymptomatic, and the window to detect viremia in serum is short. The ability to extend that window is needed to detect ZIKV at later time points after infection, particularly in high-risk individuals such as pregnant women. We evaluated RNA extraction methods to optimize detection of ZIKV in various body fluids using RT-qPCR as a means of improving the analytical sensitivity of detection. We optimized methods for ZIKV RNA recovery from a number of body fluids by spiking with three varying concentrations of virus, then comparing recovery with that of spiked buffer control. RNA extraction protocols were adjusted as necessary for maximum RNA recovery. Adjustment of the elution step was essential for improved ZIKV RNA recovery from whole blood, saliva, vaginal secretions, and breast milk. Optimal recovery from urine samples required the addition of Urine Conditioning Buffer, and the use of RLT Plus buffer and RNeasy Mini Spin Columns was necessary for RNA extractions from semen samples. Optimized QIAamp MinElute Virus Spin Kit (QIAGEN, Valencia, CA) protocol followed by the singleplex ZIKV RT-qPCR assay provided a reliable method for detection of ZIKV RNA in a variety of biological samples. Improved diagnostics are crucial for timely detection and diagnosis, particularly during pregnancy when the consequences of ZIKV infection can greatly impact the developing fetus.
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Affiliation(s)
- Rodion Gorchakov
- Department of Pediatrics-Tropical Medicine, Baylor College of Medicine and Texas Children's Hospital, Houston, Texas
| | - Rebecca M Berry
- Department of Pediatrics-Tropical Medicine, Baylor College of Medicine and Texas Children's Hospital, Houston, Texas
| | - Shital M Patel
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Hana M El Sahly
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Shannon E Ronca
- Department of Pediatrics-Tropical Medicine, Baylor College of Medicine and Texas Children's Hospital, Houston, Texas
| | - Kristy O Murray
- Department of Pediatrics-Tropical Medicine, Baylor College of Medicine and Texas Children's Hospital, Houston, Texas
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16
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Oreskovic A, Brault ND, Panpradist N, Lai JJ, Lutz BR. Analytical Comparison of Methods for Extraction of Short Cell-Free DNA from Urine. J Mol Diagn 2019; 21:1067-1078. [PMID: 31442674 DOI: 10.1016/j.jmoldx.2019.07.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 07/02/2019] [Accepted: 07/23/2019] [Indexed: 11/19/2022] Open
Abstract
Urine cell-free DNA (cfDNA) is a valuable noninvasive biomarker for cancer mutation detection, infectious disease diagnosis (eg, tuberculosis), organ transplantation monitoring, and prenatal screening. Conventional silica DNA extraction does not efficiently capture urine cfDNA, which is dilute (ng/mL) and highly fragmented [30 to 100 nucleotides (nt)]. The clinical sensitivity of urine cfDNA detection increases with decreasing target length, motivating use of sample preparation methods designed for short fragments. We compared the analytical performance of two published protocols (Wizard resin/guanidinium thiocyanate and Q Sepharose), three commercial kits (Norgen, QIAamp, and MagMAX), and an in-house sequence-specific hybridization capture technique. Dependence on fragment length (25 to 150 nt), performance at low concentrations (10 copies/mL), tolerance to variable urine conditions, and susceptibility to PCR inhibition were characterized. Hybridization capture and Q Sepharose performed best overall (60% to 90% recovery), although Q Sepharose had reduced recovery (<10%) of the shortest 25-nt fragment. Wizard resin/guanidinium thiocyanate recovery was dependent on pH and background DNA concentration and was limited to <35%, even under optimal conditions. The Norgen kit led to consistent PCR inhibition but had high recovery of short fragments. The QIAamp and MagMAX kits had minimal recovery of fragments <150 and <80 nt, respectively. Urine cfDNA extraction methods differ widely in ability to capture short, dilute cfDNA in urine; using suboptimal methods may profoundly impair clinical results.
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Affiliation(s)
- Amy Oreskovic
- Department of Bioengineering, University of Washington, Seattle, Washington
| | - Norman D Brault
- Department of Bioengineering, University of Washington, Seattle, Washington
| | - Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, Washington
| | - James J Lai
- Department of Bioengineering, University of Washington, Seattle, Washington
| | - Barry R Lutz
- Department of Bioengineering, University of Washington, Seattle, Washington.
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17
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Gorchakov R, Gulas-Wroblewski BE, Ronca SE, Ruff JC, Nolan MS, Berry R, Alvarado RE, Gunter SM, Murray KO. Optimizing PCR Detection of West Nile Virus from Body Fluid Specimens to Delineate Natural History in an Infected Human Cohort. Int J Mol Sci 2019; 20:ijms20081934. [PMID: 31010160 PMCID: PMC6514913 DOI: 10.3390/ijms20081934] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 04/15/2019] [Accepted: 04/16/2019] [Indexed: 12/14/2022] Open
Abstract
West Nile virus (WNV), a mosquito-borne arbovirus, remains a major global health concern. In this study, we optimized PCR methods then assessed serially-collected whole blood (WB), urine (UR), saliva, and semen specimens from a large cohort of WNV-positive participants to evaluate the natural history of infection and persistent shedding of WNV RNA. Viral RNA extraction protocols for frozen WB and UR specimens were optimized and validated through spiking experiments to maximize recovery of viral RNA from archived specimens and to assess the degradation of WNV RNA in stored UR specimens. The resultant procedures were used in conjunction with PCR detection to identify WNV-positive specimens and to quantify their viral loads. A total of 59 of 352 WB, 10 of 38 UR, and 2 of 34 saliva specimens tested positive for WNV RNA. Although a single semen specimen was positive 22 days post onset, we could not definitively confirm the presence of WNV RNA in the remaining specimens. WNV RNA-positive UR specimens exhibited profound loss of viral RNA during storage, highlighting the need for optimal preservation pre-storage. This study provides optimized methods for WNV RNA detection among different fluid types and offers alternative options for diagnostic testing during the acute stages of WNV.
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Affiliation(s)
- Rodion Gorchakov
- Department of Pediatrics, National School of Tropical Medicine, Baylor College of Medicine and Texas Children's Hospital, Houston, TX 77030, USA.
| | - Bonnie E Gulas-Wroblewski
- Department of Pediatrics, National School of Tropical Medicine, Baylor College of Medicine and Texas Children's Hospital, Houston, TX 77030, USA.
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX 77843, USA.
| | - Shannon E Ronca
- Department of Pediatrics, National School of Tropical Medicine, Baylor College of Medicine and Texas Children's Hospital, Houston, TX 77030, USA.
| | - Jeanne C Ruff
- Department of Pediatrics, National School of Tropical Medicine, Baylor College of Medicine and Texas Children's Hospital, Houston, TX 77030, USA.
| | - Melissa S Nolan
- University of South Carolina, Arnold School of Public Health, Columbia, SC 29208, USA.
| | - Rebecca Berry
- Department of Pediatrics, National School of Tropical Medicine, Baylor College of Medicine and Texas Children's Hospital, Houston, TX 77030, USA.
| | - R Elias Alvarado
- Department of Pediatrics, National School of Tropical Medicine, Baylor College of Medicine and Texas Children's Hospital, Houston, TX 77030, USA.
| | - Sarah M Gunter
- Department of Pediatrics, National School of Tropical Medicine, Baylor College of Medicine and Texas Children's Hospital, Houston, TX 77030, USA.
| | - Kristy O Murray
- Department of Pediatrics, National School of Tropical Medicine, Baylor College of Medicine and Texas Children's Hospital, Houston, TX 77030, USA.
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18
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Abstract
PURPOSE OF REVIEW Epigenetic variations have been shown to reveal vulnerability to diabetes and its complications. Although it has become clear that metabolic derangements, especially hyperglycemia, can impose a long-term metabolic memory that predisposes to diabetic complications, the underlying mechanisms remain to be understood. It has been suggested that epigenetics (e.g., histone modification, DNA methylation, and non-coding RNAs) help link metabolic disruption to aberrancies related to diabetic kidney disease (DKD). In this review, we discuss the key findings and advances made in the epigenetic risk profile of DKD and provide perspectives on the emerging topics that implicate epigenetics in DKD. RECENT FINDINGS Epigenetic profiles can be profoundly altered in patients with diabetes, in circulating blood cells as well as in renal tissues. These changes provide useful insight into the mechanisms of diabetic kidney injury and progressive kidney dysfunction. Increasing evidence supports the role of epigenetic regulation in DKD. More studies are needed to elucidate the mechanism and importance of epigenetic changes in the initiation and progression of DKD and to further explore their diagnostic and therapeutic potential in the clinical management of patients with diabetes who have a high risk for DKD.
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Affiliation(s)
- Lixia Xu
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, 1500 E. Duarte Rd., Duarte, CA, 91010, USA
- Division of Nephrology, Guangdong Academy of Medical Science and Guangdong General Hospital, 106 Zhongshan Er Rd, Guangzhou, 510080, China
| | - Rama Natarajan
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, 1500 E. Duarte Rd., Duarte, CA, 91010, USA
| | - Zhen Chen
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, 1500 E. Duarte Rd., Duarte, CA, 91010, USA.
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19
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An efficient and cost-effective method for purification of small sized DNAs and RNAs from human urine. PLoS One 2019; 14:e0210813. [PMID: 30721243 PMCID: PMC6363378 DOI: 10.1371/journal.pone.0210813] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 01/02/2019] [Indexed: 02/06/2023] Open
Abstract
Urine holds great promise as a non-invasive sampling method for molecular diagnostics. The cell-free nucleic acids of urine however are small, labile, and difficult to purify. Here an efficient method for the purification of these nucleic acids is presented. An empirically derived protocol was devised by first identifying conditions that allowed recovery of a 100 base pair (bp) DNA, followed by optimization using a quantitative polymerase chain reaction (qPCR) assay. The resulting method efficiently purifies both small sized DNAs and RNAs from urine, which when combined with quantitative reverse transcription PCR (qRTPCR), demonstrably improves detection sensitivity. Fractionation experiments reveal that nucleic acids in urine exist both in the cell-free and cellular fraction, roughly in equal proportion. Consistent with previous studies, amplicons > 180bp show a marked loss in PCR sensitivity for cell-free nucleic acids. Finally, the lysis buffer developed here also doubles as an effective preservative, protecting against nucleic acid degradation for at least two weeks under simulated field conditions. With this method, volumes of up to 25ml of whole urine can be purified in a high-throughput and cost-effective manner. Coupled with its ability to purify both DNA and RNA, the described method may have broad applicability for improving the diagnostic utility of urine, particularly for the detection of low abundant targets.
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20
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Lecamwasam A, Sexton-Oates A, Carmody J, Ekinci EI, Dwyer KM, Saffery R. DNA methylation profiling of genomic DNA isolated from urine in diabetic chronic kidney disease: A pilot study. PLoS One 2018; 13:e0190280. [PMID: 29462136 PMCID: PMC5819761 DOI: 10.1371/journal.pone.0190280] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Accepted: 12/09/2017] [Indexed: 11/18/2022] Open
Abstract
Aim To characterise the genomic DNA (gDNA) yield from urine and quality of derived methylation data generated from the widely used Illuminia Infinium MethylationEPIC (HM850K) platform and compare this with buffy coat samples. Background DNA methylation is the most widely studied epigenetic mark and variations in DNA methylation profile have been implicated in diabetes which affects approximately 415 million people worldwide. Methods QIAamp Viral RNA Mini Kit and QIAamp DNA micro kit were used to extract DNA from frozen and fresh urine samples as well as increasing volumes of fresh urine. Matched buffy coats to the frozen urine were also obtained and DNA was extracted from the buffy coats using the QIAamp DNA Mini Kit. Genomic DNA of greater concentration than 20μg/ml were used for methylation analysis using the HM850K array. Results Irrespective of extraction technique or the use of fresh versus frozen urine samples, limited genomic DNA was obtained using a starting sample volume of 5ml (0–0.86μg/mL). In order to optimize the yield, we increased starting volumes to 50ml fresh urine, which yielded only 0–9.66μg/mL A different kit, QIAamp DNA Micro Kit, was trialled in six fresh urine samples and ten frozen urine samples with inadequate DNA yields from 0–17.7μg/mL and 0–1.6μg/mL respectively. Sufficient genomic DNA was obtained from only 4 of the initial 41 frozen urine samples (10%) for DNA methylation profiling. In comparison, all four buffy coat samples (100%) provided sufficient genomic DNA. Conclusion High quality data can be obtained provided a sufficient yield of genomic DNA is isolated. Despite optimizing various extraction methodologies, the modest amount of genomic DNA derived from urine, may limit the generalisability of this approach for the identification of DNA methylation biomarkers of chronic diabetic kidney disease.
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Affiliation(s)
- Ashani Lecamwasam
- Clinical and Disease Epigenetics Group, Murdoch Childrens Research Institute, Victoria, Australia
- Department of Endocrinology, Austin Health, Victoria, Australia
- School of Medicine, Faculty of Health Deakin University, Victoria, Australia
- * E-mail:
| | - Alexandra Sexton-Oates
- Clinical and Disease Epigenetics Group, Murdoch Childrens Research Institute, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Victoria, Australia
| | - Jake Carmody
- Clinical and Disease Epigenetics Group, Murdoch Childrens Research Institute, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Victoria, Australia
| | - Elif I. Ekinci
- Department of Endocrinology, Austin Health, Victoria, Australia
| | - Karen M. Dwyer
- School of Medicine, Faculty of Health Deakin University, Victoria, Australia
| | - Richard Saffery
- Clinical and Disease Epigenetics Group, Murdoch Childrens Research Institute, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Victoria, Australia
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Felt JR, Yurkovich C, Garshott DM, Kamat D, Farooqi A, Fribley AM, Callaghan MU, Hebert K. The Utility of Real-Time Quantitative Polymerase Chain Reaction Genotype Detection in the Diagnosis of Urinary Tract Infections in Children. Clin Pediatr (Phila) 2017; 56:912-919. [PMID: 28436231 DOI: 10.1177/0009922817706144] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Urinary tract infections (UTIs) are the most common serious bacterial infection in children with significant morbidity with delayed diagnosis. Polymerase chain reaction (PCR) is very accurate in detecting bacteria and widely available, but has never been evaluated to detect UTIs in children. To assess the utility of PCR as a rapid diagnostic tool, we conducted a prospective cohort study of 193 urine samples from children younger than 36 months undergoing evaluation for UTI in the emergency department over a 10-month period. A quantification cycle (Cq) threshold of 26.15 identified all Escherichia coli positive samples with sensitivity and specificity of 100% and 99.5%, respectively (95% CI = 71.5%-100% and 97.9%-99.5%, respectively). A Cq threshold of 19.03 identified E coli infections >100 000 colony forming units/mL with sensitivity and specificity of 100% (95% CI = 72.2%-100% and 98.6%-100%, respectively). PCR is very accurate in diagnosing E coli UTIs in young children and could be useful as a rapid diagnostic tool.
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Affiliation(s)
- Jon R Felt
- 1 Children's Hospital of Michigan, Wayne State University, Detroit, MI, USA
| | - Chelsey Yurkovich
- 1 Children's Hospital of Michigan, Wayne State University, Detroit, MI, USA
| | | | - Deepak Kamat
- 1 Children's Hospital of Michigan, Wayne State University, Detroit, MI, USA
| | - Ahmad Farooqi
- 1 Children's Hospital of Michigan, Wayne State University, Detroit, MI, USA
| | - Andrew M Fribley
- 1 Children's Hospital of Michigan, Wayne State University, Detroit, MI, USA
| | | | - Katherine Hebert
- 1 Children's Hospital of Michigan, Wayne State University, Detroit, MI, USA
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22
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Guha P, Das A, Dutta S, Chaudhuri TK. A rapid and efficient DNA extraction protocol from fresh and frozen human blood samples. J Clin Lab Anal 2017; 32. [PMID: 28233351 DOI: 10.1002/jcla.22181] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 01/22/2017] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Different methods available for extraction of human genomic DNA suffer from one or more drawbacks including low yield, compromised quality, cost, time consumption, use of toxic organic solvents, and many more. Herein, we aimed to develop a method to extract DNA from 500 μL of fresh or frozen human blood. METHODS Five hundred microliters of fresh and frozen human blood samples were used for standardization of the extraction procedure. Absorbance at 260 and 280 nm, respectively, (A260 /A280 ) were estimated to check the quality and quantity of the extracted DNA sample. Qualitative assessment of the extracted DNA was checked by Polymerase Chain reaction and double digestion of the DNA sample. RESULTS Our protocol resulted in average yield of 22±2.97 μg and 20.5±3.97 μg from 500 μL of fresh and frozen blood, respectively, which were comparable to many reference protocols and kits. CONCLUSION Besides yielding bulk amount of DNA, our protocol is rapid, economical, and avoids toxic organic solvents such as Phenol. Due to unaffected quality, the DNA is suitable for downstream applications. The protocol may also be useful for pursuing basic molecular researches in laboratories having limited funds.
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Affiliation(s)
- Pokhraj Guha
- Cellular Immunology Laboratory, Department of Zoology, University of North Bengal, Siliguri, India
| | - Avishek Das
- Cellular Immunology Laboratory, Department of Zoology, University of North Bengal, Siliguri, India
| | - Somit Dutta
- Cellular Immunology Laboratory, Department of Zoology, University of North Bengal, Siliguri, India
| | - Tapas Kumar Chaudhuri
- Cellular Immunology Laboratory, Department of Zoology, University of North Bengal, Siliguri, India
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23
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Song B, Shen M, Jiang D, Malla S, Mosa IM, Choudhary D, Rusling JF. Microfluidic array for simultaneous detection of DNA oxidation and DNA-adduct damage. Analyst 2016; 141:5722-5729. [PMID: 27517117 PMCID: PMC5048564 DOI: 10.1039/c6an01237j] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Exposure to chemical pollutants and pharmaceuticals may cause health issues caused by metabolite-related toxicity. This paper reports a new microfluidic electrochemical sensor array with the ability to simultaneously detect common types of DNA damage including oxidation and nucleobase adduct formation. Sensors in the 8-electrode screen-printed carbon array were coated with thin films of metallopolymers osmium or ruthenium bipyridyl-poly(vinylpyridine) chloride (OsPVP, RuPVP) along with DNA and metabolic enzymes by layer-by-layer electrostatic assembly. After a reaction step in which test chemicals and other necessary reagents flow over the array, OsPVP selectively detects oxidized guanines on the DNA strands, and RuPVP detects DNA adduction by metabolites on nucleobases. We demonstrate array performance for test chemicals including 17β-estradiol (E2), its metabolites 4-hydroxyestradiol (4-OHE2), 2-hydroxyestradiol (2-OHE2), catechol, 2-nitrosotoluene (2-NO-T), 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK), and 2-acetylaminofluorene (2-AAF). Results revealed DNA-adduct and oxidation damage in a single run to provide a metabolic-genotoxic chemistry screen. The array measures damage directly in unhydrolyzed DNA, and is less expensive, faster, and simpler than conventional methods to detect DNA damage. The detection limit for oxidation is 672 8-oxodG per 106 bases. Each sensor requires only 22 ng of DNA, so the mass detection limit is 15 pg (∼10 pmol) 8-oxodG.
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Affiliation(s)
- Boya Song
- Department of Chemistry, University of Connecticut, Storrs, CT 06269, USA.
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24
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Koshy L, Anju AL, Harikrishnan S, Kutty VR, Jissa VT, Kurikesu I, Jayachandran P, Jayakumaran Nair A, Gangaprasad A, Nair GM, Sudhakaran PR. Evaluating genomic DNA extraction methods from human whole blood using endpoint and real-time PCR assays. Mol Biol Rep 2016; 44:97-108. [PMID: 27686559 DOI: 10.1007/s11033-016-4085-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 09/22/2016] [Indexed: 11/29/2022]
Abstract
The extraction of genomic DNA is the crucial first step in large-scale epidemiological studies. Though there are many popular DNA isolation methods from human whole blood, only a few reports have compared their efficiencies using both end-point and real-time PCR assays. Genomic DNA was extracted from coronary artery disease patients using solution-based conventional protocols such as the phenol-chloroform/proteinase-K method and a non-phenolic non-enzymatic Rapid-Method, which were evaluated and compared vis-a-vis a commercially available silica column-based Blood DNA isolation kit. The appropriate method for efficiently extracting relatively pure DNA was assessed based on the total DNA yield, concentration, purity ratios (A260/A280 and A260/A230), spectral profile and agarose gel electrophoresis analysis. The quality of the isolated DNA was further analysed for PCR inhibition using a murine specific ATP1A3 qPCR assay and mtDNA/Y-chromosome ratio determination assay. The suitability of the extracted DNA for downstream applications such as end-point SNP genotyping, was tested using PCR-RFLP analysis of the AGTR1-1166A>C variant, a mirSNP having pharmacogenetic relevance in cardiovascular diseases. Compared to the traditional phenol-chloroform/proteinase-K method, our results indicated the Rapid-Method to be a more suitable protocol for genomic DNA extraction from human whole blood in terms of DNA quantity, quality, safety, processing time and cost. The Rapid-Method, which is based on a simple salting-out procedure, is not only safe and cost-effective, but also has the added advantage of being scaled up to process variable sample volumes, thus enabling it to be applied in large-scale epidemiological studies.
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Affiliation(s)
- Linda Koshy
- Department of Biotechnology, Inter-University Centre for Genomics and Gene Technology, University of Kerala, Trivandrum, 695 581, India.
| | - A L Anju
- Department of Biotechnology, Inter-University Centre for Genomics and Gene Technology, University of Kerala, Trivandrum, 695 581, India
| | - S Harikrishnan
- Department of Cardiology, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Trivandrum, 695 011, India
| | - V R Kutty
- Achutha Menon Centre for Health Science Studies, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Trivandrum, 695 011, India
| | - V T Jissa
- Achutha Menon Centre for Health Science Studies, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Trivandrum, 695 011, India
| | - Irin Kurikesu
- Department of Biotechnology, Inter-University Centre for Genomics and Gene Technology, University of Kerala, Trivandrum, 695 581, India
| | - Parvathy Jayachandran
- Department of Biotechnology, Inter-University Centre for Genomics and Gene Technology, University of Kerala, Trivandrum, 695 581, India
| | - A Jayakumaran Nair
- Department of Biotechnology, Inter-University Centre for Genomics and Gene Technology, University of Kerala, Trivandrum, 695 581, India
| | - A Gangaprasad
- Department of Biotechnology, Inter-University Centre for Genomics and Gene Technology, University of Kerala, Trivandrum, 695 581, India.,Deparment of Botany, University of Kerala, Trivandrum, 695 581, India
| | - G M Nair
- Department of Biotechnology, Inter-University Centre for Genomics and Gene Technology, University of Kerala, Trivandrum, 695 581, India
| | - P R Sudhakaran
- Department of Biotechnology, Inter-University Centre for Genomics and Gene Technology, University of Kerala, Trivandrum, 695 581, India.,Department of Computational Biology and Bioinformatics, University of Kerala, Trivandrum, 695 581, India
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25
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Dimethyl adipimidate/Thin film Sample processing (DTS); A simple, low-cost, and versatile nucleic acid extraction assay for downstream analysis. Sci Rep 2015; 5:14127. [PMID: 26370251 PMCID: PMC4569962 DOI: 10.1038/srep14127] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 08/18/2015] [Indexed: 11/30/2022] Open
Abstract
Sample processing, especially that involving nucleic acid extraction, is a prerequisite step for the isolation of high quantities of relatively pure DNA for downstream analyses in many life science and biomedical engineering studies. However, existing methods still have major problems, including labor-intensive time-consuming methods and high costs, as well as requirements for a centrifuge and the complex fabrication of filters and membranes. Here, we first report a versatile Dimethyl adipimidate/Thin film based Sample processing (DTS) procedure without the limitations of existing methods. This procedure is useful for the extraction of DNA from a variety of sources, including 6 eukaryotic cells, 6 bacteria cells, and 2 body fluids in a single step. Specifically, the DTS procedure does not require a centrifuge and has improved time efficiency (30 min), affordability, and sensitivity in downstream analysis. We validated the DTS procedure for the extraction of DNA from human body fluids, as well as confirmed that the quality and quantity of the extracted DNA were sufficient to allow robust detection of genetic and epigenetic biomarkers in downstream analysis.
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26
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Majer W, Kluzek K, Bluyssen H, Wesoły J. Potential Approaches and Recent Advances in Biomarker Discovery in Clear-Cell Renal Cell Carcinoma. J Cancer 2015; 6:1105-13. [PMID: 26516358 PMCID: PMC4615346 DOI: 10.7150/jca.12145] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 06/12/2015] [Indexed: 02/06/2023] Open
Abstract
The early diagnosis and monitoring of clear-cell Renal Cell Carcinoma (ccRCC), which is the most common renal malignancy, remains challenging. The late diagnosis and lack of tools that can be used to assess the progression of the disease and metastasis significantly influence the chance of survival of ccRCC patients. Molecular biomarkers have been shown to aid the diagnosis and disease monitoring for other cancers, but such markers are not currently available for ccRCC. Recently, plasma and serum circulating nucleic acids, nucleic acids present in urine, and plasma and urine proteins gained interest in the field of cancer biomarker discovery. Here, we describe the applicability of plasma and urine nucleic acids as cancer biomarkers with a particular focus on DNA, small RNA, and protein markers for ccRCC.
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Affiliation(s)
- Weronika Majer
- 1. Laboratory of High Throughput Technologies, Institute of Molecular Biology and Biotechnology, Faculty of Biology, University of Adam Mickiewicz, Umultowska 89, 61-614 Poznan, Poland, Tel. +4861 829 5832, Fax. +4861 829 5949
| | - Katarzyna Kluzek
- 2. Department of Human Molecular Genetics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, University of Adam Mickiewicz, Umultowska 89, 64-614 Poznan, Tel. +4861 829 5832
| | - Hans Bluyssen
- 2. Department of Human Molecular Genetics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, University of Adam Mickiewicz, Umultowska 89, 64-614 Poznan, Tel. +4861 829 5832
| | - Joanna Wesoły
- 1. Laboratory of High Throughput Technologies, Institute of Molecular Biology and Biotechnology, Faculty of Biology, University of Adam Mickiewicz, Umultowska 89, 61-614 Poznan, Poland, Tel. +4861 829 5832, Fax. +4861 829 5949
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27
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Gandasegui J, Fernández-Soto P, Carranza-Rodríguez C, Pérez-Arellano JL, Vicente B, López-Abán J, Muro A. The Rapid-Heat LAMPellet Method: A Potential Diagnostic Method for Human Urogenital Schistosomiasis. PLoS Negl Trop Dis 2015; 9:e0003963. [PMID: 26230990 PMCID: PMC4521856 DOI: 10.1371/journal.pntd.0003963] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 07/07/2015] [Indexed: 12/25/2022] Open
Abstract
Background Urogenital schistosomiasis due to Schistosoma haematobium is a serious underestimated public health problem affecting 112 million people - particularly in sub-Saharan Africa. Microscopic examination of urine samples to detect parasite eggs still remains as definitive diagnosis. This work was focussed on developing a novel loop-mediated isothermal amplification (LAMP) assay for detection of S. haematobium DNA in human urine samples as a high-throughput, simple, accurate and affordable diagnostic tool to use in diagnosis of urogenital schistosomiasis. Methodology/Principal Findings A LAMP assay targeting a species specific sequence of S. haematobium ribosomal intergenic spacer was designed. The effectiveness of our LAMP was assessed in a number of patients´ urine samples with microscopy confirmed S. haematobium infection. For potentially large-scale application in field conditions, different DNA extraction methods, including a commercial kit, a modified NaOH extraction method and a rapid heating method were tested using small volumes of urine fractions (whole urine, supernatants and pellets). The heating of pellets from clinical samples was the most efficient method to obtain good-quality DNA detectable by LAMP. The detection limit of our LAMP was 1 fg/µL of S. haematobium DNA in urine samples. When testing all patients´ urine samples included in our study, diagnostic parameters for sensitivity and specificity were calculated for LAMP assay, 100% sensitivity (95% CI: 81.32%-100%) and 86.67% specificity (95% CI: 75.40%-94.05%), and also for microscopy detection of eggs in urine samples, 69.23% sensitivity (95% CI: 48.21% -85.63%) and 100% specificity (95% CI: 93.08%-100%). Conclusions/Significance We have developed and evaluated, for the first time, a LAMP assay for detection of S. haematobium DNA in heated pellets from patients´ urine samples using no complicated requirement procedure for DNA extraction. The procedure has been named the Rapid-Heat LAMPellet method and has the potential to be developed further as a field diagnostic tool for use in urogenital schistosomiasis-endemic areas. Human schistosomiasis is a disease caused by several species of parasitic worms of the genus Schistosoma that is affecting 200 million people, especially in sub-Saharan Africa. Most people are infected with Schistosoma haematobium, the species that causes urogenital schistosomiasis and also bladder cancer in many chronic infections. The definitive diagnostic test is based on microscopic examination of urine samples to detect parasite eggs. This method has low sensitivity, high day-to-day variability and cannot be carried out in the acute phase of the disease since the parasite has not started yet to lay eggs. New high-throughput diagnostic tools would be desirable, permitting early treatment and preventing the pathology associated with chronic infections. An interesting approach is the loop-mediated isothermal amplification (LAMP) technique because of its simplicity in operation and potential use in clinical diagnosis and surveillance of infectious diseases. In this study, we developed and evaluated a LAMP assay for detection of S. haematobium DNA in patients´ urine samples using heated pellets with no complicated requirement procedure for DNA extraction, namely the Rapid-Heat LAMPellet method. This is a new, easy, rapid and cost-effective LAMP method that should prove useful for mass screening in limited-resource settings in urogenital schistosomiasis-endemic areas.
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Affiliation(s)
- Javier Gandasegui
- IBSAL-CIETUS (Instituto de Investigación Biomédica de Salamanca-Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca), Facultad de Farmacia, Universidad de Salamanca, Salamanca, Spain
| | - Pedro Fernández-Soto
- IBSAL-CIETUS (Instituto de Investigación Biomédica de Salamanca-Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca), Facultad de Farmacia, Universidad de Salamanca, Salamanca, Spain
- * E-mail:
| | - Cristina Carranza-Rodríguez
- Departamento de Ciencias Médicas y Quirúrgicas, Facultad de Ciencias de la Salud, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - José Luis Pérez-Arellano
- Departamento de Ciencias Médicas y Quirúrgicas, Facultad de Ciencias de la Salud, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Belén Vicente
- IBSAL-CIETUS (Instituto de Investigación Biomédica de Salamanca-Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca), Facultad de Farmacia, Universidad de Salamanca, Salamanca, Spain
| | - Julio López-Abán
- IBSAL-CIETUS (Instituto de Investigación Biomédica de Salamanca-Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca), Facultad de Farmacia, Universidad de Salamanca, Salamanca, Spain
| | - Antonio Muro
- IBSAL-CIETUS (Instituto de Investigación Biomédica de Salamanca-Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca), Facultad de Farmacia, Universidad de Salamanca, Salamanca, Spain
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