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Vanhie A, Caron E, Vermeersch E, O D, Tomassetti C, Meuleman C, Mestdagh P, D’Hooghe TM. Circulating microRNAs as Non-Invasive Biomarkers in Endometriosis Diagnosis-A Systematic Review. Biomedicines 2024; 12:888. [PMID: 38672242 PMCID: PMC11048084 DOI: 10.3390/biomedicines12040888] [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: 09/01/2023] [Revised: 12/18/2023] [Accepted: 01/25/2024] [Indexed: 04/28/2024] Open
Abstract
The aim of this systematic review is to assess the power of circulating miRNAs as biomarkers as a diagnostic tool in endometriosis. In endometriosis-suspected women with uncertain imaging, the only way to confirm or exclude endometriosis with certainty is currently laparoscopy. This creates a need for non-invasive diagnostics. We searched the literature through the PubMed database using the Mesh terms 'endometriosis' and 'miRNAs'. Some, but limited, overlap was found between the 32 articles included, with a total of 20 miRNAs reported as dysregulated in endometriosis in two or more studies. MiR-17-5p was reported as dysregulated in six studies, followed by miR-451a and let-7b-5p in four studies and miR-20a-5p, miR-143-3p, miR-199a-5p and miR-3613-5p in three studies. Furthermore, a possible impact of the menstrual phase on miRNA expression was noted in five studies, while no influence of hormonal intake was observed in any included study. The modest reproducibility between studies may be attributable to biological variability as well as to the lack of universal protocols, resulting in pre- and analytical variability. Despite the identification of several suitable candidate biomarkers among the miRNAs, the need for high-quality studies with larger and well-defined population cohorts and the use of standardized protocols lingers.
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Affiliation(s)
- Arne Vanhie
- Department of Development and Regeneration, KU Leuven, 3000 Leuven, Belgium
| | - Ellen Caron
- Department of Obstetrics and Gynecology, University Hospital Leuven, 3000 Leuven, Belgium
| | - Eveline Vermeersch
- Department of Obstetrics and Gynecology, University Hospital Leuven, 3000 Leuven, Belgium
| | - Dorien O
- Department of Obstetrics and Gynecology, University Hospital Leuven, 3000 Leuven, Belgium
| | - Carla Tomassetti
- Department of Obstetrics and Gynecology, University Hospital Leuven, 3000 Leuven, Belgium
| | - Christel Meuleman
- Department of Obstetrics and Gynecology, University Hospital Leuven, 3000 Leuven, Belgium
| | - Pieter Mestdagh
- UGent, Center for Medical Genetics, Thent University, 9000 Ghent, Belgium
- UGent, Cancer Research Institute Ghen, Ghent University, 9000 Ghent, Belgium
| | - Thomas M. D’Hooghe
- Department of Obstetrics and Gynecology, University Hospital Leuven, 3000 Leuven, Belgium
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Greytak SR, Engel KB, Hoon DSB, Elias KM, Lockwood CM, Guan P, Moore HM. Evidence-based procedures to improve the reliability of circulating miRNA biomarker assays. Clin Chem Lab Med 2024; 62:60-66. [PMID: 37129007 DOI: 10.1515/cclm-2023-0131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 04/18/2023] [Indexed: 05/03/2023]
Abstract
Circulating cell-free microRNAs (cfmiRNA) are an emerging class of biomarkers that have shown great promise in the clinical diagnosis, treatment, and monitoring of several pathological conditions, including cancer. However, validation and clinical implementation of cfmiRNA biomarkers has been hindered by the variability introduced during different or suboptimal specimen collection and handling practices. To address the need for standardization and evidence-based guidance, the National Cancer Institute (NCI) developed a new Biospecimen Evidenced-Based Practices (BEBP) document, entitled "Cell-free miRNA (cfmiRNA): Blood Collection and Processing". The BEBP, the fourth in the document series, contains step-by-step procedural guidelines on blood collection, processing, storage, extraction, and quality assessment that are tailored specifically for cfmiRNA analysis of plasma and serum. The workflow outlined in the BEBP is based on the available literature and recommendations of an expert panel. The BEBP contains the level of detail required for development of evidence-based standard operating procedures (SOPs) as well as the flexibility needed to accomodate (i) discovery- and inquiry-based studies and (ii) the different constraints faced by research labs, industry, clinical and academic institutions to foster widespread implementation. Guidance from the expert panel also included recommendations on study design, validating changes in workflow, and suggested quality thresholds to delineate meaningful changes in cfmiRNA levels. The NCI cfmiRNA: Blood Collection and Processing BEBP is available here as supplementary information as well as through the NCI Biorepositories and Biospecimen Research Branch (BBRB) (https://biospecimens.cancer.gov/resources/bebp.asp).
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Affiliation(s)
| | | | - Dave S B Hoon
- Department of Translational Molecular Medicine & Sequencing Center, Saint Johns' Cancer Institute, Providence Health and Service, Santa Monica, CA, USA
| | - Kevin M Elias
- Gynecologic Oncology Laboratory, Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Harvard Medical School, Brigham and Women's Hospital, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Christina M Lockwood
- Genetics and Solid Tumors Laboratory, Department of Laboratory Medicine and Pathology, Brotman Baty Institute for Precision Medicine, UW Medicine, Seattle, WA, USA
| | - Ping Guan
- Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD, USA
| | - Helen M Moore
- Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD, USA
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Ye F, Feldman DR, Valentino A, So R, Bromberg M, Khan S, Funt SA, Sheinfeld J, Solit DB, Pessin MS, Peerschke EI. Analytical Validation and Performance Characteristics of Molecular Serum Biomarkers, miR-371a-3p and miR-372-3p, for Male Germ Cell Tumors, in a Clinical Laboratory Setting. J Mol Diagn 2022; 24:867-877. [PMID: 35934321 PMCID: PMC9379668 DOI: 10.1016/j.jmoldx.2022.04.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 03/17/2022] [Accepted: 04/22/2022] [Indexed: 12/12/2022] Open
Abstract
Detection of serum embryonic miRNAs miR-371a-3p and miR-372-3p has been proposed to aid in diagnosis, prognosis, and management of patients with testicular germ cell tumors (GCTs). This study describes the analytical validation and performance of a laboratory-developed test to detect these miRNA targets by stem loop real-time quantitative RT-PCR (RT-qPCR) in serum from patients with GCTs. The assay was standardized using an exogenous spike-in control of nonhuman miRNA from Caenorhabditis elegans (cel-miR-39-3p) to assess extraction efficiency, and an endogenous housekeeping miRNA, miR-30b-5p, to control for miRNA normalization. miRNA results were expressed as relative expression level, using the comparative threshold cycle method (2ΔΔCT). Analytical sensitivity of miR-371a-3p and miR-372-3p was 12.5 and 1.25 copies/μL, respectively. Clinical accuracy was evaluated using GCT patients with (n = 34) and without (n = 17) active disease. Positive/negative cutoffs and indeterminate findings were established on the basis of results from healthy volunteers (n = 25) and assay precision. miR-371a-3p and miR-372-3p exhibited a sensitivity of 81.8% and 87.5%, respectively, and a specificity of 100% and 94%, respectively, and an area under the receiver operating characteristic curve of 0.93 and 0.95, respectively. Taken together, RT-qPCR testing for serum miR-371a-3p and miR-372-3p represents a robust, sensitive, and specific clinical assay to aid in the clinical management of patients with GCT.
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Considerations and Suggestions for the Reliable Analysis of miRNA in Plasma Using qRT-PCR. Genes (Basel) 2022; 13:genes13020328. [PMID: 35205372 PMCID: PMC8872398 DOI: 10.3390/genes13020328] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/08/2022] [Accepted: 02/08/2022] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) are promising molecules that can regulate gene expression, and their expression level and type have been associated with early diagnosis, targeted therapy, and prognosis of various diseases. Therefore, analysis of miRNA in the plasma or serum is useful for the discovery of biomarkers and the diagnosis of implicated diseases to achieve potentially unprecedented progress in early treatment. Numerous methods to improve sensitivity have recently been proposed and confirmed to be valuable in miRNA detection. Specifically, quantitative reverse-transcription polymerase chain reaction (qRT-PCR) is an effective and common method for sensitive and specific analysis of miRNA from biological fluids, such as plasma or serum. Despite this, the application of qRT-PCR is limited, as it can be affected by various contaminants. Therefore, extraction studies have been frequently conducted to maximize the extracted miRNA amount while simultaneously minimizing contaminants. Moreover, studies have evaluated extraction efficiency and normalization of the extracted sample. However, variability in results among laboratories still exists. In this review, we aimed to summarize the factors influencing the qualification and quantification of miRNAs in the plasma using qRT-PCR. Factors influencing reliable analysis of miRNA using qRT-PCR are described in detail. Additionally, we aimed to describe the importance of evaluating extraction and normalization for reliable miRNA analysis and to explore how miRNA detection accuracy, especially from plasma, can be improved.
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Parker VL, Cushen BF, Gavriil E, Marshall B, Waite S, Pacey A, Heath PR. Comparison and optimisation of microRNA extraction from the plasma of healthy pregnant women. Mol Med Rep 2021; 23:1. [PMID: 33576446 PMCID: PMC7893782 DOI: 10.3892/mmr.2021.11897] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 12/15/2020] [Indexed: 01/01/2023] Open
Abstract
Circulating microRNA (miRNA) biomarkers are implicated in the diagnosis, monitoring and prediction of various disease processes. Before embarking upon biomarker discovery, miRNA extraction techniques must first be optimised in the biofluid and population under study. Using plasma from a healthy pregnant woman, it was attempted to optimise and compare the performance of two commercially available miRNA extraction kits; Qiagen (miRNeasy Serum/Plasma) and Promega (Maxwell® RSC miRNA from Tissue or Plasma or Serum). Sample miRNA content (concentration and percentage) was assessed using Agilent Bioanalyzer Small RNA chips and reverse transcription-quantitative PCR (RT-qPCR) using four constitutively expressed miRNAs (hsa-miR-222-3p, hsa-let-7i-3p, hsa-miR-148-3p and hsa-miR-30e-5p). Quality control spike-ins monitored RNA extraction (UniSp2, 4 and 5) and cDNA synthesis (UniSp6, cel-miR-39-3p) efficiency. Optimisation approaches included: i) Starting volume of plasma; the addition of ii) Proteinase K; iii) a RNA bacteriophage carrier (MS2); and iv) a glycogen carrier. The two kits exhibited equivalence in terms of miRNA recovery based on Bioanalyzer and RT-qPCR ΔΔCq results. Optimisation attempts for both kits failed to improve upon miRNA content compared with standard methodology. Comparing the standard methodology, the Qiagen kit was more consistent (smaller variance of ΔCq values) compared with the Promega kit. The standard methodology of either kit would be suitable for the investigation of miRNA biomarkers in a healthy pregnant population.
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Affiliation(s)
- Victoria L Parker
- Department of Oncology and Metabolism, The University of Sheffield, Sheffield S10 2SF, UK
| | - Bryony F Cushen
- Department of Oncology and Metabolism, The University of Sheffield, Sheffield S10 2SF, UK
| | - Eleftherios Gavriil
- Department of Oncology and Metabolism, The University of Sheffield, Sheffield S10 2SF, UK
| | - Benjamin Marshall
- Department of Oncology and Metabolism, The University of Sheffield, Sheffield S10 2SF, UK
| | - Sarah Waite
- Department of Oncology and Metabolism, The University of Sheffield, Sheffield S10 2SF, UK
| | - Allan Pacey
- Department of Oncology and Metabolism, The University of Sheffield, Sheffield S10 2SF, UK
| | - Paul R Heath
- Sheffield Institute of Translational Neuroscience, The University of Sheffield, Sheffield S10 2HQ, UK
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Carmona A, Guerrero F, Jimenez MJ, Ariza F, Agüera ML, Obrero T, Noci V, Muñoz-Castañeda JR, Rodríguez M, Soriano S, Moreno JA, Martin-Malo A, Aljama P. Inflammation, Senescence and MicroRNAs in Chronic Kidney Disease. Front Cell Dev Biol 2020; 8:739. [PMID: 32850849 PMCID: PMC7423998 DOI: 10.3389/fcell.2020.00739] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/16/2020] [Indexed: 12/11/2022] Open
Abstract
Background Patients with chronic kidney disease (CKD) show a chronic microinflammatory state that promotes premature aging of the vascular system. Currently, there is a growth interest in the search of novel biomarkers related to vascular aging to identify CKD patients at risk to develop cardiovascular complications. Methods Forty-five CKD patients were divided into three groups according to CKD-stages [predialysis (CKD4-5), hemodialysis (HD) and kidney transplantation (KT)]. In all these patients, we evaluated the quantitative changes in microRNAs (miRNAs), CD14+C16++ monocytes number, and microvesicles (MV) concentration [both total MV, and monocytes derived MV (CD14+Annexin V+CD16+)]. To understand the molecular mechanism involved in senescence and osteogenic transdifferentation of vascular smooth muscle cells (VSMC), these cells were stimulated with MV isolated from THP-1 monocytes treated with uremic toxins (txMV). Results A miRNA array was used to investigate serum miRNAs profile in CKD patients. Reduced expression levels of miRNAs-126-3p, -191-5p and -223-3p were observed in CKD4-5 and HD patients as compared to KT. This down-regulation disappeared after KT, even when lower glomerular filtration rates (eGFR) persisted. Moreover, HD patients had higher percentage of proinflammatory monocytes (CD14+CD16++) and MV derived of proinflammatory monocytes (CD14+Annexin V+CD16+) than the other groups. In vitro studies showed increased expression of osteogenic markers (BMP2 and miRNA-223-3p), expression of cyclin D1, β-galactosidase activity and VSMC size in those cells treated with txMV. Conclusion CKD patients present a specific circulating miRNAs expression profile associated with the microinflammatory state. Furthermore, microvesicles generated by monocytes treated with uremic toxins induce early senescence and osteogenic markers (BMP2 and miRNA-223-3p) in VSMC.
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Affiliation(s)
- Andres Carmona
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Reina Sofia University Hospital, Córdoba, Spain
| | - Fatima Guerrero
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Reina Sofia University Hospital, Córdoba, Spain.,Department of Medicine, University of Córdoba, Córdoba, Spain
| | - Maria Jose Jimenez
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Reina Sofia University Hospital, Córdoba, Spain
| | - Francisco Ariza
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Reina Sofia University Hospital, Córdoba, Spain
| | - Marisa L Agüera
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Reina Sofia University Hospital, Córdoba, Spain.,Nephrology Unit, Reina Sofia University Hospital, University of Córdoba, Córdoba, Spain
| | - Teresa Obrero
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Reina Sofia University Hospital, Córdoba, Spain
| | - Victoria Noci
- Anesthesia Unit, Reina Sofía University Hospital, Córdoba, Spain
| | - Juan Rafael Muñoz-Castañeda
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Reina Sofia University Hospital, Córdoba, Spain.,Nephrology Unit, Reina Sofia University Hospital, University of Córdoba, Córdoba, Spain
| | - Mariano Rodríguez
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Reina Sofia University Hospital, Córdoba, Spain.,Department of Medicine, University of Córdoba, Córdoba, Spain.,Nephrology Unit, Reina Sofia University Hospital, University of Córdoba, Córdoba, Spain.,Spanish Renal Research Network (REDinREN), Institute of Health Carlos III, Madrid, Spain
| | - Sagrario Soriano
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Reina Sofia University Hospital, Córdoba, Spain.,Nephrology Unit, Reina Sofia University Hospital, University of Córdoba, Córdoba, Spain.,Spanish Renal Research Network (REDinREN), Institute of Health Carlos III, Madrid, Spain
| | - Juan Antonio Moreno
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Reina Sofia University Hospital, Córdoba, Spain.,Department of Cell Biology, Physiology and Immunology, University of Córdoba, Córdoba, Spain
| | - Alejandro Martin-Malo
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Reina Sofia University Hospital, Córdoba, Spain.,Department of Medicine, University of Córdoba, Córdoba, Spain.,Nephrology Unit, Reina Sofia University Hospital, University of Córdoba, Córdoba, Spain.,Spanish Renal Research Network (REDinREN), Institute of Health Carlos III, Madrid, Spain
| | - Pedro Aljama
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Reina Sofia University Hospital, Córdoba, Spain.,Department of Medicine, University of Córdoba, Córdoba, Spain
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Feng X, Liu Y, Wan N. Plasma microRNA detection standardization test. J Clin Lab Anal 2019; 34:e23058. [PMID: 31617231 PMCID: PMC7031554 DOI: 10.1002/jcla.23058] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 09/16/2019] [Accepted: 09/17/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) can be used for early diagnosis of myocardial infarction. However, due to a lack of standardized operating procedures, their value for clinical application is low. METHODS Detection of plasma miRNAs was optimized by analyzing factors influencing miRNA variance and myocardial infarction risk scores during analysis (extraction, reverse transcription, and real-time PCR) and pre-analysis (dietary status, anticoagulants, storage conditions, and hemolysis). RESULTS Regarding variable factors during analysis, the centrifugal column method was superior to Trizol LS reagent when extracting miRNA from plasma. Recovery rate was highest with plasma volumes of 200 and 300 µL. During analysis, the main source of miRNA detection inaccuracy was derived from RNA extraction (mainly organic extraction), and not reverse transcription or PCR. MiRNA variance could be reduced by use of an internal reference. During analysis, 95% of risk score variation fluctuated within a range of 6.267. The variable factors pre-analysis mainly involved dietary status, anticoagulant selection, and storage conditions. Hemolysis positively correlated with miRNA levels, but there was no significant change in risk score after internal reference calibration. CONCLUSION Preliminary standardization for miRNA detection provides a reference for clinical blood testing of miRNAs.
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Affiliation(s)
- Xiaomin Feng
- Dalian Medical University, Dalian, Liaoning, China
| | - Yuwei Liu
- Dalian Medical University, Dalian, Liaoning, China
| | - Nan Wan
- Department of Laboratory Medicine Science Center, General Hospital of Northern Theater Command, Shenyang, Liaoning, China
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