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Maiocchi S, Collins EN, Peterson AR, Alexander KC, McGlamery DJ, Cassidy NA, Ikonomidis JS, Akerman AW. Plasma microrna quantification protocol. VESSEL PLUS 2023; 7:27. [PMID: 38445249 PMCID: PMC10914336 DOI: 10.20517/2574-1209.2023.69] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate translation and are involved in many pathological processes. They have emerged as promising biomarkers for diagnosis of conditions such as aortic aneurysm disease. Quantifying miRNAs in plasma is uniquely challenging because of the lack of standardized reproducible protocols. To facilitate the independent verification of conclusions, it is necessary to provide a thorough disclosure of all pertinent experimental details. In this technical note, we present a comprehensive protocol for quantifying plasma miRNAs using droplet digital PCR. We detail the entire workflow, including blood collection, plasma processing, cryo-storage, miRNA isolation, reverse transcription, droplet generation, PCR amplification, fluorescence reading, and data analysis. We offer comprehensive guidance regarding optimization, assay conditions, expected results, and insight into the troubleshooting of common issues. The stepwise normalization and detailed methodological guide enhance reproducibility. Moreover, multiple portions of this protocol may be automated. The data provided in this technical note is demonstrative of the values typically obtained when following its steps. To facilitate standardization in data reporting, we include a table of expected aortic aneurysm-related miRNA levels in healthy human plasma. This versatile protocol can be easily adapted to quantify most circulating miRNAs in plasma, making it a valuable resource for diagnostic development.
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Affiliation(s)
- Sophie Maiocchi
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7545, USA
| | - Elizabeth N. Collins
- Department of Surgery, Division of Cardiothoracic Surgery, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7065, USA
| | - Andrew R. Peterson
- Department of Surgery, Division of Cardiothoracic Surgery, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7065, USA
| | - Kyle C. Alexander
- Department of Surgery, Division of Cardiothoracic Surgery, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7065, USA
| | - Dalton J. McGlamery
- Department of Surgery, Division of Cardiothoracic Surgery, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7065, USA
| | - Noah A. Cassidy
- University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - John S. Ikonomidis
- Department of Surgery, Division of Cardiothoracic Surgery, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7065, USA
| | - Adam W. Akerman
- Department of Surgery, Division of Cardiothoracic Surgery, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7065, USA
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2
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McIlwraith EK, He W, Belsham DD. Promise and Perils of MicroRNA Discovery Research: Working Toward Quality Over Quantity. Endocrinology 2023; 164:bqad111. [PMID: 37453100 DOI: 10.1210/endocr/bqad111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/07/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
Since the first microRNA (miRNA) was described in 1993 in the humble worm Caenorhabditis elegans, the miRNA field has boomed, with more than 100 000 related patents filed and miRNAs now in ongoing clinical trials. Despite an advanced understanding of the biogenesis and action of miRNAs, applied miRNA research faces challenges and irreproducibility due to a lack of standardization. This review provides guidelines regarding miRNA investigation, while focusing on the pitfalls and considerations that are often overlooked in prevailing applied miRNA research. These include miRNA annotation and quantification, to modulation, target prediction, validation, and the study of circulating miRNAs.
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Affiliation(s)
- Emma K McIlwraith
- Department of Physiology, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Wenyuan He
- Department of Physiology, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Denise D Belsham
- Department of Physiology, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
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3
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Diehl JN, Ray A, Collins LB, Peterson A, Alexander KC, Boutros JG, Ikonomidis JS, Akerman AW. A standardized method for plasma extracellular vesicle isolation and size distribution analysis. PLoS One 2023; 18:e0284875. [PMID: 37115777 PMCID: PMC10146456 DOI: 10.1371/journal.pone.0284875] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
The following protocol describes our workflow for isolation and quantification of plasma extracellular vesicles (EVs). It requires limited sample volume so that the scientific value of specimens is maximized. These steps include isolation of vesicles by automated size exclusion chromatography and quantification by tunable resistive pulse sensing. This workflow optimizes reproducibility by minimizing variations in processing, handling, and storage of EVs. EVs have significant diagnostic and therapeutic potential, but clinical application is limited by disparate methods of data collection. This standardized protocol is scalable and ensures efficient recovery of physiologically intact EVs that may be used in a variety of downstream biochemical and functional analyses. Simultaneous measurement quantifies EV concentration and size distribution absolutely. Absolute quantification corrects for variations in EV number and size, offering a novel method of standardization in downstream applications.
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Affiliation(s)
- J. Nathaniel Diehl
- University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Amelia Ray
- University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Lauren B. Collins
- University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Andrew Peterson
- Department of Surgery, University of North Carolina–Chapel Hill, Chapel Hill, North Carolina, United States of America
- Division of Cardiothoracic Surgery, University of North Carolina–Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Kyle C. Alexander
- Department of Surgery, University of North Carolina–Chapel Hill, Chapel Hill, North Carolina, United States of America
- Division of Cardiothoracic Surgery, University of North Carolina–Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jacob G. Boutros
- Campbell University School of Osteopathic Medicine, Lillington, North Carolina, United States of America
| | - John S. Ikonomidis
- Department of Surgery, University of North Carolina–Chapel Hill, Chapel Hill, North Carolina, United States of America
- Division of Cardiothoracic Surgery, University of North Carolina–Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Adam W. Akerman
- Department of Surgery, University of North Carolina–Chapel Hill, Chapel Hill, North Carolina, United States of America
- Division of Cardiothoracic Surgery, University of North Carolina–Chapel Hill, Chapel Hill, North Carolina, United States of America
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4
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Sritong N, Sala de Medeiros M, Basing LA, Linnes JC. Promise and perils of paper-based point-of-care nucleic acid detection for endemic and pandemic pathogens. LAB ON A CHIP 2023; 23:888-912. [PMID: 36688463 PMCID: PMC10028599 DOI: 10.1039/d2lc00554a] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
From HIV and influenza to emerging pathogens like COVID-19, each new infectious disease outbreak has highlighted the need for massively-scalable testing that can be performed outside centralized laboratory settings at the point-of-care (POC) in order to prevent, track, and monitor endemic and pandemic threats. Nucleic acid amplification tests (NAATs) are highly sensitive and can be developed and scaled within weeks while protein-based rapid tests require months for production. Combining NAATs with paper-based detection platforms are promising due to the manufacturability, scalability, and simplicity of each of these components. Typically, paper-based NAATs consist of three sequential steps: sample collection and preparation, amplification of DNA or RNA from pathogens of interest, and detection. However, these exist within a larger ecosystem of sample collection and interpretation workflow, usability, and manufacturability which can be vastly perturbed during a pandemic emergence. This review aims to explore the challenges of paper-based NAATs covering sample-to-answer procedures along with three main types of clinical samples; blood, urine, and saliva, as well as broader operational, scale up, and regulatory aspects of device development and implementation. To fill the technological gaps in paper-based NAATs, a sample-in-result-out system that incorporates the integrated sample collection, sample preparation, and integrated internal amplification control while also balancing needs of users and manufacturability upfront in the early design process is required.
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Affiliation(s)
- Navaporn Sritong
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA.
| | | | - Laud Anthony Basing
- Department of Medical Diagnostics, Kwame Nkrumah University of Science and Technology, Kumasi, Ashanti, Ghana
| | - Jacqueline C Linnes
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA.
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5
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Beránek M, Koblížek V, Dulíček P, Hegerová J, Palička V. Whole blood samples for faster real-time PCR analysis of thrombophilic mutations in SARS-CoV-2 virus positive patients. Physiol Res 2022; 71:439-445. [PMID: 35616044 DOI: 10.33549/physiolres.934883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
High incidence of thrombosis and venous thromboembolism was reported in patients with COVID-19. In this study, we focused on analysis of thrombophilic mutations performed without a standard DNA extraction step. In one hundred of COVID-19 positive outpatients, real-time PCR for Leiden mutation in the FV gene and G20210A mutation in the FII gene was carried out from DNA extracts and modified whole blood samples, and their cycle threshold (Ct) values were evaluated. In the extracts, healthy homozygotes (wt/wt), heterozygotes (M/wt), and homozygous carriers of Leiden mutation (M/M) provided median Ct values of 18.5, 19.4/22.0, and 20.9. In the whole blood, Ct values were 25.3 (wt/wt), 24.8/27.2 (M/wt), and 26.9 (M/M). Median Ct values for G20210A in the extracts were 19.6 for homozygotes (wt/wt), and 19.7/20.4 for heterozygous carriers. The whole blood samples provided Ct values of 23.9 in healthy homozygotes and 26.3/27.2 in heterozygotes for G20210A mutation. No homozygous subjects for G20210A and no double heterozygotes (for Leiden and G20210A mutations) were found. Despite significant differences in the Ct values, genotyping showed complete result concordance of the DNA extracts and the whole blood samples. The integrity and amplificability of DNA molecules in the whole blood samples during 28 days of deep freezing, interrupted by four cycles of thawing, did not significantly change. In conclusion, we demonstrated a new protocol for the detection of the thrombophilic mutations via real time PCR on the modified whole blood of COVID-19 positive patients. The blood modification was reliable, easy, cheap, and saving costs and turnaround time of the whole laboratory process.
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Affiliation(s)
- M Beránek
- Institute of Clinical Biochemistry and Diagnostics, Charles University Hospital, Hradec Králové, Czech Republic.
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6
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Yunga ST, Gower AJ, Melrose AR, Fitzgerald MK, Rajendran A, Lusardi TA, Armstrong RJ, Minnier J, Jordan KR, McCarty OJT, David LL, Wilmarth PA, Reddy AP, Aslan JE. Effects of ex vivo blood anticoagulation and preanalytical processing time on the proteome content of platelets. J Thromb Haemost 2022; 20:1437-1450. [PMID: 35253976 PMCID: PMC9887642 DOI: 10.1111/jth.15694] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/03/2022] [Indexed: 02/03/2023]
Abstract
BACKGROUND Ex vivo assays of platelet function critically inform mechanistic and clinical hematology studies, where effects of divergent blood processing methods on platelet composition are apparent, but unspecified. OBJECTIVE Here, we evaluate how different blood anticoagulation options and processing times affect platelet function and protein content ex vivo. METHODS Parallel blood samples were collected from healthy human donors into sodium citrate, acid citrate dextrose, EDTA or heparin, and processed over an extended time course for functional and biochemical experiments, including platelet proteome quantification with multiplexed tandem mass tag (TMT) labeling and triple quadrupole mass spectrometry (MS). RESULTS Each anticoagulant had time-dependent effects on platelet function in whole blood. For instance, heparin enhanced platelet agonist reactivity, platelet-monocyte aggregate formation and platelet extracellular vesicle release, while EDTA increased platelet α-granule secretion. Following platelet isolation, TMT-MS quantified 3357 proteins amongst all prepared platelet samples. Altogether, >400 proteins were differentially abundant in platelets isolated from blood processed at 24 h versus 1 h post-phlebotomy, including proteins pertinent to membrane trafficking and exocytosis. Anticoagulant-specific effects on platelet proteomes included increased complement system and decreased α-granule proteins in platelets from EDTA-anticoagulated blood. Platelets prepared from heparinized blood had higher levels of histone and neutrophil-associated proteins in a manner related to neutrophil extracellular trap (NET) formation and platelet:NET interactions in whole blood ex vivo. CONCLUSION Our results demonstrate that different anticoagulants routinely used for blood collection have varying effects on platelets ex vivo, where methodology-associated alterations in platelet proteome may influence mechanistic, translational and biomarker studies.
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Affiliation(s)
- Samuel Tassi Yunga
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
- Department of Biomedical Engineering, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Austin J. Gower
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Alexander R. Melrose
- Knight Cardiovascular Institute, Division of Cardiology, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Meghan K. Fitzgerald
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Ashmitha Rajendran
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Theresa A. Lusardi
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Randall J. Armstrong
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Jessica Minnier
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
- Knight Cardiovascular Institute, Division of Cardiology, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Kelley R. Jordan
- Department of Biomedical Engineering, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Owen J. T. McCarty
- Department of Biomedical Engineering, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Larry L. David
- Proteomics Shared Resource; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
- Department of Chemical Physiology & Biochemistry, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Phillip A. Wilmarth
- Proteomics Shared Resource; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Ashok P. Reddy
- Proteomics Shared Resource; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Joseph E. Aslan
- Department of Biomedical Engineering, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
- Knight Cardiovascular Institute, Division of Cardiology, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
- Department of Chemical Physiology & Biochemistry, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
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7
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MicroRNA Signatures in the Upper Urinary Tract Urothelial Carcinoma Scenario: Ready for the Game Changer? Int J Mol Sci 2022; 23:ijms23052602. [PMID: 35269744 PMCID: PMC8910117 DOI: 10.3390/ijms23052602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/20/2022] [Accepted: 02/24/2022] [Indexed: 12/18/2022] Open
Abstract
Upper urinary tract urothelial carcinoma (UTUC) represents a minor subgroup of malignancies arising in the urothelium of the renal pelvis or ureter. The estimated annual incidence is around 2 cases per 100,000 people, with a mean age at diagnosis of 73 years. UTUC is more frequently diagnosed in an invasive or metastatic stage. However, even though the incidence of UTUC is not high, UTUC tends to be aggressive and rapidly progressing with a poor prognosis in some patients. A significant challenge in UTUC is ensuring accurate and timely diagnosis, which is complicated by the non-specific nature of symptoms seen at the onset of disease. Moreover, there is a lack of biomarkers capable of identifying the early presence of the malignancy and guide-tailored medical treatment. However, the growing understanding of the molecular biology underlying UTUC has led to the discovery of promising new biomarkers. Among these biomarkers, there is a class of small non-coding RNA biomarkers known as microRNAs (miRNAs) that are particularly promising. In this review, we will analyze the main characteristics of UTUC and focus on microRNAs as possible novel tools that could enter clinical practice in order to optimize the current diagnostic and prognostic algorithm.
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8
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Enhanced Antiviral Function of Magnesium Chloride-Modified Heparin on a Broad Spectrum of Viruses. Int J Mol Sci 2021; 22:ijms221810075. [PMID: 34576237 PMCID: PMC8466540 DOI: 10.3390/ijms221810075] [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: 08/20/2021] [Revised: 09/13/2021] [Accepted: 09/15/2021] [Indexed: 12/12/2022] Open
Abstract
Previous studies reported on the broad-spectrum antiviral function of heparin. Here we investigated the antiviral function of magnesium-modified heparin and found that modified heparin displayed a significantly enhanced antiviral function against human adenovirus (HAdV) in immortalized and primary cells. Nuclear magnetic resonance analyses revealed a conformational change of heparin when complexed with magnesium. To broadly explore this discovery, we tested the antiviral function of modified heparin against herpes simplex virus type 1 (HSV-1) and found that the replication of HSV-1 was even further decreased compared to aciclovir. Moreover, we investigated the antiviral effect against the new severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) and measured a 55-fold decreased viral load in the supernatant of infected cells associated with a 38-fold decrease in virus growth. The advantage of our modified heparin is an increased antiviral effect compared to regular heparin.
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9
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Mee PT, Wong S, O’Riley KJ, da Conceição F, Bendita da Costa Jong J, Phillips DE, Rodoni BC, Rawlin GT, Lynch SE. Field Verification of an African Swine Fever Virus Loop-Mediated Isothermal Amplification (LAMP) Assay During an Outbreak in Timor-Leste. Viruses 2020; 12:v12121444. [PMID: 33334037 PMCID: PMC7765541 DOI: 10.3390/v12121444] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 12/11/2020] [Indexed: 02/07/2023] Open
Abstract
Recent outbreaks of African swine fever virus (ASFV) have seen the movement of this virus into multiple new regions with devastating impact. Many of these outbreaks are occurring in remote, or resource-limited areas, that do not have access to molecular laboratories. Loop-mediated isothermal amplification (LAMP) is a rapid point of care test that can overcome a range of inhibitors. We outline further development of a real-time ASFV LAMP, including field verification during an outbreak in Timor-Leste. To increase field applicability, the extraction step was removed and an internal amplification control (IAC) was implemented. Assay performance was assessed in six different sample matrices and verified for a range of clinical samples. A LAMP detection limit of 400 copies/rxn was determined based on synthetic positive control spikes. A colourmetric LAMP assay was also assessed on serum samples. Comparison of the LAMP assay to a quantitative polymerase chain reaction (qPCR) was performed on clinical ASFV samples, using both serum and oral/rectal swabs, with a substantial level of agreement observed. The further verification of the ASFV LAMP assay, removal of extraction step, implementation of an IAC and the assessment of a range of sample matrix, further support the use of this assay for rapid in-field detection of ASFV.
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Affiliation(s)
- Peter T. Mee
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, VIC 3083, Australia; (S.W.); (K.J.O.); (B.C.R.); (G.T.R.); (S.E.L.)
- Correspondence: ; Tel.: +61-390-327-143
| | - Shani Wong
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, VIC 3083, Australia; (S.W.); (K.J.O.); (B.C.R.); (G.T.R.); (S.E.L.)
| | - Kim J. O’Riley
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, VIC 3083, Australia; (S.W.); (K.J.O.); (B.C.R.); (G.T.R.); (S.E.L.)
| | - Felisiano da Conceição
- Ministry of Agriculture and Fisheries, Government of Timor-Leste, Av. Nicolao Lobato, Comoro, Dili 0332, Timor-Leste; (F.d.C.); (J.B.d.C.J.)
| | - Joanita Bendita da Costa Jong
- Ministry of Agriculture and Fisheries, Government of Timor-Leste, Av. Nicolao Lobato, Comoro, Dili 0332, Timor-Leste; (F.d.C.); (J.B.d.C.J.)
| | - Dianne E. Phillips
- Agriculture Victoria, Biosecurity and Agriculture Services, Bairnsdale, VIC 3857, Australia;
| | - Brendan C. Rodoni
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, VIC 3083, Australia; (S.W.); (K.J.O.); (B.C.R.); (G.T.R.); (S.E.L.)
| | - Grant T. Rawlin
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, VIC 3083, Australia; (S.W.); (K.J.O.); (B.C.R.); (G.T.R.); (S.E.L.)
| | - Stacey E. Lynch
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, VIC 3083, Australia; (S.W.); (K.J.O.); (B.C.R.); (G.T.R.); (S.E.L.)
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10
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Armitage JD, Bolitho EM, Moodley YP, Tan DBA. A simplified protocol for profiling heparin-contaminated circulating miRNAs: by microfluidic array. Mol Biol Rep 2020; 47:9973-9977. [PMID: 33170428 DOI: 10.1007/s11033-020-05964-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 10/29/2020] [Indexed: 11/30/2022]
Abstract
Peripheral blood is a valuable, non-invasive source of biomarkers which include circulating miRNAs. Using microfluidic array-based techniques, miRNAs can be successfully measured in small amounts of blood plasma (< 0.5 mL) using cDNA pre-amplification. However, the use of heparin-based anticoagulants for blood collection hinders the detection of circulating miRNAs due to its inhibitory effect on PCR components. Although pre-treatment with heparinase have been shown to overcome heparin contamination in blood, its effect has not been described in array-based analyses or more sensitive applications with smaller sample volumes (i.e. 200 μL plasma) requiring pre-amplification. We show that the treatment of miRNA extracted from heparinised plasma with an optimised concentration of Bacteroides heparinase I prior to cDNA pre-amplification dramatically improves the number of detectable miRNA from 2 to 67 targets on the TaqMan® Array Human MicroRNA Cards. Furthermore, the titrated amount of heparinase (3 U) gave the best miRNA detection compared to those used in previous studies (6-24 U). This study provides novel data which demonstrates that heparinase treatment is compatible with protocols that involve pre-amplification of cDNA and microfluidic array-based techniques. This an improved methodology that permits miRNA-based biomarker analysis from small volume of heparinised plasma.
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Affiliation(s)
- Jesse D Armitage
- Centre for Respiratory Health, School of Biomedical Sciences, University of Western Australia, Level 5, Harry Perkins Institute of Medical Research, 6 Verdun Street, Nedlands, Perth, WA, 6000, Australia.,Stem Cell Unit, Institute for Respiratory Health, Perth, WA, Australia
| | - Erin M Bolitho
- Research Centre, Royal Perth Hospital, Perth, WA, Australia
| | - Yuben P Moodley
- Centre for Respiratory Health, School of Biomedical Sciences, University of Western Australia, Level 5, Harry Perkins Institute of Medical Research, 6 Verdun Street, Nedlands, Perth, WA, 6000, Australia.,Stem Cell Unit, Institute for Respiratory Health, Perth, WA, Australia.,Department of Respiratory Medicine, Fiona Stanley Hospital, Murdoch, WA, Australia
| | - Dino B A Tan
- Centre for Respiratory Health, School of Biomedical Sciences, University of Western Australia, Level 5, Harry Perkins Institute of Medical Research, 6 Verdun Street, Nedlands, Perth, WA, 6000, Australia. .,Stem Cell Unit, Institute for Respiratory Health, Perth, WA, Australia.
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11
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Guy GP, Hargrave J, Dunn R, Price K, Short J, Thilaganathan B. Secondary non-invasive prenatal screening for fetal trisomy: an effectiveness study in a public health setting. BJOG 2020; 128:440-446. [PMID: 32790109 DOI: 10.1111/1471-0528.16464] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/04/2020] [Indexed: 02/06/2023]
Abstract
OBJECTIVE To evaluate the effectiveness of secondary screening using non-invasive prenatal testing (NIPT) in a routine NHS setting including test performance, turn-around times (TATs) and no-call (failure to obtain result) rates. To examine the influence of maternal and fetal characteristics on test performance. DESIGN Retrospective cohort. SETTING London teaching hospital. SAMPLE A total of 8651 pregnancies undergoing screening for fetal trisomy using NIPT provided by an NHS cell-free DNA screening laboratory - the SAFE laboratory. METHODS Screening test evaluation and TATs. Univariate and multivariate logistic regression analysis to identify significant predictors of no-call results and reported by low fetal fraction (<2%), very high fetal fraction (>40%) and processing failure. MAIN OUTCOME MEASURES Test performance, TATs and no-call rates, factors affecting no-call results. RESULTS Average TAT was 4.0 days (95% CI 4.0-4.2 days). Test sensitivities for trisomies 21 and 13/18 were 98.9% (95% CI 95.9-99.9%) and 90.4% (95% CI 80.0-96.8%), respectively. The overall no-call rate was 32/8651 (0.37%, 95% CI 0.26-0.52%). The overall risk of a no-call result was influenced by gestational age, dichorionic twin pregnancy, history of malignancy and pregnancies affected by trisomy 13/18, but not by maternal weight or use of low-molecular-weight heparin. CONCLUSIONS High-throughput NIPT can be effectively embedded into a public health NHS setting. TATs of 4 days and no-calls of <0.5% were well within clinically desirable tolerances. Gestational age, maternal weight, assisted reproductive techniques, use of low-molecular-weight heparin and past history of malignancy did not have major impacts on test no-call rates and should not constitute reasons for withholding the option of NIPT from women. TWEETABLE ABSTRACT Turn-around times of 4 days, no-call (test failure) rates of 0.37% and highly accurate NIPT can be successfully embedded in the NHS.
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Affiliation(s)
- G P Guy
- Fetal Medicine Unit, St George's University Hospitals NHS Foundation Trust, London, UK.,Vascular Biology Research Centre, Molecular and Clinical Sciences Research Institute, St George's University of London, London, UK
| | - J Hargrave
- Fetal Medicine Unit, St George's University Hospitals NHS Foundation Trust, London, UK.,St George's Antenatal Fetal Evaluation (SAFE) Laboratory, St George's Hospital, St George's University of London, London, UK
| | - R Dunn
- St George's Antenatal Fetal Evaluation (SAFE) Laboratory, St George's Hospital, St George's University of London, London, UK
| | - K Price
- St George's Antenatal Fetal Evaluation (SAFE) Laboratory, St George's Hospital, St George's University of London, London, UK
| | - J Short
- St George's Antenatal Fetal Evaluation (SAFE) Laboratory, St George's Hospital, St George's University of London, London, UK
| | - B Thilaganathan
- Fetal Medicine Unit, St George's University Hospitals NHS Foundation Trust, London, UK.,Vascular Biology Research Centre, Molecular and Clinical Sciences Research Institute, St George's University of London, London, UK.,St George's Antenatal Fetal Evaluation (SAFE) Laboratory, St George's Hospital, St George's University of London, London, UK
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12
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Heeroma AJ, Gwenin C. Development of Solid-Phase RPA on a Lateral Flow Device for the Detection of Pathogens Related to Sepsis. SENSORS (BASEL, SWITZERLAND) 2020; 20:E4182. [PMID: 32731402 PMCID: PMC7436017 DOI: 10.3390/s20154182] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/19/2020] [Accepted: 07/21/2020] [Indexed: 12/19/2022]
Abstract
Population extended life expectancy has significantly increased the risk of septic shock in an ageing population. Sepsis affects roughly 20 million people every year, resulting in over 11 million deaths. The need for faster more accurate diagnostics and better management is therefore paramount in the fight to prevent these avoidable deaths. Here we report the development of a POC device with the ability to identify a broad range of pathogens on a lateral flow platform. Namely Gram-positive and Gram-negative bacteria. The simple to use laboratory device has the potential to be automated, thus enabling an operator to carry out solid-phase lysis and room temperature RPA in situ, providing accurate results in hours rather than days. Results show there is a potential for a fully automated device in which concepts described in this paper can be integrated into a lateral flow device.
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Affiliation(s)
- Alice Jane Heeroma
- School of Natural Sciences, Bangor University, post code Bangor, Gwynedd, Wales LL57 2UW, UK;
| | - Christopher Gwenin
- School of Natural Sciences, Bangor University, post code Bangor, Gwynedd, Wales LL57 2UW, UK;
- Department of Chemistry, Xi’an Jiaotong-Liverpool University, 111 Ren’ai Road, Suzhou Industrial Park, Suzhou 215123, China
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13
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Long S, Berkemeier B. Maximizing viral detection with SIV droplet digital PCR (ddPCR) assays. PLoS One 2020; 15:e0233085. [PMID: 32407343 PMCID: PMC7224504 DOI: 10.1371/journal.pone.0233085] [Citation(s) in RCA: 8] [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: 01/21/2020] [Accepted: 04/28/2020] [Indexed: 11/19/2022] Open
Abstract
Highly sensitive detection of HIV-1 nucleic acids is of critical importance for evaluating treatment interventions superimposed on combination antiretroviral therapy (cART) in HIV-1 infected individuals. SIV infection of rhesus macaques models many key aspects of human HIV-1 infection and plays a key role in evaluation of approaches for prevention, treatment and attempted eradication of HIV infection. Here we describe two droplet digital PCR (ddPCR) assays, a ddPCR DNA assay and an RT-ddPCR RNA assay for detecting simian immunodeficiency virus (SIV) on the RainDance platform. We demonstrate that RainDance ddPCR can tolerate significantly higher cell DNA input without inhibition on a per reaction basis (compared to both qPCR and Bio-Rad ddPCR), thus allowing a large quantity of sample to be analyzed in each reaction. In addition, the combination of a high processivity RT enzyme and RainDance ddPCR could overcome inhibition in severely inhibited (99.99% inhibition in qPCR quantification) viral RNA samples. These assays offer valuable tools for assessing low level viral production/replication and strategies for targeting residual virus in the setting of cART suppression of viral replication. The methodologies presented here can be adapted for a broad range of applications where highly sensitive nucleic acid detection is required.
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Affiliation(s)
- Samuel Long
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
- * E-mail:
| | - Brian Berkemeier
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
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14
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Morinha F, Magalhães P, Blanco G. Standard guidelines for the publication of telomere qPCR results in evolutionary ecology. Mol Ecol Resour 2020; 20. [PMID: 32133733 DOI: 10.1111/1755-0998.13152] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 02/25/2020] [Accepted: 02/27/2020] [Indexed: 12/14/2022]
Abstract
Telomere length has been used as a proxy of fitness, aging and lifespan in vertebrates. In the last decade, dozens of articles reporting on telomere dynamics in the fields of ecology and evolution have been published for a wide range of taxa. With this growing interest, it is necessary to ensure the accuracy and reproducibility of telomere length measurement techniques. Real-time quantitative PCR (qPCR) is routinely applied to measure relative telomere length. However, this technique is highly sensitive to several methodological variables and the optimization of qPCR telomere assays remains highly variable between studies. Therefore, standardized guidelines are required to enable the optimization of robust protocols, and to help in judging the validity of the presented results. This review provides an overview of preanalytical and analytical factors that can lead to qPCR inconsistencies and biases, including: (a) sample type, collection and storage; (b) DNA extraction, storage and quality; (c) qPCR primers, laboratory reagents, and assay conditions; and (d) data analysis. We propose a minimum level of information for publication of qPCR telomere assays in evolutionary ecology considering the methodological pitfalls and sources of error. This review highlights the complexity of the optimization and validation of qPCR for telomere measurement per se, demonstrating the importance of transparency and clarity of reporting methodological details required for reliable, reproducible and comparable qPCR telomere assays. We encourage efforts to implement standardized protocols that ensure the rigour and quality of telomere dynamics studies.
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Affiliation(s)
- Francisco Morinha
- Department of Evolutionary Ecology, National Museum of Natural Sciences (MNCN), Spanish National Research Council (CSIC), Madrid, Spain
| | - Paula Magalhães
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Guillermo Blanco
- Department of Evolutionary Ecology, National Museum of Natural Sciences (MNCN), Spanish National Research Council (CSIC), Madrid, Spain
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15
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Felekkis K, Papaneophytou C. Challenges in Using Circulating Micro-RNAs as Biomarkers for Cardiovascular Diseases. Int J Mol Sci 2020; 21:ijms21020561. [PMID: 31952319 PMCID: PMC7013987 DOI: 10.3390/ijms21020561] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/07/2020] [Accepted: 01/09/2020] [Indexed: 12/12/2022] Open
Abstract
Micro-RNAs (miRNAs) play a pivotal role in the development and physiology of the cardiovascular system while they have been associated with multiple cardiovascular diseases (CVDs). Several cardiac miRNAs are detectable in circulation (circulating miRNAs; c-miRNAs) and are emerging as diagnostic and therapeutic biomarkers for CVDs. c-miRNAs exhibit numerous essential characteristics of biomarkers while they are extremely stable in circulation, their expression is tissue-/disease-specific, and they can be easily detected using sequence-specific amplification methods. These features of c-miRNAs are helpful in the development of non-invasive assays to monitor the progress of CVDs. Despite significant progress in the detection of c-miRNAs in serum and plasma, there are many contradictory publications on the alterations of cardiac c-miRNAs concentration in circulation. The aim of this review is to examine the pre-analytical and analytical factors affecting the quantification of c-miRNAs and provide general guidelines to increase the accuracy of the diagnostic tests in order to improve future research on cardiac c-miRNAs.
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16
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Yan L, Toohey-Kurth KL, Crossley BM, Bai J, Glaser AL, Tallmadge RL, Goodman LB. Inhibition monitoring in veterinary molecular testing. J Vet Diagn Invest 2019; 32:758-766. [PMID: 31735123 DOI: 10.1177/1040638719889315] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Many of the sample matrices typically used for veterinary molecular testing contain inhibitory factors that can potentially reduce analytic sensitivity or produce false-negative results by masking the signal produced by the nucleic acid target. Inclusion of internal controls in PCR-based assays is a valuable strategy not only for monitoring for PCR inhibitors, but also for monitoring nucleic acid extraction efficiency, and for identifying technology errors that may interfere with the ability of an assay to detect the intended target. The Laboratory Technology Committee of the American Association of Veterinary Laboratory Diagnosticians reviewed the different types of internal controls related to monitoring inhibition of PCR-based assays, and provides information here to encourage veterinary diagnostic laboratories to incorporate PCR internal control strategies as a routine quality management component of their molecular testing.
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Affiliation(s)
- Lifang Yan
- Mississippi Veterinary Research and Diagnostic Laboratory, Mississippi State University, Pearl, MS (Yan).,California Animal Health and Food Safety Laboratory, University of California-Davis, Davis, CA (Toohey-Kurth, Crossley).,Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS (Bai).,Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY (Glaser, Tallmadge, Goodman)
| | - Kathy L Toohey-Kurth
- Mississippi Veterinary Research and Diagnostic Laboratory, Mississippi State University, Pearl, MS (Yan).,California Animal Health and Food Safety Laboratory, University of California-Davis, Davis, CA (Toohey-Kurth, Crossley).,Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS (Bai).,Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY (Glaser, Tallmadge, Goodman)
| | - Beate M Crossley
- Mississippi Veterinary Research and Diagnostic Laboratory, Mississippi State University, Pearl, MS (Yan).,California Animal Health and Food Safety Laboratory, University of California-Davis, Davis, CA (Toohey-Kurth, Crossley).,Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS (Bai).,Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY (Glaser, Tallmadge, Goodman)
| | - Jianfa Bai
- Mississippi Veterinary Research and Diagnostic Laboratory, Mississippi State University, Pearl, MS (Yan).,California Animal Health and Food Safety Laboratory, University of California-Davis, Davis, CA (Toohey-Kurth, Crossley).,Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS (Bai).,Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY (Glaser, Tallmadge, Goodman)
| | - Amy L Glaser
- Mississippi Veterinary Research and Diagnostic Laboratory, Mississippi State University, Pearl, MS (Yan).,California Animal Health and Food Safety Laboratory, University of California-Davis, Davis, CA (Toohey-Kurth, Crossley).,Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS (Bai).,Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY (Glaser, Tallmadge, Goodman)
| | - Rebecca L Tallmadge
- Mississippi Veterinary Research and Diagnostic Laboratory, Mississippi State University, Pearl, MS (Yan).,California Animal Health and Food Safety Laboratory, University of California-Davis, Davis, CA (Toohey-Kurth, Crossley).,Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS (Bai).,Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY (Glaser, Tallmadge, Goodman)
| | - Laura B Goodman
- Mississippi Veterinary Research and Diagnostic Laboratory, Mississippi State University, Pearl, MS (Yan).,California Animal Health and Food Safety Laboratory, University of California-Davis, Davis, CA (Toohey-Kurth, Crossley).,Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS (Bai).,Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY (Glaser, Tallmadge, Goodman)
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17
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Bottani M, Banfi G, Lombardi G. Perspectives on miRNAs as Epigenetic Markers in Osteoporosis and Bone Fracture Risk: A Step Forward in Personalized Diagnosis. Front Genet 2019; 10:1044. [PMID: 31737038 PMCID: PMC6831724 DOI: 10.3389/fgene.2019.01044] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 09/30/2019] [Indexed: 02/06/2023] Open
Abstract
Aging is associated with an increased incidence of age-related bone diseases. Current diagnostics (e.g., conventional radiology, biochemical markers), because limited in specificity and sensitivity, can distinguish between healthy or osteoporotic subjects but they are unable to discriminate among different underlying causes that lead to the same bone pathological condition (e.g., bone fracture risk). Among recent, more sensitive biomarkers, miRNAs — the non-coding RNAs involved in the epigenetic regulation of gene expression, have emerged as fundamental post-transcriptional modulators of bone development and homeostasis. Each identified miRNA carries out a specific role in osteoblast and osteoclast differentiation and functional pathways (osteomiRs). miRNAs bound to proteins or encapsulated in exosomes and/or microvesicles are released into the bloodstream and biological fluids where they can be detected and measured by highly sensitive and specific methods (e.g., quantitative PCR, next-generation sequencing). As such, miRNAs provide a prompt and easily accessible tool to determine the subject-specific epigenetic environment of a specific condition. Their use as biomarkers opens new frontiers in personalized medicine. While miRNAs circulating levels are lower than those found in the tissue/cell source, their quantification in biological fluids may be strategic in the diagnosis of diseases that affect tissues, such as bone, in which biopsy may be especially challenging. For a biomarker to be valuable in clinical practice and support medical decisions, it must be (easily) measurable, validated by independent studies, and strongly and significantly associated with a disease outcome. Currently, miRNAs analysis does not completely satisfy these criteria, however. Starting from in vitro and in vivo observations describing their biological role in bone cell development and metabolism, this review describes the potential use of bone-associated circulating miRNAs as biomarkers for determining predisposition, onset, and development of osteoporosis and bone fracture risk. Moreover, the review focuses on their clinical relevance and discusses the pre-analytical, analytical, and post-analytical issues in their measurement, which still limits their routine application. Taken together, research and clinical findings may be helpful for creating miRNA-based diagnostic tools in the diagnosis and treatment of bone diseases.
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Affiliation(s)
- Michela Bottani
- IRCCS Istituto Ortopedico Galeazzi, Laboratory of Experimental Biochemistry & Moelcular Biology, Milano, Italy
| | - Giuseppe Banfi
- IRCCS Istituto Ortopedico Galeazzi, Laboratory of Experimental Biochemistry & Moelcular Biology, Milano, Italy.,Vita-Salute San Raffaele University, Milano, Italy
| | - Giovanni Lombardi
- IRCCS Istituto Ortopedico Galeazzi, Laboratory of Experimental Biochemistry & Moelcular Biology, Milano, Italy.,Department of Physiology & Pharmacology, Gdańsk University of Physical Education & Sport, Gdańsk, Poland
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18
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Pilecky M, Schildberger A, Knabl L, Orth-Höller D, Weber V. Influence of antibiotic treatment on the detection of S. aureus in whole blood following pathogen enrichment. BMC Microbiol 2019; 19:180. [PMID: 31387527 PMCID: PMC6683330 DOI: 10.1186/s12866-019-1559-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 07/30/2019] [Indexed: 02/06/2023] Open
Abstract
Background Early pathogen detection and identification are crucial for an effective and targeted antibiotic therapy in patients suffering from blood stream infection. Molecular diagnostic methods can accelerate pathogen identification as compared to blood culture, but frequently suffer from the inhibition of polymerase chain reation (PCR) by sample matrix components, such as host DNA, anticoagulants, or plasma proteins. To overcome this limitation, molecular diagnostic methods commonly rely on pathogen enrichment by selective lysis of blood cells and pelleting of intact pathogens prior to analysis. Results Here, we investigated the impact of antibiotic treatment on the recovery of pathogen DNA using an established pathogen enrichment protocol. Based on the hypothesis that induction of bacterial cell wall disintegration following antibiotic administration leads to incomplete pelleting of pathogen DNA, S. aureus was grown in human whole blood with or without addition of cell wall active (vancomycin, piperacillin) or non cell wall active (ciprofloxacin, clindamycin) antibiotics at clinically relevant concentrations. Pathogen detection remained unaffected by non cell wall active antibiotics or even increased in the presence of cell wall active antibiotics, indicating improved accessibility of pathogen DNA. Likewise, mechanical lysis of S. aureus prior to pathogen enrichment resulted in increased recovery of pathogen DNA. Quantification of pathogen and human DNA after selective lysis of blood cells and pathogen enrichment confirmed partial depletion of human DNA, leading to a net enrichment of pathogen DNA over human DNA. Conclusion Concurrent antibiotic administration does not reduce the recovery of pathogen DNA during pathogen enrichment by selective lysis and centrifugation. Leads to a 10-fold human DNA depletion as compared to pathogen DNA. Moreover, we confirm that the recovery of pathogen DNA after pathogen enrichment is not negatively influenced by concurrent antibiotic administration. Electronic supplementary material The online version of this article (10.1186/s12866-019-1559-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Matthias Pilecky
- Center for Biomedical Technology, Department for Health Sciences and Biomedicine, Danube University Krems, Dr.-Karl-Dorrek-Strasse 30, 3500, Krems, Austria
| | - Anita Schildberger
- Center for Biomedical Technology, Department for Health Sciences and Biomedicine, Danube University Krems, Dr.-Karl-Dorrek-Strasse 30, 3500, Krems, Austria
| | - Ludwig Knabl
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Schöpfstraße 41, A-6020, Innsbruck, Austria
| | - Dorothea Orth-Höller
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Schöpfstraße 41, A-6020, Innsbruck, Austria
| | - Viktoria Weber
- Center for Biomedical Technology, Department for Health Sciences and Biomedicine, Danube University Krems, Dr.-Karl-Dorrek-Strasse 30, 3500, Krems, Austria. .,Christian Doppler Laboratory for Innovative Therapy Approaches in Sepsis, Department for Health Sciences and Biomedicine, Danube University Krems, Dr.-Karl-Dorrek-Strasse 30, 3500, Krems, Austria. .,Department for Biomedical Research, Danube University Krems, Dr.-Karl-Dorrek-Strasse 30, 3500, Krems, Austria.
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19
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Meddeb R, Pisareva E, Thierry AR. Guidelines for the Preanalytical Conditions for Analyzing Circulating Cell-Free DNA. Clin Chem 2019; 65:623-633. [DOI: 10.1373/clinchem.2018.298323] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 02/05/2019] [Indexed: 12/13/2022]
Abstract
Abstract
Circulating cell-free DNA (cfDNA) isolated from blood has been identified as a potential biomarker in numerous fields, and has been the object of intensive research over the past decade, although its original discovery dates back 60 years. While it is already used routinely in commercial and clinical practice in oncology and prenatal testing, other potential applications have emerged, including for diabetes, cardiovascular diseases, organ transplantation, autoimmune diseases, sepsis, trauma, and sport management. As with the discovery and development of any biomarker, preanalytical requirements and documentation are as important as analytical requirements. Except for the case of noninvasive prenatal testing and prenatal diagnosis, the implementation of cfDNA in a clinical setting remains limited because of the lack of standardization of cfDNA analysis. In particular, only a few attempts have been made to collect and pool scientific data on the relevant preanalytical factors, and no standard operating procedure has yet been set. For this report, we have performed a thorough and systematic search via MEDLINE® for relevant preanalytical variables and patient factors. These form the basis of the guidelines we propose for analyzing nuclear cfDNA.
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Affiliation(s)
- Romain Meddeb
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier, France
- INSERM, U1194, Montpellier, France
- University of Montpellier, Montpellier, France
- Regional Institute of Cancer of Montpellier, Montpellier, France
| | - Ekaterina Pisareva
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier, France
- INSERM, U1194, Montpellier, France
- University of Montpellier, Montpellier, France
- Regional Institute of Cancer of Montpellier, Montpellier, France
| | - Alain R Thierry
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier, France
- INSERM, U1194, Montpellier, France
- University of Montpellier, Montpellier, France
- Regional Institute of Cancer of Montpellier, Montpellier, France
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20
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Beall SG, Cantera J, Diaz MH, Winchell JM, Lillis L, White H, Kalnoky M, Gallarda J, Boyle DS. Performance and workflow assessment of six nucleic acid extraction technologies for use in resource limited settings. PLoS One 2019; 14:e0215753. [PMID: 30998749 PMCID: PMC6472818 DOI: 10.1371/journal.pone.0215753] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 02/16/2019] [Indexed: 01/20/2023] Open
Abstract
Infectious disease nucleic acid amplification technologies (NAAT) have superior sensitivity, specificity, and rapid time to result compared to traditional microbiological methods. Recovery of concentrated, high quality pathogen nucleic acid (NA) from complex specimen matrices is required for optimal performance of several NA amplification/detection technologies such as polymerase chain reaction (PCR). Fully integrated NAAT platforms that enable rapid sample-to-result workflows with minimal user input are generally restricted to larger reference lab settings, and their complexity and cost are prohibitive to widespread implementation in resource limited settings (RLS). Identification of component technologies for incorporation of reliable and affordable sample preparation with pathogen NA amplification/detection into an integrated platform suitable for RLS, is a necessary first step toward achieving the overarching goal of reducing infectious disease-associated morbidity and mortality globally. In the current study, we evaluate the performance of six novel NA extraction technologies from different developers using blinded panels of stool, sputum and blood spiked with variable amounts of quality-controlled DNA- and/or RNA-based microbes. The extraction efficiencies were semi-quantitatively assessed using validated real-time reverse transcription (RT)-PCR assays specific for each microbe and comparing target-specific RT-PCR results to those obtained with reference NA extraction methods. The technologies were ranked based on overall diagnostic accuracy (analytical sensitivity and specificity). Sample input and output volumes, total processing time, user-required manual steps and cost estimates were also examined for suitability in RLS. Together with the performance analysis, these metrics were used to select the more suitable candidate technologies for further optimization of integrated NA amplification and detection technologies for RLS.
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Affiliation(s)
- Shivani G. Beall
- Centers for Disease Control and Prevention, Division of Bacterial Diseases, Respiratory Diseases Branch, Atlanta, Georgia, United States of America
| | | | - Maureen H. Diaz
- Centers for Disease Control and Prevention, Division of Bacterial Diseases, Respiratory Diseases Branch, Atlanta, Georgia, United States of America
| | - Jonas M. Winchell
- Centers for Disease Control and Prevention, Division of Bacterial Diseases, Respiratory Diseases Branch, Atlanta, Georgia, United States of America
| | | | | | | | - James Gallarda
- Bill and Melinda Gates Foundation, Seattle, Washington, United States of America
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21
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Hoey C, Liu SK. Circulating blood miRNAs for prostate cancer risk stratification: miRroring the underlying tumor biology with liquid biopsies. Res Rep Urol 2019; 11:29-42. [PMID: 30881943 PMCID: PMC6398395 DOI: 10.2147/rru.s165625] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Current risk stratification methods for prostate cancer – although they have seen marked improvements over the past decades – are far from perfect. Despite the significant utility of prostate-specific antigen as a biomarker to monitor for disease recurrence, it cannot predict which tumors will recur or recommend the best treatment for patients. Similarly, although biopsies are imperative for diagnosis and staging, they are saddled with limitations and risks. We must move toward a noninvasive biomarker that has predictive and prognostic efficacy. We therefore review the current literature on circulating miRNA biomarkers, apply their use to two significant clinical problems (ie, how limitations of prostate biopsies can impact diagnosis and treatment management, and the need to tailor treatment for a clinically heterogeneous disease), and evaluate how circulating miRNAs have inherent properties that make them ideal liquid biomarkers. We also outline current gaps in knowledge that must be addressed before they can be implemented into routine clinical practice. With further research on their function and validation of their biomarker utility in large prospective cohorts, circulating miRNAs will likely prove to be the liquid biopsies of tomorrow.
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Affiliation(s)
- Christianne Hoey
- Biological Sciences, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada, .,Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada,
| | - Stanley K Liu
- Biological Sciences, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada, .,Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada, .,Department of Radiation Oncology, University of Toronto, Toronto, ON M5S 3E2, Canada,
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22
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Li TT, Wang JL, Zhang NZ, Li WH, Yan HB, Li L, Jia WZ, Fu BQ. Rapid and Visual Detection of Trichinella Spp. Using a Lateral Flow Strip-Based Recombinase Polymerase Amplification (LF-RPA) Assay. Front Cell Infect Microbiol 2019; 9:1. [PMID: 30719427 PMCID: PMC6348712 DOI: 10.3389/fcimb.2019.00001] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 01/03/2019] [Indexed: 12/23/2022] Open
Abstract
Trichinella spp., are amongst the most widespread parasitic nematodes, primarily live in the muscles of a wide range of vertebrate animals and humans. Human infection occurs by ingestion of raw or undercooked meat containing Trichinella larvae. Accurate diagnosis of Trichinella spp. infection in domestic animals is crucial for the effective prevention and control of human trichinellosis. In the present study, a simple, rapid and accurate diagnostic assay was developed combining recombinase polymerase amplification and a lateral flow strip (LF-RPA) to detect Trichinella spp. infection. The LF-RPA assay targets Trichinella spp. mitochondrial small-subunit ribosomal RNA (rrnS) gene and can detect as low as 100 fg DNA of Trichinella strains, which was approximately 10 times more sensitive than a conventional PCR assay. The LF-RPA assay can be performed within 10–25 min, at a wide range of temperatures (25–45°C) and showed no cross-reactivity with DNA of other parasites and related host species of Trichinella. The performance of the LF-RPA assay in the presence of high concentration of PCR inhibitor was better than that of a conventional PCR assay. Results obtained by LF-RPA assay for the detection of experimentally infected mice were comparable to the results obtained by using a conventional PCR, achieving 100% specificity and high sensitivity. These results present the developed LF-RPA assay as a new simple, specific, sensitive, rapid and convenient method for the detection of Trichinella infection in domestic animals.
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Affiliation(s)
- Ting-Ting Li
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jin-Lei Wang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Nian-Zhang Zhang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Wen-Hui Li
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Hong-Bin Yan
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Li Li
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Wan-Zhong Jia
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Jiangsu Co-innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University College of Veterinary Medicine, Yangzhou, China
| | - Bao-Quan Fu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Jiangsu Co-innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University College of Veterinary Medicine, Yangzhou, China
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23
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Barnes RA, White PL, Morton CO, Rogers TR, Cruciani M, Loeffler J, Donnelly JP. Diagnosis of aspergillosis by PCR: Clinical considerations and technical tips. Med Mycol 2018; 56:60-72. [PMID: 29087518 DOI: 10.1093/mmy/myx091] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 08/29/2017] [Indexed: 12/25/2022] Open
Abstract
Standardization of Aspergillus polymerase chain reaction (PCR) protocols has progressed, and analytical validity of blood-based assays has been formally established. It remains necessary to consider how the tests can be used in practice to maximize clinical utility. To determine the optimal diagnostic strategies and influence on patient management, several factors require consideration, including the patient population, incidence of invasive aspergillosis (and other fungal disease), and the local antifungal prescribing policy. Technical issues such as specimen type, ease of sampling, frequency of testing, access to testing centers, and time to reporting will also influence the use of PCR in clinical practice. Interpretation of all diagnostic tests is dependent on the clinical context and molecular assays are no exception, but with the proposal to incorporate Aspergillus PCR into the second revision of the consensus guidelines for defining invasive fungal disease the acceptance and understanding of molecular tests should improve.
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Affiliation(s)
| | - P Lewis White
- Public Health Wales Microbiology Cardiff, Cardiff, UK
| | | | | | - Mario Cruciani
- Center of Community Medicine and Infectious Diseases Service, ULSS 20 Verona
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Pilecky M, Schildberger A, Orth-Höller D, Weber V. Pathogen enrichment from human whole blood for the diagnosis of bloodstream infection: Prospects and limitations. Diagn Microbiol Infect Dis 2018; 94:7-14. [PMID: 30579657 DOI: 10.1016/j.diagmicrobio.2018.11.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 11/20/2018] [Accepted: 11/20/2018] [Indexed: 02/07/2023]
Abstract
Blood culture represents the current reference method for the detection of bacteria or fungi in the circulation. To accelerate pathogen identification, molecular diagnostic methods, mainly based on polymerase chain reaction (PCR), have been introduced to ensure early and targeted antibiotic treatment of patients suffering from bloodstream infection. Still, these approaches suffer from a lack of sensitivity and from inhibition of PCR in a number of clinical samples, leading to false negative results. To overcome these limitations, various approaches aiming at the enrichment of pathogens from larger blood volumes prior to the extraction of pathogen DNA, thereby also depleting factors interfering with PCR, have been developed. Here, we provide an overview of current systems for diagnosing bloodstream infection, with a focus on approaches for pre-analytical pathogen enrichment, and highlight emerging applications of pathogen depletion for therapeutic purposes as a potential adjunctive treatment of sepsis patients.
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Affiliation(s)
- Matthias Pilecky
- Center for Biomedical Technology, Department for Biomedical Research, Danube University Krems, Dr.-Karl-Dorrek-Strasse 30, 3500 Krems, Austria.
| | - Anita Schildberger
- Center for Biomedical Technology, Department for Biomedical Research, Danube University Krems, Dr.-Karl-Dorrek-Strasse 30, 3500 Krems, Austria.
| | - Dorothea Orth-Höller
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Schöpfstraße 41, A-6020 Innsbruck, Austria.
| | - Viktoria Weber
- Center for Biomedical Technology, Department for Biomedical Research, Danube University Krems, Dr.-Karl-Dorrek-Strasse 30, 3500 Krems, Austria; Christian Doppler Laboratory for Innovative Therapy Approaches in Sepsis, Department for Biomedical Research, Danube University Krems, Dr.-Karl-Dorrek-Strasse 30, 3500 Krems, Austria.
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25
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Aswani A, Manson J, Itagaki K, Chiazza F, Collino M, Wupeng WL, Chan TK, Wong WSF, Hauser CJ, Thiemermann C, Brohi K. Scavenging Circulating Mitochondrial DNA as a Potential Therapeutic Option for Multiple Organ Dysfunction in Trauma Hemorrhage. Front Immunol 2018; 9:891. [PMID: 29867926 PMCID: PMC5951958 DOI: 10.3389/fimmu.2018.00891] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 04/10/2018] [Indexed: 12/15/2022] Open
Abstract
Trauma is a leading cause of death worldwide with 5.8 million deaths occurring yearly. Almost 40% of trauma deaths are due to bleeding and occur in the first few hours after injury. Of the remaining severely injured patients up to 25% develop a dysregulated immune response leading to multiple organ dysfunction syndrome (MODS). Despite improvements in trauma care, the morbidity and mortality of this condition remains very high. Massive traumatic injury can overwhelm endogenous homeostatic mechanisms even with prompt treatment. The underlying mechanisms driving MODS are also not fully elucidated. As a result, successful therapies for trauma-related MODS are lacking. Trauma causes tissue damage that releases a large number of endogenous damage-associated molecular patterns (DAMPs). Mitochondrial DAMPs released in trauma, such as mitochondrial DNA (mtDNA), could help to explain part of the immune response in trauma given the structural similarities between mitochondria and bacteria. MtDNA, like bacterial DNA, contains an abundance of highly stimulatory unmethylated CpG DNA motifs that signal through toll-like receptor-9 to produce inflammation. MtDNA has been shown to be highly damaging when injected into healthy animals causing acute organ injury to develop. Elevated circulating levels of mtDNA have been reported in trauma patients but an association with clinically meaningful outcomes has not been established in a large cohort. We aimed to determine whether mtDNA released after clinical trauma hemorrhage is sufficient for the development of MODS. Secondly, we aimed to determine the extent of mtDNA release with varying degrees of tissue injury and hemorrhagic shock in a clinically relevant rodent model. Our final aim was to determine whether neutralizing mtDNA with the nucleic acid scavenging polymer, hexadimethrine bromide (HDMBr), at a clinically relevant time point in vivo would reduce the severity of organ injury in this model. CONCLUSIONS We have shown that the release of mtDNA is sufficient for the development of multiple organ injury. MtDNA concentrations likely peak at different points in the early postinjury phase dependent on the degree of isolated trauma vs combined trauma and hemorrhagic shock. HDMBr scavenging of circulating mtDNA (and nuclear DNA, nDNA) is associated with rescue from severe multiple organ injury in the animal model. This suggests that HDMBr could have utility in rescue from human trauma-induced MODS.
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Affiliation(s)
- Andrew Aswani
- Department of Critical Care Medicine, Guy's and St Thomas' NHS Foundation Trust, London, United Kingdom
| | - Joanna Manson
- Centre for Trauma Sciences, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Kiyoshi Itagaki
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Fausto Chiazza
- Department of Drug Science and Technology, Università degli Studi di Torino, Turin, Italy
| | - Massimo Collino
- Department of Drug Science and Technology, Università degli Studi di Torino, Turin, Italy
| | - Winston Liao Wupeng
- Department of Pharmacology and Immunology Program, National University Health System, Singapore, Singapore
| | - Tze Khee Chan
- Department of Pharmacology and Immunology Program, National University Health System, Singapore, Singapore
| | - W S Fred Wong
- Department of Pharmacology and Immunology Program, National University Health System, Singapore, Singapore
| | - Carl J Hauser
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Chris Thiemermann
- Department of Translational Medicine and Therapeutics, Queen Mary University of London, London, United Kingdom
| | - Karim Brohi
- Centre for Trauma Sciences, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
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26
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Mauk MG, Song J, Liu C, Bau HH. Simple Approaches to Minimally-Instrumented, Microfluidic-Based Point-of-Care Nucleic Acid Amplification Tests. BIOSENSORS 2018; 8:E17. [PMID: 29495424 PMCID: PMC5872065 DOI: 10.3390/bios8010017] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 01/29/2018] [Accepted: 02/09/2018] [Indexed: 01/10/2023]
Abstract
Designs and applications of microfluidics-based devices for molecular diagnostics (Nucleic Acid Amplification Tests, NAATs) in infectious disease testing are reviewed, with emphasis on minimally instrumented, point-of-care (POC) tests for resource-limited settings. Microfluidic cartridges ('chips') that combine solid-phase nucleic acid extraction; isothermal enzymatic nucleic acid amplification; pre-stored, paraffin-encapsulated lyophilized reagents; and real-time or endpoint optical detection are described. These chips can be used with a companion module for separating plasma from blood through a combined sedimentation-filtration effect. Three reporter types: Fluorescence, colorimetric dyes, and bioluminescence; and a new paradigm for end-point detection based on a diffusion-reaction column are compared. Multiplexing (parallel amplification and detection of multiple targets) is demonstrated. Low-cost detection and added functionality (data analysis, control, communication) can be realized using a cellphone platform with the chip. Some related and similar-purposed approaches by others are surveyed.
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Affiliation(s)
- Michael G Mauk
- Mechanical Engineering and Applied Mechanics (MEAM), School of Engineering and Applied Science, University of Pennsylvania, Towne Building, 220 33rd Street, Philadelphia, PA 19104, USA.
| | - Jinzhao Song
- Mechanical Engineering and Applied Mechanics (MEAM), School of Engineering and Applied Science, University of Pennsylvania, Towne Building, 220 33rd Street, Philadelphia, PA 19104, USA.
| | - Changchun Liu
- Mechanical Engineering and Applied Mechanics (MEAM), School of Engineering and Applied Science, University of Pennsylvania, Towne Building, 220 33rd Street, Philadelphia, PA 19104, USA.
| | - Haim H Bau
- Mechanical Engineering and Applied Mechanics (MEAM), School of Engineering and Applied Science, University of Pennsylvania, Towne Building, 220 33rd Street, Philadelphia, PA 19104, USA.
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27
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Direct DNA and RNA detection from large volumes of whole human blood. Sci Rep 2018; 8:3410. [PMID: 29467420 PMCID: PMC5821888 DOI: 10.1038/s41598-018-21224-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 01/21/2018] [Indexed: 11/25/2022] Open
Abstract
PCR inhibitors in clinical specimens negatively affect the sensitivity of diagnostic PCR and RT-PCR or may even cause false-negative results. To overcome PCR inhibition, increase the sensitivity of the assays and simplify the detection protocols, simple methods based on quantitative nested real-time PCR and RT-PCR were developed to detect exogenous DNA and RNA directly from large volumes of whole human blood (WHB). Thermus thermophilus (Tth) polymerase is resistant to several common PCR inhibitors and exhibits reverse transcriptase activity in the presence of manganese ions. In combination with optimized concentrations of magnesium ions and manganese ions, Tth polymerase enabled efficient detection of DNA and RNA from large volumes of WHB treated with various anticoagulants. The applicability of these methods was further demonstrated by examining WHB specimens collected from different healthy individuals and those stored under a variety of conditions. The detection limit of these methods was determined by detecting exogenous DNA, RNA, and bacteria spiked in WHB. To the best of our knowledge, direct RNA detection from large volumes of WHB has not been reported. The results of the developed methods can be obtained within 4 hours, making them possible for rapid and accurate detection of disease-causing agents from WHB.
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28
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Lai MY, Ooi CH, Lau YL. Recombinase Polymerase Amplification Combined with a Lateral Flow Strip for the Detection of Plasmodium knowlesi. Am J Trop Med Hyg 2017; 98:700-703. [PMID: 29260656 DOI: 10.4269/ajtmh.17-0738] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The aim of this study was to develop a recombinase polymerase amplification (RPA) combined with a lateral flow (LF) strip method for specific diagnosis of Plasmodium knowlesi. With incubation at 37°C, the 18S rRNA gene of P. knowlesi was successfully amplified within 12 minutes. By adding a specifically designed probe to the reaction solution, the amplified RPA product can be visualized on a LF strip. The RPA assay exhibited high sensitivity with limits of detection down to 10 parasites/μL of P. knowlesi. Nonetheless, it was demonstrated that all P. knowlesi (N = 41) and other Plasmodium sp. (N = 25) were positive while negative samples (N = 8) were negative. Therefore, a combination of RPA and LF strip detection is a highly promising approach with the potential to be suitable for use in resource-limited settings.
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Affiliation(s)
- Meng-Yee Lai
- Department of Parasitology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Choo-Huck Ooi
- Sarawak State Health Department, Kuching, Sarawak, Malaysia
| | - Yee-Ling Lau
- Department of Parasitology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
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29
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Sefrioui D, Beaussire L, Clatot F, Delacour J, Perdrix A, Frebourg T, Michel P, Di Fiore F, Sarafan-Vasseur N. Heparinase enables reliable quantification of circulating tumor DNA from heparinized plasma samples by droplet digital PCR. Clin Chim Acta 2017; 472:75-79. [PMID: 28729136 DOI: 10.1016/j.cca.2017.07.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 07/15/2017] [Indexed: 01/26/2023]
Abstract
BACKGROUND Heparin is often used as a blood anticoagulant for tumor marker analysis but results in the inhibition of PCR detection of circulating tumor DNA (ctDNA), which has been deemed a potential "liquid biopsy". We aimed to evaluate the impact of heparinase addition on heparinized plasma samples to allow ctDNA analysis. METHODS Plasma samples were collected in heparinized (n=194) and EDTA (n=8) tubes from hormone receptor-positive metastatic breast cancer (HR+MBC) (n=144) and pancreatic adenocarcinoma (PA) patients (n=50). Circulating ESR1 and KRAS mutations were detected with or without heparinase by digital PCR in HR+MBC and PA patients, respectively. Patients were classified into 2 subgroups i) inhibition, I+ and ii) no inhibition, I- based on a threshold of 200copies/μL for PCR inhibition by heparin. RESULTS In the I+ subgroup (91/144 HR+MBC and 26/50 PA), heparinase treatment significantly improved PCR efficacy, enabling ctDNA detection in 22/91 and 13/26 patients. Moreover, comparable results for ctDNA detection (4/8) were obtained with heparinized and EDTA PA samples. In the I- subgroup, heparinase addition did not quantitatively and qualitatively alter ctDNA detection. CONCLUSION Heparinase addition removes the heparin inhibition and allows accurate ctDNA detection in heparinized samples. These findings could make the samples from heparinized blood suitable for ctDNA analysis.
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Affiliation(s)
- David Sefrioui
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine and Digestive Oncology Unit, F 76000 Rouen, France
| | - Ludivine Beaussire
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, F 76000 Rouen, France
| | - Florian Clatot
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine and Department of Medical Oncology, Henri Becquerel Centre, F 76000 Rouen, France
| | - Julien Delacour
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, F 76000 Rouen, France
| | - Anne Perdrix
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine and Department of Biopathology, Henri Becquerel Centre, F 76000 Rouen, France
| | - Thierry Frebourg
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, F 76000 Rouen, France
| | - Pierre Michel
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine and Digestive Oncology Unit, F 76000 Rouen, France
| | - Frédéric Di Fiore
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, Digestive Oncology Unit and Department of Medical Oncology, Henri Becquerel Centre, F 76000 Rouen, France
| | - Nasrin Sarafan-Vasseur
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, F 76000 Rouen, France.
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30
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Kappel A, Keller A. miRNA assays in the clinical laboratory: workflow, detection technologies and automation aspects. Clin Chem Lab Med 2017; 55:636-647. [PMID: 27987355 DOI: 10.1515/cclm-2016-0467] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 11/01/2016] [Indexed: 12/27/2022]
Abstract
microRNAs (miRNAs) are short non-coding RNA molecules that regulate gene expression in eukaryotes. Their differential abundance is indicative or even causative for a variety of pathological processes including cancer or cardiovascular disorders. Due to their important biological function, miRNAs represent a promising class of novel biomarkers that may be used to diagnose life-threatening diseases, and to monitor disease progression. Further, they may guide treatment selection or dosage of drugs. miRNAs from blood or derived fractions are particularly interesting candidates for routine laboratory applications, as they can be measured in most clinical laboratories already today. This assures a good accessibility of respective tests. Albeit their great potential, miRNA-based diagnostic tests have not made their way yet into the clinical routine, and hence no standardized workflows have been established to measure miRNAs for patients' benefit. In this review we summarize the detection technologies and workflow options that exist to measure miRNAs, and we describe the advantages and disadvantages of each of these options. Moreover, we also provide a perspective on data analysis aspects that are vital for translation of raw data into actionable diagnostic test results.
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Affiliation(s)
- Andreas Kappel
- Siemens Healthcare GmbH, Guenther-Scharowsky-Str.1, Erlangen
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, University Hospital, Saarbruecken
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31
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Williams MR, Stedtfeld RD, Waseem H, Stedtfeld T, Upham B, Khalife W, Etchebarne B, Hughes M, Tiedje JM, Hashsham SA. Implications of direct amplification for measuring antimicrobial resistance using point-of-care devices. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2017; 9:1229-1241. [PMID: 29657581 PMCID: PMC5898395 DOI: 10.1039/c6ay03405e] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Antimicrobial resistance (AMR) is recognized as a global threat to human health. Rapid detection and characterization of AMR is a critical component of most antibiotic stewardship programs. Methods based on amplification of nucleic acids for detection of AMR are generally faster than culture-based approaches but they still require several hours to more than a day due to the need for transporting the sample to a centralized laboratory, processing of sample, and sometimes DNA purification and concentration. Nucleic acids-based point-of-care (POC) devices are capable of rapidly diagnosing antibiotic-resistant infections which may help in making timely and correct treatment decisions. However, for most POC platforms, sample processing for nucleic acids extraction and purification is also generally required prior to amplification. Direct amplification, an emerging possibility for a number of polymerases, has the potential to eliminate these steps without significantly impacting diagnostic performance. This review summarizes direct amplification methods and their implication for rapid measurement of AMR. Future research directions that may further strengthen the possibility of integrating direct amplification methods with POC devices are also summarized.
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Affiliation(s)
- M R Williams
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - R D Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - H Waseem
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - T Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - B Upham
- Pediatrics and Human Development, Michigan State University, East Lansing, MI 48824, USA
| | - W Khalife
- Department of Microbiology, Sparrow Laboratories, Sparrow Health System, Lansing, MI 48912, USA
| | - B Etchebarne
- Osteopathic Medical Specialties, Section of Emergency Medicine, Michigan State University, East Lansing, MI 4882, USA
| | - M Hughes
- Osteopathic Medical Specialties, Section of Emergency Medicine, Michigan State University, East Lansing, MI 4882, USA
| | - J M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - S A Hashsham
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
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32
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Zampetaki A, Mayr M. Circulating microRNAs as Novel Biomarkers in Cardiovascular Disease: Basic and Technical Principles. NON-CODING RNAS IN THE VASCULATURE 2017. [DOI: 10.1007/978-3-319-52945-5_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Abstract
PCR can aid in the diagnosis of invasive fungal disease (IFD). While the large number of "in-house" methodologies drives technological diversity, providing robustness, they make it difficult to identify optimal strategies, limiting standardization, and widespread acceptance. No matter how efficient, PCR utility will be limited by the quality of extracted nucleic acid. This chapter highlights benefits and limitations affecting the nucleic acid extraction process, before focusing on recent recommendations that through multicenter evaluation have provided optimal and standardized methodology.
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Affiliation(s)
- P Lewis White
- Public Health Wales Microbiology Cardiff, University Hospital of Wales, Heath Park, Cardiff, CF14 4XW, UK.
| | - Rosemary A Barnes
- Public Health Wales Microbiology Cardiff, University Hospital of Wales, Heath Park, Cardiff, CF14 4XW, UK.,Department of Infection and Immunity, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
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34
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Michell DL, Allen RM, Landstreet SR, Zhao S, Toth CL, Sheng Q, Vickers KC. Isolation of High-density Lipoproteins for Non-coding Small RNA Quantification. J Vis Exp 2016. [PMID: 27929461 DOI: 10.3791/54488] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The diversity of small non-coding RNAs (sRNA) is rapidly expanding and their roles in biological processes, including gene regulation, are emerging. Most interestingly, sRNAs are also found outside of cells and are stably present in all biological fluids. As such, extracellular sRNAs represent a novel class of disease biomarkers and are likely involved in cell signaling and intercellular communication networks. To assess their potential as biomarkers, sRNAs can be quantified in plasma, urine, and other fluids. Nevertheless, to fully understand the impact of extracellular sRNAs as endocrine signals, it is important to determine which carriers are transporting and protecting them in biological fluids (e.g., plasma), which cells and tissues contribute to extracellular sRNA pools, and cells and tissues capable of accepting and utilizing extracellular sRNA. To accomplish these goals, it is critical to isolate highly pure populations of extracellular carriers for sRNA profiling and quantification. We have previously demonstrated that lipoproteins, particularly high-density lipoproteins (HDL), transport functional microRNAs (miRNA) between cells and HDL-miRNAs are significantly altered in disease. Here, we detail a new protocol that utilizes tandem HDL isolation with density-gradient ultracentrifugation (DGUC) and fast-protein-liquid chromatography (FPLC) to obtain highly pure HDL for downstream profiling and quantification of all sRNAs, including miRNAs, using both high-throughput sequencing and real-time PCR approaches. This protocol will be a valuable resource for the investigation of sRNAs on HDL.
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Affiliation(s)
| | - Ryan M Allen
- Department of Medicine, Vanderbilt University School of Medicine
| | | | - Shilin Zhao
- Center for Quantitative Sciences, Vanderbilt University School of Medicine
| | - Cynthia L Toth
- Department of Medicine, Vanderbilt University School of Medicine
| | - Quanhu Sheng
- Department of Cancer Biology, Vanderbilt University School of Medicine
| | - Kasey C Vickers
- Department of Medicine, Vanderbilt University School of Medicine; Center for Quantitative Sciences, Vanderbilt University School of Medicine;
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35
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Roest HP, Verhoeven CJ, de Haan JE, de Jonge J, IJzermans JN, van der Laan LJ. Improving Accuracy of Urinary miRNA Quantification in Heparinized Patients Using Heparinase I Digestion. J Mol Diagn 2016; 18:825-833. [DOI: 10.1016/j.jmoldx.2016.06.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 05/31/2016] [Accepted: 06/16/2016] [Indexed: 10/21/2022] Open
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Calvopina DA, Coleman MA, Lewindon PJ, Ramm GA. Function and Regulation of MicroRNAs and Their Potential as Biomarkers in Paediatric Liver Disease. Int J Mol Sci 2016; 17:ijms17111795. [PMID: 27801781 PMCID: PMC5133796 DOI: 10.3390/ijms17111795] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 10/18/2016] [Accepted: 10/20/2016] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) are short non-coding RNAs involved in biological and pathological processes of every cell type, including liver cells. Transcribed from specific genes, miRNA precursors are processed in the cytoplasm into mature miRNAs and as part of the RNA-induced silencing complex (RISC) complex binds to messenger RNA (mRNA) by imperfect complementarity. This leads to the regulation of gene expression at a post-transcriptional level. The function of a number of different miRNAs in fibrogenesis associated with the progression of chronic liver disease has recently been elucidated. Furthermore, miRNAs have been shown to be both disease-and tissue-specific and are stable in the circulation, which has led to increasing investigation on their utility as biomarkers for the diagnosis of chronic liver diseases, including those in children. Here, we review the current knowledge on the biogenesis of microRNA, the mechanisms of translational repression and the use of miRNA as circulatory biomarkers in chronic paediatric liver diseases including cystic fibrosis associated liver disease, biliary atresia and viral hepatitis B.
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Affiliation(s)
- Diego A Calvopina
- Hepatic Fibrosis Group, QIMR Berghofer Medical Research Institute, 300 Herston Rd, Herston, QLD 4006, Australia.
| | - Miranda A Coleman
- Hepatic Fibrosis Group, QIMR Berghofer Medical Research Institute, 300 Herston Rd, Herston, QLD 4006, Australia.
| | - Peter J Lewindon
- Hepatic Fibrosis Group, QIMR Berghofer Medical Research Institute, 300 Herston Rd, Herston, QLD 4006, Australia.
- Department of Gastroenterology and Hepatology, Lady Cilento Children's Hospital, 501 Stanley St, South Brisbane, QLD 4101, Australia.
- Faculty of Medicine and Biomedical Sciences, The University of Queensland, Brisbane, QLD 4006, Australia.
| | - Grant A Ramm
- Hepatic Fibrosis Group, QIMR Berghofer Medical Research Institute, 300 Herston Rd, Herston, QLD 4006, Australia.
- Faculty of Medicine and Biomedical Sciences, The University of Queensland, Brisbane, QLD 4006, Australia.
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Markowitz J, Abrams Z, Jacob NK, Zhang X, Hassani JN, Latchana N, Wei L, Regan KE, Brooks TR, Uppati SR, Levine KM, Bekaii-Saab T, Kendra KL, Lesinski GB, Howard JH, Olencki T, Payne PR, Carson WE. MicroRNA profiling of patient plasma for clinical trials using bioinformatics and biostatistical approaches. Onco Targets Ther 2016; 9:5931-5941. [PMID: 27729802 PMCID: PMC5047719 DOI: 10.2147/ott.s106288] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Background MicroRNAs (miRNAs) are short noncoding RNAs that function to repress translation of mRNA transcripts and contribute to the development of cancer. We hypothesized that miRNA array-based technologies work best for miRNA profiling of patient-derived plasma samples when the techniques and patient populations are precisely defined. Methods Plasma samples were obtained from five sources: melanoma clinical trial of interferon and bortezomib (12), purchased normal donor plasma samples (four), gastrointestinal tumor bank (nine), melanoma tumor bank (ten), or aged-matched normal donors (eight) for the tumor bank samples. Plasma samples were purified for miRNAs and quantified using NanoString® arrays or by the company Exiqon. Standard biostatistical array approaches were utilized for data analysis and compared to a rank-based analytical approach. Results With the prospectively collected samples, fewer plasma samples demonstrated visible hemolysis due to increased attention to eliminating factors, such as increased pressure during phlebotomy, small gauge needles, and multiple punctures. Cancer patients enrolled in a melanoma clinical study exhibited the clearest pattern of miRNA expression as compared to normal donors in both the rank-based analytical method and standard biostatistical array approaches. For the patients from the tumor banks, fewer miRNAs (<5) were found to be differentially expressed and the false positive rate was relatively high. Conclusion In order to obtain consistent results for NanoString miRNA arrays, it is imperative that patient cohorts have similar clinical characteristics with a uniform sample preparation procedure. A clinical workflow has been optimized to collect patient samples to study plasma miRNAs.
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Affiliation(s)
- Joseph Markowitz
- Department of Cutaneous Oncology, Moffitt Cancer Center, Tampa, FL; Comprehensive Cancer Center, The Ohio State University, Columbus, OH; Department of Oncologic Sciences, USF Morsani School of Medicine, Tampa, FL; Division of Medical Oncology, The Ohio State University Wexner Medical Center
| | - Zachary Abrams
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH; Department of Biomedical Informatics
| | - Naduparambil K Jacob
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH; Department of Radiation Oncology
| | - Xiaoli Zhang
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH; Center for Biostatistics
| | - John N Hassani
- Department of Cutaneous Oncology, Moffitt Cancer Center, Tampa, FL
| | | | - Lai Wei
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH; Center for Biostatistics
| | - Kelly E Regan
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH; Department of Biomedical Informatics
| | - Taylor R Brooks
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH
| | - Sarvani R Uppati
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH
| | - Kala M Levine
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH
| | - Tanios Bekaii-Saab
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH; Division of Medical Oncology, The Ohio State University Wexner Medical Center
| | - Kari L Kendra
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH; Division of Medical Oncology, The Ohio State University Wexner Medical Center
| | - Gregory B Lesinski
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH; Division of Medical Oncology, The Ohio State University Wexner Medical Center
| | - J Harrison Howard
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH; Department of Surgery, The Ohio State University, Columbus, OH, USA
| | - Thomas Olencki
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH; Division of Medical Oncology, The Ohio State University Wexner Medical Center
| | - Philip R Payne
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH; Department of Biomedical Informatics
| | - William E Carson
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH; Department of Surgery, The Ohio State University, Columbus, OH, USA
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Circulating miRNA as fine regulators of the physiological responses to physical activity: Pre-analytical warnings for a novel class of biomarkers. Clin Biochem 2016; 49:1331-1339. [PMID: 27693050 DOI: 10.1016/j.clinbiochem.2016.09.017] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 09/22/2016] [Accepted: 09/23/2016] [Indexed: 12/29/2022]
Abstract
MicroRNAs are endogenous non-coding RNAs that post-transcriptionally regulate gene expression by specifically binding the target mRNA and by consequently inducing its degradation. miRNAs can be released into the circulation where they remain stable and they can be measured. Their changes reflect individual biologic adaptation to exposures to specific environmental conditions. As such, measurement of circulating microRNAs represents an opportunity to evaluate biologic changes associated with interventions such as exercise and diet. Physical activity is, indeed, a very important modifying factor for circulating miRNAs. Toward their use in clinical settings several issues should be still solved. Their clinical application is hindered by the high heterogeneity of the analytical procedures used for their measurements. Furthermore, several pre-analytical concerns equally reduce the clinical applicability of miRNA. Pre-analytical phase in sports medicine is an important issue both because, often the conditions in which sampling are performed are peculiar (and not always canonical) and because some of the tested parameters, in the case of professional athletes, enters in routine anti-doping testing and, as such, they should be treated according to precise rules in order to avoid any false positive results. Aim of this review is to give an overview of the main available knowledges about the pre-analytical management of the sample for circulating miRNA evaluation along with the importance of miRNA as regulators of the response to physical activity and their possible future use in anti-doping settings.
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Hackl M, Heilmeier U, Weilner S, Grillari J. Circulating microRNAs as novel biomarkers for bone diseases - Complex signatures for multifactorial diseases? Mol Cell Endocrinol 2016; 432:83-95. [PMID: 26525415 DOI: 10.1016/j.mce.2015.10.015] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 10/20/2015] [Accepted: 10/20/2015] [Indexed: 02/07/2023]
Abstract
Biomarkers are essential tools in clinical research and practice. Useful biomarkers must combine good measurability, validated association with biological processes or outcomes, and should support clinical decision making if used in clinical practice. Several types of validated biomarkers have been reported in the context of bone diseases. However, because these biomarkers face certain limitations there is an interest in the identification of novel biomarkers for bone diseases, specifically in those that are tightly linked to the disease pathology leading to increased fracture-risk. MicroRNAs (miRNAs) are the most abundant RNA species to be found in cell-free blood. Encapsulated within microvesicles or bound to proteins, circulating miRNAs are remarkably stable analytes that can be measured using gold-standard technologies such as quantitative polymerase-chain-reaction (qPCR). Nevertheless, the analysis of circulating miRNAs faces several pre-analytical as well as analytical challenges. From a biological view, there is accumulating evidence that miRNAs play essential roles in the regulation of various biological processes including bone homeostasis. Moreover, specific changes in miRNA transcription levels or miRNA secretory levels have been linked to the development and progression of certain bone diseases. Only recently, results from circulating miRNAs analysis in patients with osteopenia, osteoporosis and fragility fractures have been reported. By comparing these findings to studies on circulating miRNAs in cellular senescence and aging or muscle physiology and sarcopenia, several overlaps were observed. This suggests that signatures observed during osteoporosis might not be specific to the pathophysiology in bone, but rather integrate information from several tissue types. Despite these promising first data, more work remains to be done until circulating miRNAs can serve as established and robust diagnostic tools for bone diseases in clinical research, clinical routine and in personalized medicine.
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Affiliation(s)
| | - Ursula Heilmeier
- Musculoskeletal Quantitative Imaging Research Group, Department of Radiology & Biomedical Imaging, University of California San Francisco, San Francisco, CA, USA
| | | | - Johannes Grillari
- Evercyte GmbH, 1190 Vienna, Austria; Christian Doppler Laboratory for Biotechnology of Skin Aging, Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences Vienna, 1190 Vienna, Austria.
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Ackers-Johnson M, Li PY, Holmes AP, O'Brien SM, Pavlovic D, Foo RS. A Simplified, Langendorff-Free Method for Concomitant Isolation of Viable Cardiac Myocytes and Nonmyocytes From the Adult Mouse Heart. Circ Res 2016; 119:909-20. [PMID: 27502479 DOI: 10.1161/circresaha.116.309202] [Citation(s) in RCA: 315] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Accepted: 08/05/2016] [Indexed: 11/16/2022]
Abstract
RATIONALE Cardiovascular disease represents a global pandemic. The advent of and recent advances in mouse genomics, epigenomics, and transgenics offer ever-greater potential for powerful avenues of research. However, progress is often constrained by unique complexities associated with the isolation of viable myocytes from the adult mouse heart. Current protocols rely on retrograde aortic perfusion using specialized Langendorff apparatus, which poses considerable logistical and technical barriers to researchers and demands extensive training investment. OBJECTIVE To identify and optimize a convenient, alternative approach, allowing the robust isolation and culture of adult mouse cardiac myocytes using only common surgical and laboratory equipment. METHODS AND RESULTS Cardiac myocytes were isolated with yields comparable to those in published Langendorff-based methods, using direct needle perfusion of the LV ex vivo and without requirement for heparin injection. Isolated myocytes can be cultured antibiotic free, with retained organized contractile and mitochondrial morphology, transcriptional signatures, calcium handling, responses to hypoxia, neurohormonal stimulation, and electric pacing, and are amenable to patch clamp and adenoviral gene transfer techniques. Furthermore, the methodology permits concurrent isolation, separation, and coculture of myocyte and nonmyocyte cardiac populations. CONCLUSIONS We present a novel, simplified method, demonstrating concomitant isolation of viable cardiac myocytes and nonmyocytes from the same adult mouse heart. We anticipate that this new approach will expand and accelerate innovative research in the field of cardiac biology.
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Affiliation(s)
- Matthew Ackers-Johnson
- From the Cardiovascular Research Institute, Centre for Translational Medicine MD6, National University Health System, Singapore (M.A.-J., P.Y.L., R.S.F.); Genome Institute of Singapore (M.A.-J., R.S.F.); and Institute of Cardiovascular Sciences, University of Birmingham, UK (A.P.H., S.-M.O., D.P.)
| | - Peter Yiqing Li
- From the Cardiovascular Research Institute, Centre for Translational Medicine MD6, National University Health System, Singapore (M.A.-J., P.Y.L., R.S.F.); Genome Institute of Singapore (M.A.-J., R.S.F.); and Institute of Cardiovascular Sciences, University of Birmingham, UK (A.P.H., S.-M.O., D.P.)
| | - Andrew P Holmes
- From the Cardiovascular Research Institute, Centre for Translational Medicine MD6, National University Health System, Singapore (M.A.-J., P.Y.L., R.S.F.); Genome Institute of Singapore (M.A.-J., R.S.F.); and Institute of Cardiovascular Sciences, University of Birmingham, UK (A.P.H., S.-M.O., D.P.)
| | - Sian-Marie O'Brien
- From the Cardiovascular Research Institute, Centre for Translational Medicine MD6, National University Health System, Singapore (M.A.-J., P.Y.L., R.S.F.); Genome Institute of Singapore (M.A.-J., R.S.F.); and Institute of Cardiovascular Sciences, University of Birmingham, UK (A.P.H., S.-M.O., D.P.)
| | - Davor Pavlovic
- From the Cardiovascular Research Institute, Centre for Translational Medicine MD6, National University Health System, Singapore (M.A.-J., P.Y.L., R.S.F.); Genome Institute of Singapore (M.A.-J., R.S.F.); and Institute of Cardiovascular Sciences, University of Birmingham, UK (A.P.H., S.-M.O., D.P.)
| | - Roger S Foo
- From the Cardiovascular Research Institute, Centre for Translational Medicine MD6, National University Health System, Singapore (M.A.-J., P.Y.L., R.S.F.); Genome Institute of Singapore (M.A.-J., R.S.F.); and Institute of Cardiovascular Sciences, University of Birmingham, UK (A.P.H., S.-M.O., D.P.).
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Fritz JV, Heintz-Buschart A, Ghosal A, Wampach L, Etheridge A, Galas D, Wilmes P. Sources and Functions of Extracellular Small RNAs in Human Circulation. Annu Rev Nutr 2016; 36:301-36. [PMID: 27215587 PMCID: PMC5479634 DOI: 10.1146/annurev-nutr-071715-050711] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Various biotypes of endogenous small RNAs (sRNAs) have been detected in human circulation, including microRNAs, transfer RNAs, ribosomal RNA, and yRNA fragments. These extracellular sRNAs (ex-sRNAs) are packaged and secreted by many different cell types. Ex-sRNAs exhibit differences in abundance in several disease states and have, therefore, been proposed for use as effective biomarkers. Furthermore, exosome-borne ex-sRNAs have been reported to elicit physiological responses in acceptor cells. Exogenous ex-sRNAs derived from diet (most prominently from plants) and microorganisms have also been reported in human blood. Essential issues that remain to be conclusively addressed concern the (a) presence and sources of exogenous ex-sRNAs in human bodily fluids, (b) detection and measurement of ex-sRNAs in human circulation, (c) selectivity of ex-sRNA export and import, (d) sensitivity and specificity of ex-sRNA delivery to cellular targets, and (e) cell-, tissue-, organ-, and organism-wide impacts of ex-sRNA-mediated cell-to-cell communication. We survey the present state of knowledge of most of these issues in this review.
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MESH Headings
- Animals
- Biological Transport
- Biomarkers/blood
- Cell Communication
- Diet
- Gastrointestinal Microbiome/immunology
- Gene Expression Regulation
- Host-Parasite Interactions
- Host-Pathogen Interactions
- Humans
- Immunity, Innate
- MicroRNAs/blood
- MicroRNAs/metabolism
- Models, Biological
- RNA, Bacterial/blood
- RNA, Bacterial/metabolism
- RNA, Plant/blood
- RNA, Plant/metabolism
- RNA, Ribosomal/blood
- RNA, Ribosomal/metabolism
- RNA, Small Interfering/blood
- RNA, Small Interfering/metabolism
- RNA, Small Untranslated/blood
- RNA, Small Untranslated/metabolism
- RNA, Transfer/blood
- RNA, Transfer/metabolism
- RNA, Viral/blood
- RNA, Viral/metabolism
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Affiliation(s)
- Joëlle V Fritz
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, L-4367 Belvaux, Luxembourg; ,
| | - Anna Heintz-Buschart
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, L-4367 Belvaux, Luxembourg; ,
| | - Anubrata Ghosal
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Linda Wampach
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, L-4367 Belvaux, Luxembourg; ,
| | - Alton Etheridge
- Pacific Northwest Diabetes Research Institute, Seattle, Washington 98122
| | - David Galas
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, L-4367 Belvaux, Luxembourg; ,
- Pacific Northwest Diabetes Research Institute, Seattle, Washington 98122
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, L-4367 Belvaux, Luxembourg; ,
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Navickas R, Gal D, Laucevičius A, Taparauskaitė A, Zdanytė M, Holvoet P. Identifying circulating microRNAs as biomarkers of cardiovascular disease: a systematic review. Cardiovasc Res 2016; 111:322-37. [PMID: 27357636 PMCID: PMC4996262 DOI: 10.1093/cvr/cvw174] [Citation(s) in RCA: 248] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 05/19/2016] [Indexed: 12/31/2022] Open
Abstract
The aim of the present study is to identify microRNAs (miRs) with high potential to be used as biomarkers in plasma and/or serum to clinically diagnose, or provide accurate prognosis for survival in, patients with atherosclerosis, coronary artery disease, and acute coronary syndrome (ACS). A systematic search of published original research yielded a total of 72 studies. After review of the risk of bias of the published studies, according to Cochrane Collaboration and the QUADUAS Group standards, 19 studies were selected. Overall 52 different miRs were reported. In particular, miR-133a/b (5 studies), miR-208a/b (6 studies), and miR-499 (7 studies) were well studied and found to be significant diagnostic and/or prognostic markers across different cardiovascular disease progression stages. miR-1 and miR-145b are potential biomarkers of ACS; miR-1 with higher sensitivity for all acute myocardial infarction (AMI), and miR-145 for STEMI and worse outcome of AMI. But when miRs were studied across different ACS study populations, patients had varying degrees of coronary stenosis, which was identified as an important confounder that limited the ability to quantitatively pool the study results. The identified miRs were found to regulate endothelial function and angiogenesis (miR-1, miR-133), vascular smooth muscle cell differentiation (miR-133, miR-145), communication between vascular smooth muscle and endothelial cell to stabilize plaques (miR-145), apoptosis (miR-1, miR-133, miR-499), cardiac myocyte differentiation (miR-1, miR-133, miR-145, miR-208, miR-499), and to repress cardiac hypertrophy (miR-133). Their role in these processes may be explained by regulation of shared RNA targets such as cyclin-dependent kinase inhibitor 1A (or p21), ETS proto-oncogene 1, fascin actin-bundling protein 1, hyperpolarization-activated cyclic nucleotide-gated potassium channel 4, insulin-like growth factor 1 receptor LIM and SH3 protein 1, purine nucleoside phosphorylase, and transgelin 2. These mechanistic data further support the clinical relevance of the identified miRs. miR-1, miR-133a/b, miR-145, miR-208a/b, and miR-499(a) in plasma and/or serum show some potential for diagnosis of cardiovascular disease. However, biased selection of miRs in most studies and unexplained contrasting results are major limitations of current miR research. Inconsistencies need to be addressed in order to definitively identify clinically useful miRs. Therefore, this paper presents important aspects to improve future miR research, including unbiased selection of miRs, standardization/normalization of reference miRs, adjustment for patient comorbidities and medication, and robust protocols of data-sharing plans that could prevent selective publication and selective reporting of miR research outcomes.
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Affiliation(s)
- Rokas Navickas
- Faculty of Medicine, Vilnius University, Vilnius, Lithuania Vilnius University Hospital Santariškių Klinikos, Vilnius, Lithuania
| | - Diane Gal
- Department of Cardiovascular Sciences, Atherosclerosis and Metabolism Unit, KU Leuven, Leuven, Belgium
| | - Aleksandras Laucevičius
- Faculty of Medicine, Vilnius University, Vilnius, Lithuania Vilnius University Hospital Santariškių Klinikos, Vilnius, Lithuania
| | | | | | - Paul Holvoet
- Department of Cardiovascular Sciences, Atherosclerosis and Metabolism Unit, KU Leuven, Leuven, Belgium
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Sánchez-Fito MT, Oltra E. Optimized Treatment of Heparinized Blood Fractions to Make Them Suitable for Analysis. Biopreserv Biobank 2016; 13:287-95. [PMID: 26280503 DOI: 10.1089/bio.2015.0026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND It has been known for decades that many cytokines, such as IL-2, IL-6, and IL-12, bind to heparin. Even though some enzyme-linked immunosorbent assays (ELISA) use antibody-recognizing epitopes not affected by this binding, ELISA manufacturers often warn that heparinized plasma or serum fractions containing more than 3 IU (international units)/mL of heparin should not be used in assays so as to prevent heparin interference in the reaction. In addition, enzyme-based nucleic acid amplifications from heparinized samples have been shown defective by several research groups. The aim of this study was to determine optimal degradation and/or removal of heparin from heparinized blood samples to best turn them into fractions for appropriate ELISA and RT-PCR analysis. METHODS AND RESULTS A colorimetric reporter assay based on the metachromatic effect of the binding of heparin to toluidine blue was shown to be a low-cost effective method to discriminate assay compatible blood fractions with heparin levels below 3 IU/mL. Heparin removal from human blood fractions was best achieved by treatment with either Bacteroides Heparinase II or the less expensive Heparinase I at a final concentration of 0.1 U/μL and incubations at 30°C for a period between 30 min and 4 h, or by adsorption to Ecteola slurries at a concentration of 20 mg/mL for 20 min at room temperature (RT). The fact that both enzymatic and resin-based optimized treatments allowed for replication of the readings obtained with heparin-free equivalent fractions in both ELISA and RT-PCR assays indicates they should be appropriate for quantitative studies such as expression profiling at both the protein and nucleic acid level. CONCLUSIONS The cost-effective protocols developed in this study could make heparinized, otherwise unusable, blood-derived collections suitable for analysis by ELISA and RT-PCR amplifications, among other analyses, enhancing the possibilities for studying valuable bio-banked heparinized human samples.
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Affiliation(s)
- María Teresa Sánchez-Fito
- 1 Facultad de Medicina, Universidad Católica de Valencia "San Vicente Mártir" , Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Elisa Oltra
- 1 Facultad de Medicina, Universidad Católica de Valencia "San Vicente Mártir" , Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain .,2 Instituto Valenciano de Patología (IVP), Universidad Católica de Valencia "San Vicente Mártir" , Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
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Baoutina A, Bhat S, Zheng M, Partis L, Dobeson M, Alexander IE, Emslie KR. Synthetic certified DNA reference material for analysis of human erythropoietin transgene and transcript in gene doping and gene therapy. Gene Ther 2016; 23:708-717. [DOI: 10.1038/gt.2016.47] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 05/24/2016] [Indexed: 12/27/2022]
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Keller A, Meese E. Can circulating miRNAs live up to the promise of being minimal invasive biomarkers in clinical settings? WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 7:148-56. [PMID: 26670867 DOI: 10.1002/wrna.1320] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 10/26/2015] [Accepted: 10/28/2015] [Indexed: 12/23/2022]
Abstract
MicroRNAs have been discussed as non- or minimal invasive biomarkers with a remarkable extracellular stability. Despite a multitude of studies in basic research, there are only few independent validation studies on blood-born miRNAs as disease markers. Toward clinical applications numerous obstacles still need to be overcome. They are of technical origin but also fundamentally associated with the source and the nature of miRNAs. Here, we emphasize on potential confounding factors, the nature and the source of miRNAs. We recently showed that age and gender could influence the pattern of circulating miRNAs. On the cellular level, the miRNA pattern differs between plasma and serum preparations. On the molecular level, one has to differentiate between extracellular miRNAs that are encapsulated in microvesicles or bound to proteins or high-density lipoproteins. Using whole blood as source for miRNAs helps to minimize miRNA expression changes due to environmental influences and allows attributing miRNA changes to their cells of origin like B-cells and T-cells. Moreover, unambiguous annotation and differentiation from other noncoding RNAs can be challenging. Even not all miRNAs deposited in miRBase do necessarily represent true miRNAs, just a fraction of miRNAs in the reference database have been experimentally validated by Northern blotting. Functional evidence for a true miRNA should be obtained by cloning the precursor miRNA and by subsequent detection of the processed mature form in host cells. Surprisingly, attempts to finally confirm a true miRNA are frequently postponed until evidence has been established for a likely value as biomarker.
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Affiliation(s)
- Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, University Hospital, Saarbrücken, Germany
| | - Eckart Meese
- Institute of Human Genetics, Saarland University, University Hospital, Homburg, Germany
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McKiernan PJ, Greene CM. High-throughput profiling for discovery of non-coding RNA biomarkers of lung disease. Expert Rev Mol Diagn 2015; 16:173-85. [PMID: 26581119 DOI: 10.1586/14737159.2016.1122526] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In respiratory medicine there is a need for clinical biomarkers for diagnosis, prognosis and assessment of response to therapy. Noncoding RNA (ncRNA) is expressed in all human cells; two major classes--long ncRNA and microRNA--are detectable extracellularly in the circulation and other biofluids. Altered ncRNA expression is associated with lung disease; collectively this indicates that ncRNA represents a potential biomarker class. This article presents and compares existing platforms for detection and quantification of ncRNA, specifically hybridization, qRT-PCR and RNA sequencing, and outlines methods for data interpretation and normalization. Each approach has merits and shortcomings, which can affect the choice of method when embarking on a biomarker study. Biomarker properties and pre-analytical considerations for ncRNA profiling are also presented. Since a variety of profiling approaches are available, careful study and experimental design are important. Finally, challenges and goals for reliable, standardized high-throughput ncRNA profiling in biofluids as lung disease biomarkers are reviewed.
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Affiliation(s)
- Paul J McKiernan
- a Respiratory Research, Department of Medicine, The Royal College of Surgeons in Ireland, Education and Research Centre , Beaumont Hospital , Dublin , Ireland
| | - Catherine M Greene
- a Respiratory Research, Department of Medicine, The Royal College of Surgeons in Ireland, Education and Research Centre , Beaumont Hospital , Dublin , Ireland
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Landoni E, Miceli R, Callari M, Tiberio P, Appierto V, Angeloni V, Mariani L, Daidone MG. Proposal of supervised data analysis strategy of plasma miRNAs from hybridisation array data with an application to assess hemolysis-related deregulation. BMC Bioinformatics 2015; 16:388. [PMID: 26581577 PMCID: PMC4650369 DOI: 10.1186/s12859-015-0820-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 07/24/2015] [Indexed: 02/04/2023] Open
Abstract
Background Plasma miRNAs have the potential as cancer biomarkers but no consolidated guidelines for data mining in this field are available. The purpose of the study was to apply a supervised data analysis strategy in a context where prior knowledge is available, i.e., that of hemolysis-related miRNAs deregulation, so as to compare our results with existing evidence. Results We developed a structured strategy with innovative applications of existing bioinformatics methods for supervised analyses including: 1) the combination of two statistical (t- and Anderson-Darling) test results to detect miRNAs with significant fold change or general distributional differences in class comparison, which could reveal hidden differential biological processes worth to be considered for building predictive tools; 2) a bootstrap selection procedure together with machine learning techniques in class prediction to guarantee the transferability of results and explore the interconnections among the selected miRNAs, which is important for highlighting their inherent biological dependences. The strategy was applied to develop a classifier for discriminating between hemolyzed and not hemolyzed plasma samples, defined according to a recently published hemolysis score. We identified five miRNAs with increased expression in hemolyzed plasma samples (miR-486-5p, miR-92a, miR-451, miR-16, miR-22). Conclusions We identified four miRNAs previously reported in the literature as hemolysis related together with a new one (miR-22).which needs further investigations. Our findings confirm the validity of the proposed strategy and, in parallel, the hemolysis score capability to be used as pre-analytic hemolysis detector. R codes for implementing the approaches are provided. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0820-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elena Landoni
- Clinical Epidemiology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Venezian 1, 20133, Milan, Italy.
| | - Rosalba Miceli
- Clinical Epidemiology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Venezian 1, 20133, Milan, Italy.
| | - Maurizio Callari
- Biomarkers Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Venezian 1, 20133, Milan, Italy
| | - Paola Tiberio
- Biomarkers Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Venezian 1, 20133, Milan, Italy
| | - Valentina Appierto
- Biomarkers Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Venezian 1, 20133, Milan, Italy
| | - Valentina Angeloni
- Biomarkers Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Venezian 1, 20133, Milan, Italy
| | - Luigi Mariani
- Clinical Epidemiology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Venezian 1, 20133, Milan, Italy
| | - Maria Grazia Daidone
- Biomarkers Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Venezian 1, 20133, Milan, Italy
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Ono S, Lam S, Nagahara M, Hoon DSB. Circulating microRNA Biomarkers as Liquid Biopsy for Cancer Patients: Pros and Cons of Current Assays. J Clin Med 2015; 4:1890-907. [PMID: 26512704 PMCID: PMC4626661 DOI: 10.3390/jcm4101890] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 09/01/2015] [Accepted: 10/09/2015] [Indexed: 02/08/2023] Open
Abstract
An increasing number of studies have focused on circulating microRNAs (cmiRNA) in cancer patients’ blood for their potential as minimally-invasive biomarkers. Studies have reported the utility of assessing specific miRNAs in blood as diagnostic/prognostic biomarkers; however, the methodologies are not validated or standardized across laboratories. Unfortunately, there is often minimum limited overlap in techniques between results reported even in similar type studies on the same cancer. This hampers interpretation and reliability of cmiRNA as potential cancer biomarkers. Blood collection and processing, cmiRNA extractions, quality and quantity control of assays, defined patient population assessment, reproducibility, and reference standards all affect the cmiRNA assay results. To date, there is no reported definitive method to assess cmiRNAs. Therefore, appropriate and reliable methodologies are highly necessary in order for cmiRNAs to be used in regulated clinical diagnostic laboratories. In this review, we summarize the developments made over the past decade towards cmiRNA detection and discuss the pros and cons of the assays.
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Affiliation(s)
- Shigeshi Ono
- Department of Molecular Oncology, John Wayne Cancer Institute, Providence Saint John's Health Center, 2200 Santa Monica Blvd., Santa Monica, CA 90404, USA.
| | - Stella Lam
- Department of Molecular Oncology, John Wayne Cancer Institute, Providence Saint John's Health Center, 2200 Santa Monica Blvd., Santa Monica, CA 90404, USA.
| | - Makoto Nagahara
- Department of Molecular Oncology, John Wayne Cancer Institute, Providence Saint John's Health Center, 2200 Santa Monica Blvd., Santa Monica, CA 90404, USA.
| | - Dave S B Hoon
- Department of Molecular Oncology, John Wayne Cancer Institute, Providence Saint John's Health Center, 2200 Santa Monica Blvd., Santa Monica, CA 90404, USA.
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Loeffler J, Mengoli C, Springer J, Bretagne S, Cuenca-Estrella M, Klingspor L, Lagrou K, Melchers WJG, Morton CO, Barnes RA, Donnelly JP, White PL. Analytical Comparison of In Vitro-Spiked Human Serum and Plasma for PCR-Based Detection of Aspergillus fumigatus DNA: a Study by the European Aspergillus PCR Initiative. J Clin Microbiol 2015; 53:2838-45. [PMID: 26085614 PMCID: PMC4540929 DOI: 10.1128/jcm.00906-15] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 06/12/2015] [Indexed: 12/04/2022] Open
Abstract
The use of serum or plasma for Aspergillus PCR testing facilitates automated and standardized technology. Recommendations for serum testing are available, and while serum and plasma are regularly considered interchangeable for use in fungal diagnostics, differences in galactomannan enzyme immunoassay (GM-EIA) performance have been reported and are attributed to clot formation. Therefore, it is important to assess plasma PCR testing to determine if previous recommendations for serum are applicable and also to compare analytical performance with that of serum PCR. Molecular methods testing serum and plasma were compared through multicenter distribution of quality control panels, with additional studies to investigate the effect of clot formation and blood fractionation on DNA availability. Analytical sensitivity and time to positivity (TTP) were compared, and a regression analysis was performed to identify variables that enhanced plasma PCR performance. When testing plasma, sample volume, preextraction-to-postextraction volume ratio, PCR volume, duplicate testing, and the use of an internal control for PCR were positively associated with performance. When whole-blood samples were spiked and then fractionated, the analytical sensitivity and TTP were superior when testing plasma. Centrifugation had no effect on DNA availability, whereas the presence of clot material significantly lowered the concentration (P = 0.028). Technically, there are no major differences in the molecular processing of serum and plasma, but the formation of clot material potentially reduces available DNA in serum. During disease, Aspergillus DNA burdens in blood are often at the limits of PCR performance. Using plasma might improve performance while maintaining the methodological simplicity of serum testing.
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Affiliation(s)
| | | | | | | | | | | | - Katrien Lagrou
- National Reference Center for Mycosis, University Hospitals Leuven, Leuven, Belgium Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | | | | | | | | | - P Lewis White
- Public Health Wales Microbiology Cardiff, Cardiff, United Kingdom
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50
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Laurent LC, Abdel-Mageed AB, Adelson PD, Arango J, Balaj L, Breakefield X, Carlson E, Carter BS, Majem B, Chen CC, Cocucci E, Danielson K, Courtright A, Das S, Abd Elmageed ZY, Enderle D, Ezrin A, Ferrer M, Freedman J, Galas D, Gandhi R, Huentelman MJ, Van Keuren-Jensen K, Kalani Y, Kim Y, Krichevsky AM, Lai C, Lal-Nag M, Laurent CD, Leonardo T, Li F, Malenica I, Mondal D, Nejad P, Patel T, Raffai RL, Rubio R, Skog J, Spetzler R, Sun J, Tanriverdi K, Vickers K, Wang L, Wang Y, Wei Z, Weiner HL, Wong D, Yan IK, Yeri A, Gould S. Meeting report: discussions and preliminary findings on extracellular RNA measurement methods from laboratories in the NIH Extracellular RNA Communication Consortium. J Extracell Vesicles 2015; 4:26533. [PMID: 26320937 PMCID: PMC4553263 DOI: 10.3402/jev.v4.26533] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 04/17/2015] [Accepted: 05/03/2015] [Indexed: 01/14/2023] Open
Abstract
Extracellular RNAs (exRNAs) have been identified in all tested biofluids and have been associated with a variety of extracellular vesicles, ribonucleoprotein complexes and lipoprotein complexes. Much of the interest in exRNAs lies in the fact that they may serve as signalling molecules between cells, their potential to serve as biomarkers for prediction and diagnosis of disease and the possibility that exRNAs or the extracellular particles that carry them might be used for therapeutic purposes. Among the most significant bottlenecks to progress in this field is the lack of robust and standardized methods for collection and processing of biofluids, separation of different types of exRNA-containing particles and isolation and analysis of exRNAs. The Sample and Assay Standards Working Group of the Extracellular RNA Communication Consortium is a group of laboratories funded by the U.S. National Institutes of Health to develop such methods. In our first joint endeavour, we held a series of conference calls and in-person meetings to survey the methods used among our members, placed them in the context of the current literature and used our findings to identify areas in which the identification of robust methodologies would promote rapid advancements in the exRNA field.
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Affiliation(s)
- Louise C Laurent
- Division of Maternal Fetal Medicine, Department of Reproductive Medicine, University of California San Diego, San Diego, CA, USA.,Sanford Consortium for Regenerative Medicine, San Diego, CA, USA;
| | - Asim B Abdel-Mageed
- Department of Urology, Tulane University, School of Medicine, New Orleans, LA, USA
| | | | | | - Leonora Balaj
- Department of Neurology, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA.,Program in Neuroscience, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA
| | - Xandra Breakefield
- Department of Neurology, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA.,Program in Neuroscience, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA.,Department of Radiology, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA
| | - Elizabeth Carlson
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Bob S Carter
- Center for Theoretical and Applied Neuro-Oncology, Division of Neurosurgery, University of California San Diego, San Diego, CA, USA
| | - Blanca Majem
- School of Dentistry, University of California, Los Angeles, CA, USA
| | - Clark C Chen
- Center for Theoretical and Applied Neuro-Oncology, Division of Neurosurgery, University of California San Diego, San Diego, CA, USA
| | - Emanuele Cocucci
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Kirsty Danielson
- Cardiovascular Institute, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Amanda Courtright
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Saumya Das
- Cardiovascular Institute, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | | | | | | | - Marc Ferrer
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Bethesda, MD, USA
| | - Jane Freedman
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - David Galas
- Pacific Northwest Diabetes Research Institute, Seattle, WA, USA.,Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Roopali Gandhi
- Department of Neurology, Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | | | - Yong Kim
- School of Dentistry, University of California, Los Angeles, CA, USA
| | - Anna M Krichevsky
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Charles Lai
- Department of Neurology, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA.,Program in Neuroscience, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA
| | - Madhu Lal-Nag
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Bethesda, MD, USA
| | - Clara D Laurent
- Cardiovascular Institute, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Trevor Leonardo
- Cardiovascular Institute, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Feng Li
- School of Dentistry, University of California, Los Angeles, CA, USA
| | - Ivana Malenica
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Debasis Mondal
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Parham Nejad
- Department of Neurology, Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Tushar Patel
- Department of Transplantation, Mayo Clinic Florida, Jacksonville, FL, USA.,Department of Cancer Biology, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Robert L Raffai
- Department of Surgery, University of California San Francisco, San Francisco, CA, USA.,Department of Veteran's Affairs, San Francisco, CA, USA
| | - Renee Rubio
- Center for Cancer Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | | | | | - Jie Sun
- School of Dentistry, University of California, Los Angeles, CA, USA
| | - Kahraman Tanriverdi
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Kasey Vickers
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN, USA.,Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Liang Wang
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Yaoyu Wang
- Center for Cancer Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Zhiyun Wei
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Howard L Weiner
- Department of Neurology, Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - David Wong
- School of Dentistry, University of California, Los Angeles, CA, USA
| | - Irene K Yan
- Department of Cancer Biology, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Ashish Yeri
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Stephen Gould
- Department of Biological Chemistry, Johns Hopkins University, Baltimore, MD, USA
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