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Lee EJ, Jeong M, Lee H, Je MA, Park K, Lee DG, Xuan X, Kim S, Park S, Kim J. MiR-122, miR-133a, and miR-206 as potential biomarkers for post-mortem interval estimation. Genes Genomics 2024; 46:1175-1182. [PMID: 39207675 DOI: 10.1007/s13258-024-01559-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Accepted: 08/12/2024] [Indexed: 09/04/2024]
Abstract
BACKGROUD Accurate estimation of post-mortem interval (PMI) is crucial in forensic investigations. MicroRNAs (miRNAs or miRs) are small non-coding RNAs that remain relatively stable within the cell nucleus despite post-mortem changes. OBJECTIVE We assessed three target genes (miR-122, miR-133a, and miR-206) for PMI estimation using 72 healthy adult male BALB/c mice exposed to two different temperatures (4 and 21℃) at nine different time points over 10 days. METHODS Initially, the stability of the two reference genes (RNU6B and 5 srRNA) was evaluated using gene stability analysis tools (Delta Ct, Best Keeper, and Genorm) to select the optimal reference gene. RNU6B was found to be the most stable endogenous control. Subsequently, the expression patterns of miR-122, miR-133a, and miR-206 were analyzed within a 10-day PMI period using the heart, skeletal muscle, liver, and brain tissues. RESULTS At 4℃, miR-122 levels significantly decreased on days 8 and 10 in all tissues, with only the liver showing significant changes at 21℃. MiR-133a decreased over time in the heart, muscles, and brain, showing a dramatic decrease on days 8 and 10 in the heart and muscles at both temperatures. Although miR-206 levels decreased over time in muscles and liver at 4 ℃, these increased in the brain at 21 ℃, with no expression changes in other organs. CONCLUSION In summary, miR-122, miR-133a, and miR-206 are potential PMI markers in heart and skeletal muscle tissues.
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Affiliation(s)
- Eun Ju Lee
- Department of Clinical Laboratory Science, College of Health Sciences, Catholic University of Pusan, Busan, 46252, Republic of Korea
- Department of Research and Development, Korea Mycobacterium Resource Center (KMRC), The Korean Institute of Tuberculosis, Osong, 28158, Republic of Korea
| | - Mingyoung Jeong
- Department of Forensic Science, Graduate School, Catholic University of Pusan, Busan, 46252, Republic of Korea
| | - Haneul Lee
- Department of Forensic Science, Graduate School, Catholic University of Pusan, Busan, 46252, Republic of Korea
- Next-Generation Industrial Field-Based Specialist Program for Molecular Diagnostics, Brain Busan 21 Plus Project, Graduate School, Catholic University of Pusan, Busan, 46252, Republic of Korea
| | - Min-A Je
- Department of Clinical Laboratory Science, College of Health Sciences, Catholic University of Pusan, Busan, 46252, Republic of Korea
| | - Kwangmin Park
- Department of Clinical Laboratory Science, College of Health Sciences, Catholic University of Pusan, Busan, 46252, Republic of Korea
- Next-Generation Industrial Field-Based Specialist Program for Molecular Diagnostics, Brain Busan 21 Plus Project, Graduate School, Catholic University of Pusan, Busan, 46252, Republic of Korea
| | - Dong Geon Lee
- Department of Clinical Laboratory Science, College of Health Sciences, Catholic University of Pusan, Busan, 46252, Republic of Korea
- Next-Generation Industrial Field-Based Specialist Program for Molecular Diagnostics, Brain Busan 21 Plus Project, Graduate School, Catholic University of Pusan, Busan, 46252, Republic of Korea
| | - Xianglan Xuan
- Department of Clinical Laboratory Science, College of Health Sciences, Catholic University of Pusan, Busan, 46252, Republic of Korea
- Next-Generation Industrial Field-Based Specialist Program for Molecular Diagnostics, Brain Busan 21 Plus Project, Graduate School, Catholic University of Pusan, Busan, 46252, Republic of Korea
| | - Sunghyun Kim
- Department of Clinical Laboratory Science, College of Health Sciences, Catholic University of Pusan, Busan, 46252, Republic of Korea
- Department of Forensic Science, Graduate School, Catholic University of Pusan, Busan, 46252, Republic of Korea
- Next-Generation Industrial Field-Based Specialist Program for Molecular Diagnostics, Brain Busan 21 Plus Project, Graduate School, Catholic University of Pusan, Busan, 46252, Republic of Korea
| | - Sunyoung Park
- School of Mechanical Engineering, Yonsei University, Seoul, 03772, Republic of Korea.
| | - Jungho Kim
- Department of Clinical Laboratory Science, College of Health Sciences, Catholic University of Pusan, Busan, 46252, Republic of Korea.
- Department of Forensic Science, Graduate School, Catholic University of Pusan, Busan, 46252, Republic of Korea.
- Next-Generation Industrial Field-Based Specialist Program for Molecular Diagnostics, Brain Busan 21 Plus Project, Graduate School, Catholic University of Pusan, Busan, 46252, Republic of Korea.
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Baraldo N, Buzzoni L, Pasti L, Cavazzini A, Marchetti N, Mancia A. miRNAs as Biomolecular Markers for Food Safety, Quality, and Traceability in Poultry Meat-A Preliminary Study. Molecules 2024; 29:748. [PMID: 38398499 PMCID: PMC10891583 DOI: 10.3390/molecules29040748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/26/2024] [Accepted: 02/02/2024] [Indexed: 02/25/2024] Open
Abstract
In this study, the expression and abundance of two candidate chicken (Gallus gallus; gga) microRNAs (miRNAs, miR), gga-miR-21-5p (miR-21) and gga-miR-126-5p (miR-126), have been analyzed in order to identify biomarkers for the traceability and quality of poultry meat. Two breeds of broiler chickens were tested: the most common Ross308 (fast-growing) and the high-quality Ranger Gold (slow-growing). A preliminary analysis of the two miRNAs expressions was conducted across various tissues (liver, lung, spleen, skeletal muscle, and kidney), and the three tissues (lung, spleen, and muscle) with a higher expression were chosen for further analysis. Using quantitative reverse transcription polymerase chain reaction (RT-qPCR), the expression of miRNAs in the three tissues of a total of thirteen animals was determined. The results indicate that miR-126 could be a promising biomarker for the lung tissue in the Ranger Gold (RG) breed (p < 0.01), thus suggesting a potential applicability for tracing hybrids. RG exhibits a significantly higher miR-126 expression in the lung tissue compared to the Ross308 broilers (R308), an indication of greater respiratory capacity and, consequently, a higher oxidative metabolism of the fast-growing hybrid. During sampling, two R308 broilers presented some anomalies, including airsacculitis, hepatic steatosis, and enlarged spleen. The expression of miR-126 and miR-21 was compared in healthy animals and in those presenting anomalies. Chickens with airsacculitis and hepatic steatosis showed an up-regulation of miR-21 and miR-126 in the most commercially valuable tissue, the skeletal muscle or breast (p < 0.05).
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Affiliation(s)
- Nada Baraldo
- Department of Chemical, Pharmaceutical and Agricultural Sciences (DoCPAS), University of Ferrara, 44121 Ferrara, Italy; (N.B.); (A.C.)
| | - Luna Buzzoni
- Department of Life Science and Biotechnologies, University of Ferrara, via L. Borsari 46, 44121 Ferrara, Italy;
| | - Luisa Pasti
- Department of Environmental and Prevention Sciences, University of Ferrara, via L. Borsari 46, 44121 Ferrara, Italy;
| | - Alberto Cavazzini
- Department of Chemical, Pharmaceutical and Agricultural Sciences (DoCPAS), University of Ferrara, 44121 Ferrara, Italy; (N.B.); (A.C.)
- Council for Agricultural Research and Economics, via della Navicella 2/4, 00184 Rome, Italy
| | - Nicola Marchetti
- Department of Chemical, Pharmaceutical and Agricultural Sciences (DoCPAS), University of Ferrara, 44121 Ferrara, Italy; (N.B.); (A.C.)
| | - Annalaura Mancia
- Department of Life Science and Biotechnologies, University of Ferrara, via L. Borsari 46, 44121 Ferrara, Italy;
- Department of Biology and Marine Science, Marine Science Research Institute, 2800 University Blvd N, Jacksonville, FL 32211, USA
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Andelic M, Marchi M, Marcuzzo S, Lombardi R, Faber CG, Lauria G, Salvi E. Archival skin biopsy specimens as a tool for miRNA-based diagnosis: Technical and post-analytical considerations. Mol Ther Methods Clin Dev 2023; 31:101116. [PMID: 37808256 PMCID: PMC10550798 DOI: 10.1016/j.omtm.2023.101116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 09/13/2023] [Indexed: 10/10/2023]
Abstract
Archived specimens, taken by standardized procedures in clinical practice, represent a valuable resource in translational medicine. Their use in retrospective molecular-based studies could provide disease and therapy predictors. Microfluidic array is a user-friendly and cost-effective method allowing profiling of hundreds of microRNAs (miRNAs) from a low amount of RNA. However, even though tissue miRNAs may include potentially robust biomarkers, non-uniformed post-analytical pipelines could hinder translation into clinics. In this study, epidermal RNA from archival skin biopsy specimens was isolated from patients with peripheral neuropathy and healthy individuals. Unbiased miRNA profiling was performed using RT-qPCR-based microfluidic array. We demonstrated that RNA obtained from archival tissue is appropriate for miRNA profiling, providing evidence that different practices in threshold selection could significantly influence the final results. We showed the utility of software-based quality control for amplification curves. We revealed that selection of the most stable reference and the calculation of geometric mean are suitable when utilizing microfluidic arrays without known references. By applying appropriate post-analytical settings, we obtained miRNA profile of human epidermis associated with biological processes and a list of suitable references. Our results, which outline technical and post-analytical considerations, support the broad use of archived specimens for miRNA analysis to unravel disease-specific molecular signatures.
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Affiliation(s)
- Mirna Andelic
- Neuroalgology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
- School of Mental Health and Neuroscience, Maastricht University Medical Centre+, P.O. Box 5800, 6202 AZ Maastricht, the Netherlands
| | - Margherita Marchi
- Neuroalgology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Stefania Marcuzzo
- Neuroimmunology and Neuromuscular Diseases Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Raffaella Lombardi
- Neuroalgology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Catharina G. Faber
- Department of Neurology and School for Mental Health and Neuroscience, Maastricht University Medical Centre+, P.O. Box 5800, 6202 AZ Maastricht, the Netherlands
| | - Giuseppe Lauria
- Neuroalgology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
- Department of Medical Biotechnology and Translational Medicine, University of Milan, 20133 Milan, Italy
| | - Erika Salvi
- Neuroalgology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
- Data Science Center, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
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Varvil MS, Bailey T, Dhawan D, Knapp DW, Ramos-Vara JA, dos Santos AP. The miRNome of canine invasive urothelial carcinoma. Front Vet Sci 2022; 9:945638. [PMID: 36072391 PMCID: PMC9443663 DOI: 10.3389/fvets.2022.945638] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/01/2022] [Indexed: 11/23/2022] Open
Abstract
Urothelial carcinoma (UC) comprises up to 2% of all naturally occurring neoplasia in dogs and can be challenging to diagnose. MicroRNAs (miRNAs) have been reported to be dysregulated in numerous diseases, including neoplasia. MiRNA expression has been evaluated in human UC, but there is limited information regarding the miRNA transcriptome of UC in dogs. Our study aimed to evaluate differential miRNA expression in bladder tissue collected from normal canine urothelium and canine invasive UC (iUC) to elucidate the dysregulated pathways in canine UC. Next-Generation RNA sequencing (RNA-Seq) was performed for dogs with UC (n = 29) and normal canine urothelium (n = 4). Raw RNA data were subjected to normalization, and pairwise comparison was performed using EdgeR with Benjamini-Hochberg FDR multiple testing correction (p < 0.05; >2-fold change) comparing tissue samples of normal urothelium to canine iUC samples. Principal component analysis and hierarchical cluster analysis were performed. MiRNA of FFPE tissue samples of separate iUC (n = 5) and normal urothelium (n = 5) were used to evaluate five miRNAs using RT-qPCR. Pathway analysis was performed utilizing miRWalk, STRING database, and Metascape utilizing KEGG pathways and GO terms databases. Twenty-eight miRNAs were differentially expressed (DE) by RNA-Seq. RT-qPCR confirmed that four miRNAs are significantly downregulated in UC compared to healthy urothelial samples (miR-105a, miR-143, miR-181a, and miR-214). Principal component analysis and hierarchical cluster analysis showed separation between miRNAs in iUC and the control group. The DE miRNAs are most often associated with gene silencing by miRNA, miRNAs in cancer, and miRNAs involved in DNA damage responses. Proteins involved include HRAS, KRAS, ARAF, RAF1, MAPK1, MAP2K1, MAPK3, FGFR3, EGFR, HBEGF, RASSF1, E2F2, E2F3, ERBB2, SRC, MMP1, and UP3KA. The differential expression of miRNAs in canine iUC compared to normal canine urothelial tissue indicates that these markers should be further evaluated for their potential role as diagnostic and therapeutic targets.
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Affiliation(s)
- Mara S. Varvil
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN, United States
| | - Taylor Bailey
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN, United States
| | - Deepika Dhawan
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, IN, United States
| | - Deborah W. Knapp
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, IN, United States
- Center for Cancer Research, Purdue University Center for Cancer Research, West Lafayette, IN, United States
| | - José A. Ramos-Vara
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN, United States
- Center for Cancer Research, Purdue University Center for Cancer Research, West Lafayette, IN, United States
| | - Andrea P. dos Santos
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN, United States
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5
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Factors influencing circulating microRNAs as biomarkers for liver diseases. Mol Biol Rep 2022; 49:4999-5016. [DOI: 10.1007/s11033-022-07170-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 01/19/2022] [Indexed: 11/09/2022]
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6
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Veryaskina YA, Titov SE, Ivanov MK, Ruzankin PS, Tarasenko AS, Shevchenko SP, Kovynev IB, Stupak EV, Pospelova TI, Zhimulev IF. Selection of reference genes for quantitative analysis of microRNA expression in three different types of cancer. PLoS One 2022; 17:e0254304. [PMID: 35176014 PMCID: PMC8853544 DOI: 10.1371/journal.pone.0254304] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 01/30/2022] [Indexed: 11/18/2022] Open
Abstract
MicroRNAs (miRNAs) are promising biomarkers in cancer research. Quantitative PCR (qPCR), also known as real-time PCR, is the most frequently used technique for measuring miRNA expression levels. The use of this technique, however, requires that expression data be normalized against reference genes. The problem is that a universal internal control for quantitative analysis of miRNA expression by qPCR has yet to be known. The aim of this work was to find the miRNAs with stable expression in the thyroid gland, brain and bone marrow according to NanoString nCounter miRNA quantification data. As a results, the most stably expressed miRNAs were as follows: miR-361-3p, -151a-3p and -29b-3p in the thyroid gland; miR-15a-5p, -194-5p and -532-5p in the brain; miR-140-5p, -148b-3p and -362-5p in bone marrow; and miR-423-5p, -28-5p and -532-5p, no matter what tissue type. These miRNAs represent promising reference genes for miRNA quantification by qPCR.
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Affiliation(s)
- Yuliya A. Veryaskina
- Laboratory of Gene Engineering, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
- Department of the Structure and Function of Chromosomes, Laboratory of Molecular Genetics Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
- * E-mail:
| | - Sergei E. Titov
- Department of the Structure and Function of Chromosomes, Laboratory of Molecular Genetics Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
- AO Vector-Best, Novosibirsk, Russia
| | | | - Pavel S. Ruzankin
- Sobolev Institute of Mathematics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
- Department of Mathematics and Mechanics, Novosibirsk State University, Novosibirsk, Russia
| | - Anton S. Tarasenko
- Sobolev Institute of Mathematics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
- Department of Mathematics and Mechanics, Novosibirsk State University, Novosibirsk, Russia
| | | | - Igor B. Kovynev
- Department of Therapy, Hematology and Transfusiology, Novosibirsk State Medical University, Novosibirsk, Russia
| | - Evgenij V. Stupak
- Department of Neurosurgery, Ya.L. Tsivyan Novosibirsk Research Institute of Traumatology and Orthopedics, Novosibirsk, Russia
| | - Tatiana I. Pospelova
- Department of Therapy, Hematology and Transfusiology, Novosibirsk State Medical University, Novosibirsk, Russia
| | - Igor F. Zhimulev
- Department of the Structure and Function of Chromosomes, Laboratory of Molecular Genetics Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
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7
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Veryaskina YA, Titov SE, Zhimulev IF. Reference Genes for qPCR-Based miRNA Expression Profiling in 14 Human Tissues. Med Princ Pract 2022; 31:322-332. [PMID: 35354155 PMCID: PMC9485981 DOI: 10.1159/000524283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 03/22/2022] [Indexed: 11/19/2022] Open
Abstract
MicroRNAs (miRNAs) are promising biomarkers for the diagnosis and prognosis of various diseases. Quantitative PCR is the most frequently used method of measuring expression levels of miRNA. However, the lack of validated reference genes represents the main source of potential bias in results. It is normal practice to use small nuclear RNAs as reference genes; however, they often have variable expression. Researchers tend to prefer the most stable reference genes in each experiment. The review includes reference genes for the following tissue types: gliomas, lung cancer, melanoma, gastric cancer, liver cancer, prostate cancer, breast cancer, thyroid cancer, ovarian cancer, cervical cancer, endometrial cancer, rectal cancer, blood tumors, and placental tissues.
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Affiliation(s)
- Yulia Andreevna Veryaskina
- Laboratory of Gene Engineering, Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russian Federation
- Department of the Structure and Function of Chromosomes, Laboratory of Molecular Genetics Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russian Federation
- *Yulia Andreevna Veryaskina,
| | - Sergei Evgenievich Titov
- Department of the Structure and Function of Chromosomes, Laboratory of Molecular Genetics Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russian Federation
- AO Vector-Best, Novosibirsk, Russian Federation
| | - Igor Fyodorovich Zhimulev
- Department of the Structure and Function of Chromosomes, Laboratory of Molecular Genetics Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russian Federation
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Schofield AL, Brown JP, Brown J, Wilczynska A, Bell C, Glaab WE, Hackl M, Howell L, Lee S, Dear JW, Remes M, Reeves P, Zhang E, Allmer J, Norris A, Falciani F, Takeshita LY, Seyed Forootan S, Sutton R, Park BK, Goldring C. Systems analysis of miRNA biomarkers to inform drug safety. Arch Toxicol 2021; 95:3475-3495. [PMID: 34510227 PMCID: PMC8492583 DOI: 10.1007/s00204-021-03150-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 08/23/2021] [Indexed: 02/06/2023]
Abstract
microRNAs (miRNAs or miRs) are short non-coding RNA molecules which have been shown to be dysregulated and released into the extracellular milieu as a result of many drug and non-drug-induced pathologies in different organ systems. Consequently, circulating miRs have been proposed as useful biomarkers of many disease states, including drug-induced tissue injury. miRs have shown potential to support or even replace the existing traditional biomarkers of drug-induced toxicity in terms of sensitivity and specificity, and there is some evidence for their improved diagnostic and prognostic value. However, several pre-analytical and analytical challenges, mainly associated with assay standardization, require solutions before circulating miRs can be successfully translated into the clinic. This review will consider the value and potential for the use of circulating miRs in drug-safety assessment and describe a systems approach to the analysis of the miRNAome in the discovery setting, as well as highlighting standardization issues that at this stage prevent their clinical use as biomarkers. Highlighting these challenges will hopefully drive future research into finding appropriate solutions, and eventually circulating miRs may be translated to the clinic where their undoubted biomarker potential can be used to benefit patients in rapid, easy to use, point-of-care test systems.
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Affiliation(s)
- Amy L Schofield
- MRC Centre for Drug Safety Science, Department of Pharmacology and Therapeutics, University of Liverpool, Sherrington Buildings, Ashton Street, Liverpool, L69 3GE, UK
| | - Joseph P Brown
- MRC Centre for Drug Safety Science, Department of Pharmacology and Therapeutics, University of Liverpool, Sherrington Buildings, Ashton Street, Liverpool, L69 3GE, UK
| | - Jack Brown
- MRC Centre for Drug Safety Science, Department of Pharmacology and Therapeutics, University of Liverpool, Sherrington Buildings, Ashton Street, Liverpool, L69 3GE, UK
| | - Ania Wilczynska
- bit.bio, Babraham Research Campus, The Dorothy Hodgkin Building, Cambridge, CB22 3FH, UK
| | - Catherine Bell
- CVRM Safety, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Warren E Glaab
- Merck & Co., Inc, 770 Sumneytown Pike, West Point, PA, 19486, USA
| | | | - Lawrence Howell
- GlaxoSmithKline (GSK), Stevenage, Greater Cambridge Area, UK
| | - Stephen Lee
- ABHI, 1 Duchess St, 4th Floor, Suite 2, London, W1W 6AN, UK
| | - James W Dear
- Centre for Cardiovascular Science, The Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Mika Remes
- Genomics EMEA, QIAGEN Aarhus, Prismet, Silkeborgvej 2, 8000, Aarhus C, Denmark
| | - Paul Reeves
- Arcis Biotechnology Limited, Suite S07, Techspace One, Sci-tech Daresbury, Keckwick Lane, Daresbury, Warrington, WA4 4AB, UK
| | - Eunice Zhang
- Wolfson Centre for Personalised Medicine, Department of Pharmacology and Therapeutics, University of Liverpool, Crown Street, Liverpool, L69 3BX, UK
| | - Jens Allmer
- Applied Bioinformatics, Bioscience, Wageningen University and Research, Droevendaalsesteeg 4, 6708 PB, Wageningen, The Netherlands
| | - Alan Norris
- MRC Centre for Drug Safety Science, Department of Pharmacology and Therapeutics, University of Liverpool, Sherrington Buildings, Ashton Street, Liverpool, L69 3GE, UK
| | - Francesco Falciani
- Computational Biology Facility, MerseyBio, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Louise Y Takeshita
- Computational Biology Facility, MerseyBio, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Shiva Seyed Forootan
- MRC Centre for Drug Safety Science, Department of Pharmacology and Therapeutics, University of Liverpool, Sherrington Buildings, Ashton Street, Liverpool, L69 3GE, UK
| | - Robert Sutton
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Biosciences Building, Crown Street, Liverpool, L69 7BE, UK
| | - B Kevin Park
- MRC Centre for Drug Safety Science, Department of Pharmacology and Therapeutics, University of Liverpool, Sherrington Buildings, Ashton Street, Liverpool, L69 3GE, UK
| | - Chris Goldring
- MRC Centre for Drug Safety Science, Department of Pharmacology and Therapeutics, University of Liverpool, Sherrington Buildings, Ashton Street, Liverpool, L69 3GE, UK.
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Sun Q, Guo D, Li S, Xu Y, Jiang M, Li Y, Duan H, Zhuo W, Liu W, Zhu S, Wang L, Zhou T. Combining gene expression signature with clinical features for survival stratification of gastric cancer. Genomics 2021; 113:2683-2694. [PMID: 34129933 DOI: 10.1016/j.ygeno.2021.06.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 05/27/2021] [Accepted: 06/08/2021] [Indexed: 12/24/2022]
Abstract
The AJCC staging system is considered as the golden standard in clinical practice. However, it remains some pitfalls in assessing the prognosis of gastric cancer (GC) patients with similar clinicopathological characteristics. We aim to develop a new clinic and genetic risk score (CGRS) to improve the prognosis prediction of GC patients. We established genetic risk score (GRS) based on nine-gene signature including APOD, CCDC92, CYS1, GSDME, ST8SIA5, STARD3NL, TIMEM245, TSPYL5, and VAT1 based on the gene expression profiles of the training set from the Asian Cancer Research Group (ACRG) cohort by LASSO-Cox regression algorithms. CGRS was established by integrating GRS with clinical risk score (CRS) derived from Surveillance, Epidemiology, and End Results (SEER) database. GRS and CGRS dichotomized GC patients into high and low risk groups with significantly different prognosis in four independent cohorts with different data types, such as microarray, RNA sequencing and qRT-PCR (all HR > 1, all P < 0.001). Both GRS and CGRS were prognostic signatures independent of the AJCC staging system. Receiver operating characteristic (ROC) analysis showed that area under ROC curve of CGRS was larger than that of the AJCC staging system in most cohorts we studied. Nomogram and web tool (http://39.100.117.92/CGRS/) based on CGRS were developed for clinicians to conveniently assess GC prognosis in clinical practice. CGRS integrating genetic signature with clinical features shows strong robustness in predicting GC prognosis, and can be easily applied in clinical practice through the web application.
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Affiliation(s)
- Qiang Sun
- Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, P.R. China
| | - Dongyang Guo
- Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, P.R. China
| | - Shuang Li
- Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, P.R. China
| | - Yanjun Xu
- Zhejiang Cancer Hospital, Hangzhou 310022, P.R. China
| | - Mingchun Jiang
- Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, P.R. China
| | - Yang Li
- Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, P.R. China
| | - Huilong Duan
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou 310027, P.R. China
| | - Wei Zhuo
- Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, P.R. China
| | - Wei Liu
- Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, P.R. China
| | - Shankuan Zhu
- Department of Nutrition and Food Hygiene, Zhejiang University School of Public Health, Hangzhou 310058, P.R. China
| | - Liangjing Wang
- Institute of Gastroenterology, Zhejiang University, Hangzhou 310016, P.R. China; Department of Gastroenterology, the Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310016, P.R. China.
| | - Tianhua Zhou
- Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, P.R. China; Institute of Gastroenterology, Zhejiang University, Hangzhou 310016, P.R. China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang 310003, P.R. China; Department of Molecular Genetics, University of Toronto, Toronto, ONM5S 1A8, Canada.
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Measurements Methods for the Development of MicroRNA-Based Tests for Cancer Diagnosis. Int J Mol Sci 2021; 22:ijms22031176. [PMID: 33503982 PMCID: PMC7865473 DOI: 10.3390/ijms22031176] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/15/2021] [Accepted: 01/22/2021] [Indexed: 12/19/2022] Open
Abstract
Studies investigating microRNAs as potential biomarkers for cancer, immune-related diseases, or cardiac pathogenic diseases, among others, have exponentially increased in the last years. In particular, altered expression of specific miRNAs correlates with the occurrence of several diseases, making these molecules potential molecular tools for non-invasive diagnosis, prognosis, and response to therapy. Nonetheless, microRNAs are not in clinical use yet, due to inconsistencies in the literature regarding the specific miRNAs identified as biomarkers for a specific disease, which in turn can be attributed to several reasons, including lack of assay standardization and reproducibility. Technological limitations in circulating microRNAs measurement have been, to date, the biggest challenge for using these molecules in clinical settings. In this review we will discuss pre-analytical, analytical, and post-analytical challenges to address the potential technical biases and patient-related parameters that can have an influence and should be improved to translate miRNA biomarkers to the clinical stage. Moreover, we will describe the currently available methods for circulating miRNA expression profiling and measurement, underlining their advantages and potential pitfalls.
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11
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Dai Y, Cao Y, Köhler J, Lu A, Xu S, Wang H. Unbiased RNA-Seq-driven identification and validation of reference genes for quantitative RT-PCR analyses of pooled cancer exosomes. BMC Genomics 2021; 22:27. [PMID: 33407103 PMCID: PMC7789813 DOI: 10.1186/s12864-020-07318-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 12/09/2020] [Indexed: 01/08/2023] Open
Abstract
Background Exosomes are extracellular vesicles (EVs) derived from endocytic compartments of eukaryotic cells which contain various biomolecules like mRNAs or miRNAs. Exosomes influence the biologic behaviour and progression of malignancies and are promising candidates as non-invasive diagnostic biomarkers or as targets for therapeutic interventions. Usually, quantitative real-time polymerase chain reaction (qRT-PCR) is used to assess gene expression in cancer exosomes, however, the ideal reference genes for normalization yet remain to be identified. Results In this study, we performed an unbiased analysis of high-throughput mRNA and miRNA-sequencing data from exosomes of patients with various cancer types and identify candidate reference genes and miRNAs in cancer exosomes. The expression stability of these candidate reference genes was evaluated by the coefficient of variation “CV” and the average expression stability value “M”. We subsequently validated these candidate reference genes in exosomes from an independent cohort of ovarian cancer patients and healthy control individuals by qRT-PCR. Conclusions Our study identifies OAZ1 and hsa-miR-6835-3p as the most reliable individual reference genes for mRNA and miRNA quantification, respectively. For superior accuracy, we recommend the use of a combination of reference genes - OAZ1/SERF2/MPP1 for mRNA and hsa-miR-6835-3p/hsa-miR-4468-3p for miRNA analyses.
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Affiliation(s)
- Yao Dai
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Yumeng Cao
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Jens Köhler
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Aiping Lu
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Shaohua Xu
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
| | - Haiyun Wang
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
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Elshafie NO, Nascimento NCD, Lichti NI, Kasinski AL, Childress MO, Santos APD. MicroRNA Biomarkers in Canine Diffuse Large B-Cell Lymphoma. Vet Pathol 2020; 58:34-41. [PMID: 33287683 DOI: 10.1177/0300985820967902] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Lymphoma is among the most common cancer in dogs. Diffuse large B-cell lymphoma (DLBCL) is the predominant type, accounting for up to half of all cases. Definitive diagnosis of DLBCL relies on cytologic evaluation with immunophenotyping, or histopathology and immunohistochemistry when needed. A rapid and specific molecular test aiding in the diagnosis could be beneficial. Noncoding microRNAs (miRNAs) are regulators of gene expression involved in a variety of cellular processes, including cell differentiation, cell cycle progression, and apoptosis. Not surprisingly, miRNA expression is aberrant in diseases such as cancers. Their high stability and abundance in tissues make them promising biomarkers for diagnosing and monitoring diseases. This study aimed to identify miRNA signatures of DLBCL to develop ancillary molecular diagnostic tools. miRNA was isolated from formalin-fixed, paraffin-embedded lymph node tissue from 22 DLBCL and 14 nonneoplastic controls. Relative gene expression of 8 tumor-regulating miRNAs was achieved by RT-qPCR (reverse transcriptase quantitative polymerase chain reaction). The results showed downregulation of the let-7 family of miRNAs and miR-155, whereas miR-34a was upregulated in DLBCL compared to the controls. We demonstrated that the combination of expression levels of miR-34a and let-7f or of let-7b and let-7f achieved 100% differentiation between DLBCL and controls. Furthermore, let-7f alone discriminated DLBCL from nonneoplastic tissue in 97% of cases. Our results represent one step forward in search of a rapid and accurate ancillary diagnostic test for DLBCL in dogs.
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13
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Borisov E, Knyazeva M, Novak V, Zabegina L, Prisyazhnaya T, Karizkiy A, Berlev I, Malek A. Analysis of Reciprocally Dysregulated miRNAs in Eutopic Endometrium Is a Promising Approach for Low Invasive Diagnostics of Adenomyosis. Diagnostics (Basel) 2020; 10:E782. [PMID: 33022981 PMCID: PMC7601074 DOI: 10.3390/diagnostics10100782] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/26/2020] [Accepted: 10/01/2020] [Indexed: 01/07/2023] Open
Abstract
Endometriosis is a chronic disease characterized by the growth of endometrial tissue outside of the uterine cavity. Endometriosis affects up to 10% of women of reproductive age and has great social impact. The diagnostics of endometriosis are based on clinical appearance, ultrasound, and magnetic resonance imaging (MRI); however, a diagnosis is frequently hampered by the absence of objective criteria. Adenomyosis (AM) is a particular type of endometriosis wherein the spread of the ectopic endometrial gland is limited by the uterine myometrium. Alteration of the microRNA expression profile in the eutopic endometrium can be associated with AM, and may be assayed for diagnostic purposes. In the presented study, we aimed to explore the diagnostic potency of this approach. Eutopic endometrium specimens were collected from patients (n = 33) and healthy women (n = 30). The microRNA expression was profiled to select individual microRNAs with AM-associated expression alterations. A new method of two-tailed RT-qPCR microRNA analysis was applied to assay potential markers. The expression ratios of reciprocally dysregulated microRNAs were calculated, and the diagnostic potency of these parameters was evaluated by receiver operation curve (ROC) analysis. Mir-10b, miR-200c and miR-191 were significantly dysregulated in the eutopic endometrium of AM patients. The expression ratio of reciprocally dysregulated microRNAs allowed us to diagnose AM with a range of sensitivity from 65% to 74%, and of specificity from 72% to 86%. The analysis of microRNAs from the eutopic endometrium might present a promising low-invasive method of AM diagnostics.
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Affiliation(s)
- Evgeny Borisov
- Subcellular Technology Lab., N.N. Petrov National Medical Research Center of Oncology, 197758 Saint-Petersburg, Russia; (E.B.); (M.K.); (L.Z.); (I.B.)
- Oncosystem Ltd., 121205 Moscow, Russia
| | - Margarita Knyazeva
- Subcellular Technology Lab., N.N. Petrov National Medical Research Center of Oncology, 197758 Saint-Petersburg, Russia; (E.B.); (M.K.); (L.Z.); (I.B.)
- Oncosystem Ltd., 121205 Moscow, Russia
- Institute of Biomedical Systems and Biotechnologies, Peter the Great St. Petersburg Polytechnic University, 195251 Saint-Petersburg, Russia
| | - Veronika Novak
- Department of Obstetrics and Gynecology, North-Western State Medical University Named after I.I. Mechnikov, 195067 Saint-Petersburg, Russia; (V.N.); (T.P.)
| | - Lidia Zabegina
- Subcellular Technology Lab., N.N. Petrov National Medical Research Center of Oncology, 197758 Saint-Petersburg, Russia; (E.B.); (M.K.); (L.Z.); (I.B.)
- Oncosystem Ltd., 121205 Moscow, Russia
- Institute of Biomedical Systems and Biotechnologies, Peter the Great St. Petersburg Polytechnic University, 195251 Saint-Petersburg, Russia
| | - Tatyana Prisyazhnaya
- Department of Obstetrics and Gynecology, North-Western State Medical University Named after I.I. Mechnikov, 195067 Saint-Petersburg, Russia; (V.N.); (T.P.)
| | - Aleksey Karizkiy
- Information Technologies and Programming Faculty, Information Technologies, Mechanics and Optics University, 197101 Saint-Petersburg, Russia;
| | - Igor Berlev
- Subcellular Technology Lab., N.N. Petrov National Medical Research Center of Oncology, 197758 Saint-Petersburg, Russia; (E.B.); (M.K.); (L.Z.); (I.B.)
- Department of Obstetrics and Gynecology, North-Western State Medical University Named after I.I. Mechnikov, 195067 Saint-Petersburg, Russia; (V.N.); (T.P.)
| | - Anastasia Malek
- Subcellular Technology Lab., N.N. Petrov National Medical Research Center of Oncology, 197758 Saint-Petersburg, Russia; (E.B.); (M.K.); (L.Z.); (I.B.)
- Oncosystem Ltd., 121205 Moscow, Russia
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Jahn SC, Gay LA, Weaver CJ, Renne R, Langaee TY, Stacpoole PW, James MO. Age-Related Changes in miRNA Expression Influence GSTZ1 and Other Drug Metabolizing Enzymes. Drug Metab Dispos 2020; 48:563-569. [PMID: 32357971 DOI: 10.1124/dmd.120.090639] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 04/07/2020] [Indexed: 11/22/2022] Open
Abstract
Previous work has shown that hepatic levels of human glutathione transferase zeta 1 (GSTZ1) protein, involved in tyrosine catabolism and responsible for metabolism of the investigational drug dichloroacetate, increase in cytosol after birth before reaching a plateau around age 7. However, the mechanism regulating this change of expression is still unknown, and previous studies showed that GSTZ1 mRNA levels did not correlate with GSTZ1 protein expression. In this study, we addressed the hypothesis that microRNAs (miRNAs) could regulate expression of GSTZ1. We obtained liver samples from donors aged less than 1 year or older than 13 years and isolated total RNA for use in a microarray to identify miRNAs that were downregulated in the livers of adults compared with children. From a total of 2578 human miRNAs tested, 63 miRNAs were more than 2-fold down-regulated in adults, of which miR-376c-3p was predicted to bind to the 3' untranslated region of GSTZ1 mRNA. There was an inverse correlation of miR-376c-3p and GSTZ1 protein expression in the liver samples. Using cell culture, we confirmed that miR-376c-3p could downregulate GSTZ1 protein expression. Our findings suggest that miR-376c-3p prevents production of GSTZ1 through inhibition of translation. These experiments further our understanding of GSTZ1 regulation. Furthermore, our array results provide a database resource for future studies on mechanisms regulating human hepatic developmental expression. SIGNIFICANCE STATEMENT: Hepatic glutathione transferase zeta 1 (GSTZ1) is responsible for metabolism of the tyrosine catabolite maleylacetoacetate as well as the investigational drug dichloroacetate. Through examination of microRNA (miRNA) expression in liver from infants and adults and studies in cells, we showed that expression of GSTZ1 is controlled by miRNA. This finding has application to the dosing regimen of the drug dichloroacetate. The miRNA expression profiles are provided and will prove useful for future studies of drug-metabolizing enzymes in infants and adults.
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Affiliation(s)
- Stephan C Jahn
- Departments of Medicinal Chemistry (S.C.J., C.J.W., M.O.J.), Pharmacotherapy and Translational Research (T.Y.L.), Medicine (P.W.S.), Biochemistry and Molecular Biology (P.W.S.), and Molecular Genetics and Microbiology (L.A.G., R.R.), University of Florida, Gainesville, Florida
| | - Lauren A Gay
- Departments of Medicinal Chemistry (S.C.J., C.J.W., M.O.J.), Pharmacotherapy and Translational Research (T.Y.L.), Medicine (P.W.S.), Biochemistry and Molecular Biology (P.W.S.), and Molecular Genetics and Microbiology (L.A.G., R.R.), University of Florida, Gainesville, Florida
| | - Claire J Weaver
- Departments of Medicinal Chemistry (S.C.J., C.J.W., M.O.J.), Pharmacotherapy and Translational Research (T.Y.L.), Medicine (P.W.S.), Biochemistry and Molecular Biology (P.W.S.), and Molecular Genetics and Microbiology (L.A.G., R.R.), University of Florida, Gainesville, Florida
| | - Rolf Renne
- Departments of Medicinal Chemistry (S.C.J., C.J.W., M.O.J.), Pharmacotherapy and Translational Research (T.Y.L.), Medicine (P.W.S.), Biochemistry and Molecular Biology (P.W.S.), and Molecular Genetics and Microbiology (L.A.G., R.R.), University of Florida, Gainesville, Florida
| | - Taimour Y Langaee
- Departments of Medicinal Chemistry (S.C.J., C.J.W., M.O.J.), Pharmacotherapy and Translational Research (T.Y.L.), Medicine (P.W.S.), Biochemistry and Molecular Biology (P.W.S.), and Molecular Genetics and Microbiology (L.A.G., R.R.), University of Florida, Gainesville, Florida
| | - Peter W Stacpoole
- Departments of Medicinal Chemistry (S.C.J., C.J.W., M.O.J.), Pharmacotherapy and Translational Research (T.Y.L.), Medicine (P.W.S.), Biochemistry and Molecular Biology (P.W.S.), and Molecular Genetics and Microbiology (L.A.G., R.R.), University of Florida, Gainesville, Florida
| | - Margaret O James
- Departments of Medicinal Chemistry (S.C.J., C.J.W., M.O.J.), Pharmacotherapy and Translational Research (T.Y.L.), Medicine (P.W.S.), Biochemistry and Molecular Biology (P.W.S.), and Molecular Genetics and Microbiology (L.A.G., R.R.), University of Florida, Gainesville, Florida
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15
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Terrinoni A, Calabrese C, Basso D, Aita A, Caporali S, Plebani M, Bernardini S. The circulating miRNAs as diagnostic and prognostic markers. Clin Chem Lab Med 2020; 57:932-953. [PMID: 30838832 DOI: 10.1515/cclm-2018-0838] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Accepted: 10/23/2018] [Indexed: 02/07/2023]
Abstract
A large portion of the human genome transcribes RNA sequences that do not code for any proteins. The first of these sequences was identified in 1993, and the best known noncoding RNAs are microRNA (miRNAs). It is now fully established that miRNAs regulate approximately 30% of the known genes that codify proteins. miRNAs are involved in several biological processes, like cell proliferation, differentiation, apoptosis and metastatization. These RNA products regulate gene expression at the post-transcriptional level, modulating or inhibiting protein expression by interacting with specific sequences of mRNAs. Mature miRNAs can be detected in blood plasma, serum and also in a wide variety of biological fluids. They can be found associated with proteins, lipids as well as enclosed in exosome vesicles. We know that circulating miRNAs (C-miRNAs) can regulate several key cellular processes in tissues different from the production site. C-miRNAs behave as endogenous mediators of RNA translation, and an extraordinary knowledge on their function has been obtained in the last years. They can be secreted in different tissue cells and associated with specific pathological conditions. Significant evidence indicates that the initiation and progression of several pathologies are "highlighted" by the presence of specific C-miRNAs, underlining their potential diagnostic relevance as clinical biomarkers. Here we review the current literature on the possible use of this new class of molecules as clinical biomarkers of diseases.
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Affiliation(s)
- Alessandro Terrinoni
- Department of Experimental Medicine, University of Rome Tor Vergata, Via Montpellier, 1, 00133 Rome, Italy
| | - Cosimo Calabrese
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Daniela Basso
- Department of Medicine - DIMED; Department of Laboratory Medicine, University-Hospital of Padova, Padova, Italy
| | - Ada Aita
- Department of Medicine - DIMED; Department of Laboratory Medicine, University-Hospital of Padova, Padova, Italy
| | - Sabrina Caporali
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Mario Plebani
- Department of Medicine - DIMED; Department of Laboratory Medicine, University-Hospital of Padova, Padova, Italy
| | - Sergio Bernardini
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
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16
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Pratama MY, Cavalletto L, Tiribelli C, Chemello L, Pascut D. Selection and validation of miR-1280 as a suitable endogenous normalizer for qRT-PCR Analysis of serum microRNA expression in Hepatocellular Carcinoma. Sci Rep 2020; 10:3128. [PMID: 32081930 PMCID: PMC7035418 DOI: 10.1038/s41598-020-59682-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 01/30/2020] [Indexed: 01/26/2023] Open
Abstract
Normalization procedures for the qRT-PCR analysis of miRNA in biological samples are recommended to reduce the variability caused by pre-analytical factors. Since there is no universal standardized normalization strategy for miRNA qRT-PCR studies, we conducted a throughout study to evaluate a panel of small non-coding RNAs (sncRNAs) as reference gene candidate for biomarker studies in serum samples of patients with hepatocellular carcinoma (HCC). Five sncRNAs (miR-1280, miR-1275, SNORD-116, SNORD-68, and U6) were chosen as candidate of reference genes. This study included 122 patients with HCC and was organized into a "pilot phase" consisting of 20 serum samples of HCC patients, and a "validation phase" of 102 patients. Expression level of these candidates were analyzed by qRT-PCR. Assessment of gene stability was performed using four different integrative platforms (geNorm NormFinder, Bestkeeper, and the Delta Ct method). To determine the gene stability during the follow-up of the patient, we extend the analysis of the validation cohort at T1 (1 month after treatment) and T2 (6 month after treatment). MiR-1280 was identified as the most stably expressed reference gene in both pilot and validation phase also during the follow-up. MiR-1280 appears a reliable reference gene candidate in biomarker studies.
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Affiliation(s)
- Muhammad Yogi Pratama
- Fondazione Italiana Fegato - ONLUS, Liver Research Center, AREA Science Park, Basovizza, Trieste, Italy
- Universitas Hasanuddin, Faculty of Medicine, Makassar, Indonesia
| | - Luisa Cavalletto
- Department of Medicine - DIMED, University-Hospital of Padova, Padova, Italy
| | - Claudio Tiribelli
- Fondazione Italiana Fegato - ONLUS, Liver Research Center, AREA Science Park, Basovizza, Trieste, Italy
| | - Liliana Chemello
- Department of Medicine - DIMED, University-Hospital of Padova, Padova, Italy.
| | - Devis Pascut
- Fondazione Italiana Fegato - ONLUS, Liver Research Center, AREA Science Park, Basovizza, Trieste, Italy
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Liu J, Jia E, Shi H, Li X, Jiang G, Chi C, Liu W, Zhang D. Selection of reference genes for miRNA quantitative PCR and its application in miR-34a/Sirtuin-1 mediated energy metabolism in Megalobrama amblycephala. FISH PHYSIOLOGY AND BIOCHEMISTRY 2019; 45:1663-1681. [PMID: 31127447 DOI: 10.1007/s10695-019-00658-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 05/06/2019] [Indexed: 05/19/2023]
Abstract
MiRNAs are small, non-coding RNAs that downregulate gene expression at post-transcriptional levels. They have emerged as important regulators involved in metabolism, immunity, and cancer. Real-time quantitative PCR (RT-qPCR) is an effective and main method for quantifying target miRNA. For robust RT-qPCR method, suitable reference genes play crucial roles in data normalization. Blunt snout bream (Megalobrama amblycephala) is an economically important aquaculture species; however, no reference genes dedicated for qPCR method has been identified for this species so far. The objective of this study was to screen stable reference genes for miRNA RT-qPCR and demonstrated its application in energy metabolism in blunt snout bream. The stabilities of ten potential reference genes (miR-21-1-5p, miR-107a-3p, miR-222a-3p, miR-146a-5p, miR-101a-3p, miR-22a-3p, miR-103-3p, miR-456-3p, miR-221-3p, and U6 (RNU6A)) were evaluated in nine tissues (brain, muscle, liver, skin, spleen, heart, gill, intestine, and eye) under normal condition and in three tissues (liver, intestine, and spleen) under four stresses (heat stress, ammonia stress, bacterial challenge, and glycolipid stress). Using GeNorm, NormFinder, and RefFinder softwares, we discovered that different tissues and stresses are both important variability factors for the expression stability of miRNAs. After verifying miR-34a/Sirtuin-1 expressions in high-carbohydrate diet-induced blunt snout bream, we eventually identified that the most stable reference gene in this species was miR-221-3p, and the best combination of reference genes were miR-221-3p and miR-103-3p.
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Affiliation(s)
- Jie Liu
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing, 210095, People's Republic of China
| | - Erteng Jia
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing, 210095, People's Republic of China
| | - Huajuan Shi
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing, 210095, People's Republic of China
| | - Xiangfei Li
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing, 210095, People's Republic of China
| | - Guangzhen Jiang
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing, 210095, People's Republic of China
| | - Cheng Chi
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing, 210095, People's Republic of China
| | - Wenbin Liu
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing, 210095, People's Republic of China
| | - Dingdong Zhang
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing, 210095, People's Republic of China.
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Zárybnický T, Matoušková P, Ambrož M, Šubrt Z, Skálová L, Boušová I. The Selection and Validation of Reference Genes for mRNA and microRNA Expression Studies in Human Liver Slices Using RT-qPCR. Genes (Basel) 2019; 10:genes10100763. [PMID: 31569378 PMCID: PMC6826422 DOI: 10.3390/genes10100763] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 09/25/2019] [Accepted: 09/27/2019] [Indexed: 01/06/2023] Open
Abstract
The selection of a suitable combination of reference genes (RGs) for data normalization is a crucial step for obtaining reliable and reproducible results from transcriptional response analysis using a reverse transcription-quantitative polymerase chain reaction. This is especially so if a three-dimensional multicellular model prepared from liver tissues originating from biologically diverse human individuals is used. The mRNA and miRNA RGs stability were studied in thirty-five human liver tissue samples and twelve precision-cut human liver slices (PCLS) treated for 24 h with dimethyl sulfoxide (controls) and PCLS treated with β-naphthoflavone (10 µM) or rifampicin (10 µM) as cytochrome P450 (CYP) inducers. Validation of RGs was performed by an expression analysis of CYP3A4 and CYP1A2 on rifampicin and β-naphthoflavone induction, respectively. Regarding mRNA, the best combination of RGs for the controls was YWHAZ and B2M, while YWHAZ and ACTB were selected for the liver samples and treated PCLS. Stability of all candidate miRNA RGs was comparable or better than that of generally used short non-coding RNA U6. The best combination for the control PCLS was miR-16-5p and miR-152-3p, in contrast to the miR-16-5b and miR-23b-3p selected for the treated PCLS. Our results showed that the candidate RGs were rather stable, especially for miRNA in human PCLS.
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Affiliation(s)
- Tomáš Zárybnický
- Department of Biochemical Sciences, Charles University, Faculty of Pharmacy in Hradec Králové, 500 05 Hradec Králové, Czech Republic.
| | - Petra Matoušková
- Department of Biochemical Sciences, Charles University, Faculty of Pharmacy in Hradec Králové, 500 05 Hradec Králové, Czech Republic.
| | - Martin Ambrož
- Department of Biochemical Sciences, Charles University, Faculty of Pharmacy in Hradec Králové, 500 05 Hradec Králové, Czech Republic.
| | - Zdeněk Šubrt
- Department of General Surgery, Third Faculty of Medicine and University Hospital Královské Vinohrady, Charles University, 100 34 Prague, Czech Republic.
- Department of Surgery, University Hospital Hradec Králové, 500 05 Hradec Králové, Czech Republic.
| | - Lenka Skálová
- Department of Biochemical Sciences, Charles University, Faculty of Pharmacy in Hradec Králové, 500 05 Hradec Králové, Czech Republic.
| | - Iva Boušová
- Department of Biochemical Sciences, Charles University, Faculty of Pharmacy in Hradec Králové, 500 05 Hradec Králové, Czech Republic.
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19
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Sutliff AK, Shi J, Watson CJW, Hunt MS, Chen G, Zhu HJ, Lazarus P. Potential Regulation of UGT2B10 and UGT2B7 by miR-485-5p in Human Liver. Mol Pharmacol 2019; 96:674-682. [PMID: 31554697 PMCID: PMC6820218 DOI: 10.1124/mol.119.115881] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 09/19/2019] [Indexed: 11/22/2022] Open
Abstract
The UDP-glucuronosyltransferase (UGT) family of enzymes is important in the metabolic elimination of a variety of endogenous compounds such as bile acids, steroids, and fat-soluble vitamins, as well as exogenous compounds including many pharmaceuticals. The UGT2B subfamily is a major family of UGT enzymes expressed in human liver. The identification of novel mechanisms including post-transcriptional regulation by microRNA (miRNA) contributes to interindividual variability in UGT2B expression and is a crucial component in predicting patient drug response. In the present study, a high-resolution liquid chromatography-tandem mass spectrometry method was employed to measure UGT2B protein levels in a panel of human liver microsomal samples (n = 62). Concurrent in silico analysis identified eight candidate miRNAs as potential regulators of UGT2B enzymes. Comparison of UGT2B protein expression and candidate miRNA levels from human liver samples demonstrated a significant inverse correlation between UGT2B10 and UGT2B15 and one of these candidate miRNAs, miR-485-5p. A near-significant correlation was also observed between UGT2B7 and miR-485-5p expression. In vitro analysis using luciferase-containing vectors suggested an interaction of miR-485-5p within the UGT2B10 3'-untranslated region (UTR), and significant reduction in luciferase activity was also observed for a luciferase vector containing the UGT2B7 3'-UTR; however, none was observed for the UBT2B15 3'-UTR. UGT2B10 and UGT2B7 activities were probed using nicotine and 3'-azido-3'-deoxythymidine, respectively, and significant decreases in glucuronidation activity were observed for both substrates in HuH-7 and Hep3B cells upon overexpression of miR-485-5p mimic. This is the first study demonstrating a regulatory role of miR-485-5p for multiple UGT2B enzymes. SIGNIFICANCE STATEMENT: The purpose of this study was to identify novel epigenetic miRNA regulators of the UGT2B drug-metabolizing enzymes in healthy human liver samples. Our results indicate that miRNA 485-5p is a novel regulator of UGT2B7 and UGT2B10, which play an important role in the metabolism of many commonly prescribed medications, carcinogens, and endogenous compounds. This study identified potential miRNA-UGT2B mRNA interactions using a novel proteomic approach, with in vitro experiments undertaken to validate these interactions.
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Affiliation(s)
- Aimee K Sutliff
- Department of Pharmaceutical Sciences, Washington State University College of Pharmacy and Pharmaceutical Sciences, Spokane, Washington (A.K.S., C.J.W.W., M.H., G.C., P.L.); and Department of Clinical Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, Michigan (J.S., H.-J.Z.)
| | - Jian Shi
- Department of Pharmaceutical Sciences, Washington State University College of Pharmacy and Pharmaceutical Sciences, Spokane, Washington (A.K.S., C.J.W.W., M.H., G.C., P.L.); and Department of Clinical Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, Michigan (J.S., H.-J.Z.)
| | - Christy J W Watson
- Department of Pharmaceutical Sciences, Washington State University College of Pharmacy and Pharmaceutical Sciences, Spokane, Washington (A.K.S., C.J.W.W., M.H., G.C., P.L.); and Department of Clinical Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, Michigan (J.S., H.-J.Z.)
| | - Martina S Hunt
- Department of Pharmaceutical Sciences, Washington State University College of Pharmacy and Pharmaceutical Sciences, Spokane, Washington (A.K.S., C.J.W.W., M.H., G.C., P.L.); and Department of Clinical Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, Michigan (J.S., H.-J.Z.)
| | - Gang Chen
- Department of Pharmaceutical Sciences, Washington State University College of Pharmacy and Pharmaceutical Sciences, Spokane, Washington (A.K.S., C.J.W.W., M.H., G.C., P.L.); and Department of Clinical Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, Michigan (J.S., H.-J.Z.)
| | - Hao-Jie Zhu
- Department of Pharmaceutical Sciences, Washington State University College of Pharmacy and Pharmaceutical Sciences, Spokane, Washington (A.K.S., C.J.W.W., M.H., G.C., P.L.); and Department of Clinical Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, Michigan (J.S., H.-J.Z.)
| | - Philip Lazarus
- Department of Pharmaceutical Sciences, Washington State University College of Pharmacy and Pharmaceutical Sciences, Spokane, Washington (A.K.S., C.J.W.W., M.H., G.C., P.L.); and Department of Clinical Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, Michigan (J.S., H.-J.Z.)
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20
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Madadi S, Schwarzenbach H, Lorenzen J, Soleimani M. MicroRNA expression studies: challenge of selecting reliable reference controls for data normalization. Cell Mol Life Sci 2019; 76:3497-3514. [PMID: 31089747 PMCID: PMC11105490 DOI: 10.1007/s00018-019-03136-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 04/13/2019] [Accepted: 05/06/2019] [Indexed: 02/06/2023]
Abstract
Accurate determination of microRNA expression levels is a prerequisite in using these small non-coding RNA molecules as novel biomarkers in disease diagnosis and prognosis. Quantitative PCR is the method of choice for measuring the expression levels of microRNAs. However, a major obstacle that affects the reliability of results is the lack of validated reference controls for data normalization. Various non-coding RNAs have previously been used as reference controls, but their use may lead to variations and lack of comparability of microRNA data among the studies. Despite the growing number of studies investigating microRNA profiles to discriminate between healthy and disease stages, robust reference controls for data normalization have so far not been established. In the present article, we provide an overview of different reference controls used in various diseases, and highlight the urgent need for the identification of suitable reference controls to produce reliable data. Our analysis shows, among others, that RNU6 is not an ideal normalizer in studies using patient material from different diseases. Finally, our article tries to disclose the challenges to find a reference control which is uniformly and stably expressed across all body tissues, fluids, and diseases.
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Affiliation(s)
- Soheil Madadi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Heidi Schwarzenbach
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Johan Lorenzen
- Department of Nephrology, University Hospital Zürich, Zurich, Switzerland
| | - Meysam Soleimani
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Hamadan University of Medical Sciences, Hamadan, Iran.
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21
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Wang F, Yang QW, Zhao WJ, Du QY, Chang ZJ. Selection of suitable candidate genes for miRNA expression normalization in Yellow River Carp (Cyprinus carpio. var). Sci Rep 2019; 9:8691. [PMID: 31213623 PMCID: PMC6581906 DOI: 10.1038/s41598-019-44982-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 05/27/2019] [Indexed: 12/19/2022] Open
Abstract
Yellow River carp is widely cultivated in the world due to its economic value in aquaculture, and the faster growth of females compared to males. It is believed that microRNAs (miRNA) are involved in gonadal differentiation and development. qPCR is the most preferred method for miRNA functional analysis. Reliable reference genes for normalization in qRT-PCR are the key to ensuring the accuracy of this method. The aim of present research was to evaluate as well as identify the efficacy of reference genes for miRNA expression using qRT-PCR in Yellow River carp. Nine ncRNAs (miR-101, miR-23a, let7a, miR-26a, miR-146a, miR-451, U6, 5S, and 18S) were chosen and tested in four sample sets: (1) different tissues in adult carp, (2) different tissues in juvenile carp, (3) different early developmental stages of carp, and (4) different developmental stages of carp gonads. The stability and suitability values were calculated using NormFinder, geNorm, and BestKeeper software. The results showed that 5S was a suitable reference gene in different tissues of adult and juvenile carp. The genes 5S, 18S, and U6 were the most stable reference genes in the early developmental stages of carp. Let-7a and miR-23a were considered as the suitable reference genes in the development of gonads. All these reference genes were subsequently validated using miR-430. The results showed that genes 5S and 18S were the most suitable reference genes to normalize miRNA expression under normal growth conditions in early different developmental stages. The genes Let-7a, and miR-23a were the most suitable in different developmental stages. The present study is the first comprehensive study of the stability of miRNA reference genes in Yellow River carp, providing valuable as well as basic data for investigating more accurate miRNA expression during gonadal differentiation and development of carp.
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Affiliation(s)
- Fang Wang
- College of Life Science, Henan Normal University, Xinxiang, Henan, 453007, People's Republic of China
| | - Qian-Wen Yang
- College of Life Science, Henan Normal University, Xinxiang, Henan, 453007, People's Republic of China
| | - Wen-Jie Zhao
- College of Life Science, Henan Normal University, Xinxiang, Henan, 453007, People's Republic of China
| | - Qi-Yan Du
- College of Life Science, Henan Normal University, Xinxiang, Henan, 453007, People's Republic of China
| | - Zhong-Jie Chang
- College of Life Science, Henan Normal University, Xinxiang, Henan, 453007, People's Republic of China.
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22
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Kaija H, Pakanen L, Porvari K. RNU6B, a frequent reference in miRNA expression studies, differentiates between deaths caused by hypothermia and chronic cardiac ischemia. Int J Legal Med 2019; 134:159-162. [PMID: 30904931 PMCID: PMC6949321 DOI: 10.1007/s00414-019-02041-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 03/06/2019] [Indexed: 01/31/2023]
Abstract
Here, we tested the usefulness of small non-coding RNAs as references in quantitative RT-PCR expression analyses in hypothermia and chronic cardiac ischemia as the primary causes of death. Cq values of RNU6B, SCARNA17, SNORD25, and SNORA73A were determined from human cadaver samples of hypothermia and cardiac deaths. Average Cq values of RNU6B were higher in hypothermic and average SCARNA17 Cq values in chronic ischemic samples, but no difference in SNORD25 and SNORA73A Cq values could be seen between the groups. RNU6B expression levels were calculated using SNORD25, SNORA73A, and their combination as the reference in normalization. Expression of RNU6B, a widely used reference, was found to be significantly lower in hypothermia than in chronic cardiac ischemia. In these conditions, RNU6B is a useful marker differentiating hypothermia deaths from chronic ischemic heart disease deaths, but not a valid reference for normalization in expression studies.
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Affiliation(s)
- Helena Kaija
- Faculty of Medicine, Research Unit of Internal Medicine, Department of Forensic Medicine, Medical Research Center Oulu, Oulu University Hospital and University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland
| | - Lasse Pakanen
- Faculty of Medicine, Research Unit of Internal Medicine, Department of Forensic Medicine, Medical Research Center Oulu, Oulu University Hospital and University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland.,Forensic Medicine Unit, National Institute for Health and Welfare, P.O. Box 310, FI-90101, Oulu, Finland
| | - Katja Porvari
- Faculty of Medicine, Research Unit of Internal Medicine, Department of Forensic Medicine, Medical Research Center Oulu, Oulu University Hospital and University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland. .,Faculty of Medicine, Research Unit of Cancer Research and Translational Medicine, Department of Pathology, Medical Research Center Oulu, Oulu University Hospital and University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland.
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23
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Nilsen A, Jonsson M, Aarnes EK, Kristensen GB, Lyng H. Reference MicroRNAs for RT-qPCR Assays in Cervical Cancer Patients and Their Application to Studies of HPV16 and Hypoxia Biomarkers. Transl Oncol 2019; 12:576-584. [PMID: 30660934 PMCID: PMC6349320 DOI: 10.1016/j.tranon.2018.12.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 12/19/2018] [Accepted: 12/20/2018] [Indexed: 02/06/2023] Open
Abstract
MicroRNA (miRNA) expressions in tumor biopsies have shown potential as biomarkers in cervical cancer, but suitable reference RNAs for normalization of reverse transcription quantitative polymerase chain reaction (RT-qPCR) assays in patient cohorts with different clinicopathological characteristics are not available. We aimed to identify the optimal reference miRNAs and apply these to investigate the potential of miR-9-5p as human papilloma virus (HPV) 16 biomarker and miR-210-3p as hypoxia biomarker in cervical cancer. Candidate reference miRNAs were preselected in sequencing data of 90 patients and ranked in a stability analysis by RefFinder. A selection of the most stable miRNAs was evaluated by geNorm and NormFinder analyses of RT-qPCR data of 29 patients. U6 small nuclear RNA (RNU6) was also included in the evaluation. MiR-9-5p and miR-210-3p expression was assessed by RT-qPCR in 45 and 65 patients, respectively. Nine candidates were preselected in the sequencing data after excluding those associated with clinical markers, HPV type, hypoxia status, suboptimal expression levels, and low stability. In RT-qPCR assays, the combination of miR-151-5p, miR-152-3p, and miR-423-3p was identified as the most stable normalization factor across clinical markers, HPV type, and hypoxia status. RNU6 showed poor stability. By applying the optimal reference miRNAs, higher miR-9-5p expression in HPV16- than HPV18-positive tumors and higher miR-210-3p expression in more hypoxic than less hypoxic tumors were found in accordance with the sequencing data. MiR-210-3p was associated with poor outcome by both sequencing and RT-qPCR assays. In conclusion, miR-151-5p, miR-152-3p, and miR-423-3p are suitable reference miRNAs in cervical cancer. MiR-9-5p and miR-210-3p are promising HPV16 and hypoxia biomarkers, respectively.
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Affiliation(s)
- Anja Nilsen
- Department of Radiation Biology, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Marte Jonsson
- Department of Radiation Biology, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Eva-Katrine Aarnes
- Department of Radiation Biology, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Gunnar Balle Kristensen
- Department of Gynaecologic Oncology, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway; Institute for Cancer Genetics and Informatics, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Heidi Lyng
- Department of Radiation Biology, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.
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24
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Mergental H, Stephenson BTF, Laing RW, Kirkham AJ, Neil DAH, Wallace LL, Boteon YL, Widmer J, Bhogal RH, Perera MTPR, Smith A, Reynolds GM, Yap C, Hübscher SG, Mirza DF, Afford SC. Development of Clinical Criteria for Functional Assessment to Predict Primary Nonfunction of High-Risk Livers Using Normothermic Machine Perfusion. Liver Transpl 2018; 24:1453-1469. [PMID: 30359490 PMCID: PMC6659387 DOI: 10.1002/lt.25291] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/06/2018] [Accepted: 05/03/2018] [Indexed: 12/12/2022]
Abstract
Increased use of high-risk allografts is critical to meet the demand for liver transplantation. We aimed to identify criteria predicting viability of organs, currently declined for clinical transplantation, using functional assessment during normothermic machine perfusion (NMP). Twelve discarded human livers were subjected to NMP following static cold storage. Livers were perfused with a packed red cell-based fluid at 37°C for 6 hours. Multilevel statistical models for repeated measures were employed to investigate the trend of perfusate blood gas profiles and vascular flow characteristics over time and the effect of lactate-clearing (LC) and non-lactate-clearing (non-LC) ability of the livers. The relationship of lactate clearance capability with bile production and histological and molecular findings were also examined. After 2 hours of perfusion, median lactate concentrations were 3.0 and 14.6 mmol/L in the LC and non-LC groups, respectively. LC livers produced more bile and maintained a stable perfusate pH and vascular flow >150 and 500 mL/minute through the hepatic artery and portal vein, respectively. Histology revealed discrepancies between subjectively discarded livers compared with objective findings. There were minimal morphological changes in the LC group, whereas non-LC livers often showed hepatocellular injury and reduced glycogen deposition. Adenosine triphosphate levels in the LC group increased compared with the non-LC livers. We propose composite viability criteria consisting of lactate clearance, pH maintenance, bile production, vascular flow patterns, and liver macroscopic appearance. These have been tested successfully in clinical transplantation. In conclusion, NMP allows an objective assessment of liver function that may reduce the risk and permit use of currently unused high-risk livers.
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Affiliation(s)
- Hynek Mergental
- National Institute for Health Research Birmingham, Liver Biomedical Research Centre, College of Medical and Dental SciencesUniversity of Birmingham,Liver UnitQueen Elizabeth Hospital Birmingham, University Hospitals Birmingham National Health Service Foundation Trust
| | - Barnaby T. F. Stephenson
- National Institute for Health Research Birmingham, Liver Biomedical Research Centre, College of Medical and Dental SciencesUniversity of Birmingham
| | - Richard W. Laing
- National Institute for Health Research Birmingham, Liver Biomedical Research Centre, College of Medical and Dental SciencesUniversity of Birmingham,Liver UnitQueen Elizabeth Hospital Birmingham, University Hospitals Birmingham National Health Service Foundation Trust
| | - Amanda J. Kirkham
- Cancer Research UK Clinical Trials Unit, Institute of Cancer and Genomics SciencesUniversity of BirminghamBirminghamUnited Kingdom
| | - Desley A. H. Neil
- Liver UnitQueen Elizabeth Hospital Birmingham, University Hospitals Birmingham National Health Service Foundation Trust
| | - Lorraine L. Wallace
- National Institute for Health Research Birmingham, Liver Biomedical Research Centre, College of Medical and Dental SciencesUniversity of Birmingham
| | - Yuri L. Boteon
- National Institute for Health Research Birmingham, Liver Biomedical Research Centre, College of Medical and Dental SciencesUniversity of Birmingham,Liver UnitQueen Elizabeth Hospital Birmingham, University Hospitals Birmingham National Health Service Foundation Trust
| | - Jeannette Widmer
- National Institute for Health Research Birmingham, Liver Biomedical Research Centre, College of Medical and Dental SciencesUniversity of Birmingham
| | - Ricky H. Bhogal
- National Institute for Health Research Birmingham, Liver Biomedical Research Centre, College of Medical and Dental SciencesUniversity of Birmingham,Liver UnitQueen Elizabeth Hospital Birmingham, University Hospitals Birmingham National Health Service Foundation Trust
| | - M. Thamara P. R. Perera
- Liver UnitQueen Elizabeth Hospital Birmingham, University Hospitals Birmingham National Health Service Foundation Trust
| | - Amanda Smith
- Liver UnitQueen Elizabeth Hospital Birmingham, University Hospitals Birmingham National Health Service Foundation Trust
| | - Gary M. Reynolds
- National Institute for Health Research Birmingham, Liver Biomedical Research Centre, College of Medical and Dental SciencesUniversity of Birmingham
| | - Christina Yap
- Cancer Research UK Clinical Trials Unit, Institute of Cancer and Genomics SciencesUniversity of BirminghamBirminghamUnited Kingdom
| | - Stefan G. Hübscher
- National Institute for Health Research Birmingham, Liver Biomedical Research Centre, College of Medical and Dental SciencesUniversity of Birmingham
| | - Darius F. Mirza
- National Institute for Health Research Birmingham, Liver Biomedical Research Centre, College of Medical and Dental SciencesUniversity of Birmingham,Liver UnitQueen Elizabeth Hospital Birmingham, University Hospitals Birmingham National Health Service Foundation Trust
| | - Simon C. Afford
- National Institute for Health Research Birmingham, Liver Biomedical Research Centre, College of Medical and Dental SciencesUniversity of Birmingham
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25
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Drobna M, Szarzyńska-Zawadzka B, Daca-Roszak P, Kosmalska M, Jaksik R, Witt M, Dawidowska M. Identification of Endogenous Control miRNAs for RT-qPCR in T-Cell Acute Lymphoblastic Leukemia. Int J Mol Sci 2018; 19:ijms19102858. [PMID: 30241379 PMCID: PMC6212946 DOI: 10.3390/ijms19102858] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 09/12/2018] [Accepted: 09/18/2018] [Indexed: 02/06/2023] Open
Abstract
Optimal endogenous controls enable reliable normalization of microRNA (miRNA) expression in reverse-transcription quantitative PCR (RT-qPCR). This is particularly important when miRNAs are considered as candidate diagnostic or prognostic biomarkers. Universal endogenous controls are lacking, thus candidate normalizers must be evaluated individually for each experiment. Here we present a strategy that we applied to the identification of optimal control miRNAs for RT-qPCR profiling of miRNA expression in T-cell acute lymphoblastic leukemia (T-ALL) and in normal cells of T-lineage. First, using NormFinder for an iterative analysis of miRNA stability in our miRNA-seq data, we established the number of control miRNAs to be used in RT-qPCR. Then, we identified optimal control miRNAs by a comprehensive analysis of miRNA stability in miRNA-seq data and in RT-qPCR by analysis of RT-qPCR amplification efficiency and expression across a variety of T-lineage samples and T-ALL cell line culture conditions. We then showed the utility of the combination of three miRNAs as endogenous normalizers (hsa-miR-16-5p, hsa-miR-25-3p, and hsa-let-7a-5p). These miRNAs might serve as first-line candidate endogenous controls for RT-qPCR analysis of miRNAs in different types of T-lineage samples: T-ALL patient samples, T-ALL cell lines, normal immature thymocytes, and mature T-lymphocytes. The strategy we present is universal and can be transferred to other RT-qPCR experiments.
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Affiliation(s)
- Monika Drobna
- Institute of Human Genetics, Polish Academy of Sciences, 60-479 Poznań, Poland.
| | | | | | - Maria Kosmalska
- Institute of Human Genetics, Polish Academy of Sciences, 60-479 Poznań, Poland.
| | - Roman Jaksik
- Department, Silesian University of Technology, 44-100 Gliwice, Poland.
| | - Michał Witt
- Institute of Human Genetics, Polish Academy of Sciences, 60-479 Poznań, Poland.
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26
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Schult P, Roth H, Adams RL, Mas C, Imbert L, Orlik C, Ruggieri A, Pyle AM, Lohmann V. microRNA-122 amplifies hepatitis C virus translation by shaping the structure of the internal ribosomal entry site. Nat Commun 2018; 9:2613. [PMID: 29973597 PMCID: PMC6031695 DOI: 10.1038/s41467-018-05053-3] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 06/11/2018] [Indexed: 12/24/2022] Open
Abstract
The liver-specific microRNA-122 (miR-122) recognizes two conserved sites at the 5′ end of the hepatitis C virus (HCV) genome and contributes to stability, translation, and replication of the viral RNA. We show that stimulation of the HCV internal ribosome entry site (IRES) by miR-122 is essential for efficient viral replication. The mechanism relies on a dual function of the 5′ terminal sequence in the complementary positive (translation) and negative strand (replication), requiring different secondary structures. Predictions and experimental evidence argue for several alternative folds involving the miR-binding region (MBR) adjacent to the IRES and interfering with its function. Mutations in the MBR, designed to suppress these dysfunctional structures indeed stimulate translation independently of miR-122. Conversely, MBR mutants favoring alternative folds show impaired IRES activity. Our results therefore suggest that miR-122 binding assists the folding of a functional IRES in an RNA chaperone-like manner by suppressing energetically favorable alternative secondary structures. The liver-specific microRNA-122 is an essential proviral host factor of Hepatitis C virus replication. Here the authors show that microRNA-122 functions as an RNA chaperone that guides the formation of a functional internal ribosome entry site by preventing energetically more favorable secondary structures within the HCV RNA genome.
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Affiliation(s)
- Philipp Schult
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Im Neuenheimer Feld 344, 69120, Heidelberg, Germany
| | - Hanna Roth
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Im Neuenheimer Feld 344, 69120, Heidelberg, Germany
| | - Rebecca L Adams
- Department of Molecular, Cellular and Developmental Biology, Yale University, 219 Prospect St, New Haven, CT, 06511, USA
| | - Caroline Mas
- University Grenoble Alpes, CNRS, CEA, IBS, 71 Avenue des Martyrs, CS 10090, 38044, Grenoble CEDEX 9, France
| | - Lionel Imbert
- University Grenoble Alpes, CNRS, CEA, IBS, 71 Avenue des Martyrs, CS 10090, 38044, Grenoble CEDEX 9, France
| | - Christian Orlik
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Im Neuenheimer Feld 344, 69120, Heidelberg, Germany.,Department of Immunology, Molecular Immunology, University of Heidelberg, 69120, Heidelberg, Germany
| | - Alessia Ruggieri
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Im Neuenheimer Feld 344, 69120, Heidelberg, Germany
| | - Anna M Pyle
- Department of Molecular, Cellular and Developmental Biology, Yale University, 219 Prospect St, New Haven, CT, 06511, USA.,Howard Hughes Medical Institute, 219 Prospect St, New Haven, CT, 06511, USA
| | - Volker Lohmann
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Im Neuenheimer Feld 344, 69120, Heidelberg, Germany.
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27
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Baños-Lara MDR, Zabaleta J, Garai J, Baddoo M, Guerrero-Plata A. Comparative analysis of miRNA profile in human dendritic cells infected with respiratory syncytial virus and human metapneumovirus. BMC Res Notes 2018; 11:432. [PMID: 29970194 PMCID: PMC6029031 DOI: 10.1186/s13104-018-3541-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 06/26/2018] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVE Human metapneumovirus (HMPV) and respiratory syncytial virus (RSV) are responsible for respiratory diseases, mostly in children. Despite the clinical and epidemiological similarities between these two pneumoviruses, they elicit different immune responses. This work aims to further our understanding of the differential immune response induced by these respiratory viruses by determining the changes of small non-coding RNAs (miRNAs), which regulate gene expression and are involved in numerous cellular processes including the immune system. RESULTS In the present study, we analyzed the expression of miRNA transcripts of human dendritic cells infected with RSV or HMPV by high throughput sequencing using Illumina sequencing technology. Further validation of miRNA expression by quantitative polymerase chain reaction indicated that HMPV infection up-regulated the expression of 2 miRNAs (hsa-miR-182-5p and hsa-miR-4634), while RSV infection induced significant expression of 3 miRNAs (hsa-miR-4448, hsa-miR-30a-5p and hsa-miR-4634). The predominant miRNA induced by both viruses was hsa-miR-4634.
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Affiliation(s)
- Ma Del Rocio Baños-Lara
- Department of Pathobiological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA.,Universidad Popular Autonoma del Estado de Puebla, UPAEP, Puebla, Mexico
| | - Jovanny Zabaleta
- Department of Pediatrics, Louisiana State University Health Sciences Center, New Orleans, LA, 70112, USA.,Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA, 70112, USA
| | - Jone Garai
- Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA, 70112, USA
| | - Melody Baddoo
- Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Antonieta Guerrero-Plata
- Department of Pathobiological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA. .,Center for Experimental Infectious Disease Research, Louisiana State University, Baton Rouge, LA, 70803, USA.
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28
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Miquelestorena-Standley E, Tallet A, Collin C, Piver E, De Muret A, Salamé E, Bourlier P, Kervarrec T, Guyétant S, Pagès JC. Interest of variations in microRNA-152 and -122 in a series of hepatocellular carcinomas related to hepatitis C virus infection. Hepatol Res 2018; 48:566-573. [PMID: 28512857 DOI: 10.1111/hepr.12915] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 03/27/2017] [Accepted: 05/12/2017] [Indexed: 02/08/2023]
Abstract
AIM Hepatocellular carcinoma (HCC) is a common outcome of chronic hepatitis C virus (HCV) infection and constitutes the main burden of this disease. The molecular mechanisms underlying the development of HCC are multiple and might involve certain microRNA (miR). As discordant results have been reported concerning the detection of expression of miR-152 and miR-122 in HCC, our aim was to measure the levels of both miRs in serum and liver samples. METHODS We analyzed miR-152 and miR-122 expression by reverse transcription-quantitative polymerase chain reaction in a serum cohort from 14 HCV-infected patients who developed HCC, 20 HCV+ patients without HCC, and 19 control patients. We also studied miR-152 and miR-122 in an independent tissue cohort from 11 normal livers, and from paired HCC and non-tumor adjacent livers of 11 HCV-infected patients and 12 non-infected patients. RESULTS In serum samples, higher levels of miR-122 were found in non-HCC HCV+ compared to HCC HCV+ and control groups, whereas miR-152 was detectable in a lower range in HCC HCV+ compared to non-HCC HCV+ and control groups. We found higher signals for miR-122 and miR-152 in non-tumor liver and HCC tissues compared to control tissues. Hepatocellular carcinoma etiology had no detectable influence on miR-122 expression, whereas miR-152 was increased in HCV+ tissue samples. CONCLUSIONS Detection of low values of circulating miR-152 is a potentially interesting marker of hepatocarcinogenesis in HCV+ patients, in contrast to miR-122, which varies according to hepatocyte damage.
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Affiliation(s)
- Elodie Miquelestorena-Standley
- CHRU de Tours, Laboratoire d'anatomie et cytologie pathologiques, Tours, France.,Université François-Rabelais de Tours, PRES Centre-Val de Loire Université, Tours, France.,INSERM Unité U966, Morphogénèse et Antigénicité du VIH et des Virus des Hépatites, Tours, France
| | - Anne Tallet
- Université François-Rabelais de Tours, PRES Centre-Val de Loire Université, Tours, France.,INSERM Unité U966, Morphogénèse et Antigénicité du VIH et des Virus des Hépatites, Tours, France.,CHRU de Tours, Plateforme de Génétique Moléculaire des Cancers, Tours, France
| | - Christine Collin
- CHRU de Tours, Plateforme de Génétique Moléculaire des Cancers, Tours, France
| | - Eric Piver
- Université François-Rabelais de Tours, PRES Centre-Val de Loire Université, Tours, France.,INSERM Unité U966, Morphogénèse et Antigénicité du VIH et des Virus des Hépatites, Tours, France.,CHRU de Tours, Plateforme de Génétique Moléculaire des Cancers, Tours, France
| | - Anne De Muret
- CHRU de Tours, Laboratoire d'anatomie et cytologie pathologiques, Tours, France
| | - Ephrem Salamé
- Université François-Rabelais de Tours, PRES Centre-Val de Loire Université, Tours, France.,CHRU de Tours, Service de chirurgie digestive, endocrinienne et transplantation hépatique, Tours, France
| | - Pascal Bourlier
- CHRU de Tours, Service de chirurgie digestive, endocrinienne et transplantation hépatique, Tours, France
| | - Thibault Kervarrec
- CHRU de Tours, Laboratoire d'anatomie et cytologie pathologiques, Tours, France.,Université François-Rabelais de Tours, PRES Centre-Val de Loire Université, Tours, France
| | - Serge Guyétant
- CHRU de Tours, Laboratoire d'anatomie et cytologie pathologiques, Tours, France.,Université François-Rabelais de Tours, PRES Centre-Val de Loire Université, Tours, France
| | - Jean-Christophe Pagès
- Université François-Rabelais de Tours, PRES Centre-Val de Loire Université, Tours, France.,INSERM Unité U966, Morphogénèse et Antigénicité du VIH et des Virus des Hépatites, Tours, France.,CHRU de Tours, Plateforme de Génétique Moléculaire des Cancers, Tours, France
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Identification of Reference Genes for Analysis of microRNA Expression Patterns in Equine Chorioallantoic Membrane and Serum. Mol Biotechnol 2017; 60:62-73. [DOI: 10.1007/s12033-017-0047-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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30
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Identification and validation of the microRNA response elements in the 3'-untranslated region of the UDP glucuronosyltransferase (UGT) 2B7 and 2B15 genes by a functional genomics approach. Biochem Pharmacol 2017; 146:199-213. [PMID: 28962835 DOI: 10.1016/j.bcp.2017.09.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 09/25/2017] [Indexed: 12/15/2022]
Abstract
Posttranscriptional repression of UDP-glucuronosyltransferase (UGT) 2B7 and 2B15 expression by microRNAs (miRNAs) may be an important mechanism underlying inter-individual variability in drug glucuronidation. Furthermore, the UGT2B15 3'-UTR contains a common SNP (rs3100) that could influence miRNA binding. The aim of this study was to identify the complete complement of miRNAs that could regulate UGT2B7 and UGT2B15 expression through binding to the reference and/or variant 3'-UTRs. Luciferase reporter plasmids containing either the reference or variant 3'-UTRs were screened against a 2,048 human miRNA library to identify those miRNAs that decrease luciferase activity by at least 30% when co-transfected into HEK293 cells. Six novel miRNAs (miR-1293, miR-3664-3p, miR-4317, miR-513c-3p, miR-4483, and miR-142-3p) were identified that repressed the reference UGT2B7 3'-UTR, while twelve novel miRNAs (miR-770-5p, miR-103b, miR-3924, miR-376b-3p, miR-455-5p, miR-605, miR-624-3p, miR-4712-5p, miR-3675-3p, miR-6500-5p, miR-548as-3p, and miR-4292) repressed both the reference and rs3100 variant UGT2B15 3'-UTR. Deletion and mutagenesis studies confirmed the binding site location of each miRNA. Although the UGT2B15 rs3100 SNP was located within the miR-376c-3p response element, there was no effect on miRNA binding. miR-142-3p, miR-3664-3p, miR-4317, miR-455-5p, miR-376c-3p, miR-770-5p, miR-3675-3p, miR-331-5p, miR-605, and miR-376b-3p transcript levels were measured by quantitative PCR and correlated with UGT2B7 and UGT2B15 enzyme activities in 27 human liver samples. A significant negative correlation (Rs = -0.53; p = 0.005) was demonstrated between hepatic miR-455-5p transcript levels and UGT2B15-mediated S-oxazepam glucuronidation activities. Thus, the UGT2B7 and UGT2B15 3'-UTRs contain miRNA response elements for multiple miRNAs that may contribute to variable drug glucuronidation.
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31
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Gouin K, Peck K, Antes T, Johnson JL, Li C, Vaturi SD, Middleton R, de Couto G, Walravens AS, Rodriguez-Borlado L, Smith RR, Marbán L, Marbán E, Ibrahim AGE. A comprehensive method for identification of suitable reference genes in extracellular vesicles. J Extracell Vesicles 2017; 6:1347019. [PMID: 28815002 PMCID: PMC5549828 DOI: 10.1080/20013078.2017.1347019] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 06/19/2017] [Indexed: 01/01/2023] Open
Abstract
Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is one of the most sensitive, economical and widely used methods for evaluating gene expression. However, the utility of this method continues to be undermined by a number of challenges including normalization using appropriate reference genes. The need to develop tailored and effective strategies is further underscored by the burgeoning field of extracellular vesicle (EV) biology. EVs contain unique signatures of small RNAs including microRNAs (miRs). In this study we develop and validate a comprehensive strategy for identifying highly stable reference genes in a therapeutically relevant cell type, cardiosphere-derived cells. Data were analysed using the four major approaches for reference gene evaluation: NormFinder, GeNorm, BestKeeper and the Delta Ct method. The weighted geometric mean of all of these methods was obtained for the final ranking. Analysis of RNA sequencing identified miR-101-3p, miR-23a-3p and a previously identified EV reference gene, miR-26a-5p. Analysis of a chip-based method (NanoString) identified miR-23a, miR-217 and miR-379 as stable candidates. RT-qPCR validation revealed that the mean of miR-23a-3p, miR-101-3p and miR-26a-5p was the most stable normalization strategy. Here, we demonstrate that a comprehensive approach of a diverse data set of conditions using multiple algorithms reliably identifies stable reference genes which will increase the utility of gene expression evaluation of therapeutically relevant EVs.
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Affiliation(s)
- Kenneth Gouin
- Heart Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Kiel Peck
- Capricor Therapeutics Institute, Beverly Hills, CA, USA
| | - Travis Antes
- Capricor Therapeutics Institute, Beverly Hills, CA, USA
| | | | - Chang Li
- Capricor Therapeutics Institute, Beverly Hills, CA, USA
| | | | - Ryan Middleton
- Heart Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | | | | | | | | | - Linda Marbán
- Capricor Therapeutics Institute, Beverly Hills, CA, USA
| | - Eduardo Marbán
- Heart Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
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Identification and validation of microRNAs directly regulating the UDP-glucuronosyltransferase 1A subfamily enzymes by a functional genomics approach. Biochem Pharmacol 2017; 137:93-106. [PMID: 28433553 DOI: 10.1016/j.bcp.2017.04.017] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 04/13/2017] [Indexed: 11/23/2022]
Abstract
Posttranscriptional repression of UDP-glucuronosyltransferase (UGT) 1A expression by microRNAs (miRNAs) may be an important mechanism underlying interindividual variability in drug glucuronidation. Furthermore, the UGT1A 3'-UTR shared by all UGT1A enzymes is polymorphic, containing three linked SNPs (rs10929303, rs1042640, and rs8330) that could influence miRNA binding. The aim of this study was to identify the complete complement of miRNAs that could regulate UGT1A expression through binding to the reference and/or common variant UGT1A 3'-UTR. Luciferase reporter plasmids containing either the reference or variant UGT1A 3'-UTR were screened against a 2048 human miRNA library to identify those miRNAs that decrease luciferase activity by at least 30% when co-transfected into HEK293 cells. Four novel miRNAs (miR-103b, miR-141-3p, miR-200a-3p, and miR-376b-3p) were identified that repressed both reference and variant UGT1A 3'-UTR, while two other miRNAs selectively repressed the reference (miR-1286) or variant (miR-21-3p) 3'-UTR. Deletion and mutagenesis studies confirmed the binding site location for each miRNA. rs8330 disrupted miR-1286 binding to the reference UGT1A 3'-UTR, while rs10929303 enhanced miR-21-3p binding to the variant 3'-UTR. Transfection of miR-21-3p, miR-103b, miR-141-3p, miR-200a-3p, and miR-376b-3p mimics into LS180 human intestinal cells showed repression of UGT1A1 and UGT1A6 mediated glucuronidation and mRNA without affecting UGT2B7 activity or mRNA. Furthermore, transfection of miR-21-3p, miR-141-3p, and miR-200a-3p into primary human hepatocytes, repressed UGT1A1 activity and mRNA without affecting CYP3A activity. Finally, miR-21-3p and miR-200a-3p expression were negatively correlated with UGT1A6 activity and mRNA in human liver samples. Thus, UGT1A is regulated by multiple miRNAs with some showing allele-dependent effects.
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Masè M, Grasso M, Avogaro L, D’Amato E, Tessarolo F, Graffigna A, Denti MA, Ravelli F. Selection of reference genes is critical for miRNA expression analysis in human cardiac tissue. A focus on atrial fibrillation. Sci Rep 2017; 7:41127. [PMID: 28117343 PMCID: PMC5259703 DOI: 10.1038/srep41127] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 12/15/2016] [Indexed: 12/23/2022] Open
Abstract
MicroRNAs (miRNAs) are emerging as key regulators of complex biological processes in several cardiovascular diseases, including atrial fibrillation (AF). Reverse transcription-quantitative polymerase chain reaction is a powerful technique to quantitatively assess miRNA expression profile, but reliable results depend on proper data normalization by suitable reference genes. Despite the increasing number of studies assessing miRNAs in cardiac disease, no consensus on the best reference genes has been reached. This work aims to assess reference genes stability in human cardiac tissue with a focus on AF investigation. We evaluated the stability of five reference genes (U6, SNORD48, SNORD44, miR-16, and 5S) in atrial tissue samples from eighteen cardiac-surgery patients in sinus rhythm and AF. Stability was quantified by combining BestKeeper, delta-Cq, GeNorm, and NormFinder statistical tools. All methods assessed SNORD48 as the best and U6 as the worst reference gene. Applications of different normalization strategies significantly impacted miRNA expression profiles in the study population. Our results point out the necessity of a consensus on data normalization in AF studies to avoid the emergence of divergent biological conclusions.
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Affiliation(s)
- Michela Masè
- Department of Physics, University of Trento, Trento, Italy
| | | | - Laura Avogaro
- Department of Physics, University of Trento, Trento, Italy
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | - Elvira D’Amato
- Department of Physics, University of Trento, Trento, Italy
| | - Francesco Tessarolo
- Healthcare Research and Innovation Program (IRCS-PAT), Bruno Kessler Foundation, Trento, Italy
- Department of Industrial Engineering, University of Trento, Trento, Italy
| | - Angelo Graffigna
- Division of Cardiac Surgery, Santa Chiara Hospital, Trento, Italy
| | | | - Flavia Ravelli
- Department of Physics, University of Trento, Trento, Italy
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Corral-Vazquez C, Blanco J, Salas-Huetos A, Vidal F, Anton E. Normalization matters: tracking the best strategy for sperm miRNA quantification. Mol Hum Reprod 2016; 23:45-53. [DOI: 10.1093/molehr/gaw072] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 10/11/2016] [Accepted: 11/14/2016] [Indexed: 11/14/2022] Open
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35
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Ao R, Wang Y, Tong J, Wang BF. Altered microRNA-9 Expression Level is Directly Correlated with Pathogenesis of Nonalcoholic Fatty Liver Disease by Targeting Onecut2 and SIRT1. Med Sci Monit 2016; 22:3804-3819. [PMID: 27756894 PMCID: PMC5074799 DOI: 10.12659/msm.897207] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background MicroRNA-9 (miR-9) was detected in nonalcoholic fatty liver disease (NAFLD) patients to understand the role of miR-9 in NAFLD development. Material/Methods Between February 2014 and February 2015, 105 cases of NAFLD were recruited and confirmed by liver biopsy pathology, including patients with mild NAFLD (n=58) and moderate-severe NAFLD (n=47); nonalcoholic steatohepatitis (NASH) (n=53) and non-NASH (n=52); and 50 healthy participants were regarded as the healthy control group. MiR-9 expression was measured by qRT-PCR. For in vitro experiments, L-02 normal liver cells were divided into normal control group (cultured with original culture medium), dimethyl sulfoxide (DMSO) group (cultured with DMSO) and oleic acid group (cultured with oleic acid to induce fatty change), and MTT assay was used to measure the effect of different oleic acid concentrations on cell proliferation. Nile red staining was used to detect intracellular accumulation of lipid droplets. Further, synthetic miR-9 mimic and its control and miR-9 inhibitors and its control were independently transfected into L-02 cells. Results MiR-9 levels in the mild NAFLD group and moderate-severe NAFLD group were significantly higher than in the healthy control group (both P<0.05). Mean fluorescence intensity of lipid droplets increased with the duration of induction, and were dramatically higher in oleate-treated L-02 cells; intracellular triglyceride (TG) content was also higher. miR-9 levels significantly increased following oleate induction. Importantly, miR-9 levels were significantly elevated upon miR-9 mimic transfection. Conversely, miR-9 level was lowered with miR-9 inhibitors transfection. Additionally, Onecut2 and SIRT1 were identified as miR-9 targets. Conclusions A positive relationship between miR-9 and steatosis was established with our results that miR-9 mimic transfection decreased intracellular lipid content. Finally, we identified 2 miR-9 targets, Onecut2 and SIRT1, which may be crucial players in NAFLD development.
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Affiliation(s)
- Ran Ao
- Department of Gastroenterology, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China (mainland)
| | - Ying Wang
- Department of Gastroenterology, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China (mainland)
| | - Jing Tong
- Department of Gastroenterology, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China (mainland)
| | - Bai-Fang Wang
- Department of Gastroenterology, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China (mainland)
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Transcriptome association analysis identifies miR-375 as a major determinant of variable acetaminophen glucuronidation by human liver. Biochem Pharmacol 2016; 117:78-87. [PMID: 27531059 DOI: 10.1016/j.bcp.2016.08.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 08/09/2016] [Indexed: 12/27/2022]
Abstract
Acetaminophen is the leading cause of acute liver failure (ALF) in many countries including the United States. Hepatic glucuronidation by UDP-glucuronosyltransferase (UGT) 1A subfamily enzymes is the major route of acetaminophen elimination. Reduced glucuronidation may predispose some individuals to acetaminophen-induced ALF, but mechanisms underlying reduced glucuronidation are poorly understood. We hypothesized that specific microRNAs (miRNAs) may reduce UGT1A activity by direct effects on the UGT1A 3'-UTR shared by all UGT1A enzyme transcripts, or by indirect effects on transcription factors regulating UGT1A expression. We performed an unbiased miRNA whole transcriptome association analysis using a bank of human livers with known acetaminophen glucuronidation activities. Of 754 miRNAs evaluated, 9 miRNAs were identified that were significantly overexpressed (p<0.05; >2-fold) in livers with low acetaminophen glucuronidation activities compared with those with high activities. miR-375 showed the highest difference (>10-fold), and was chosen for further mechanistic validation. We demonstrated using in silico analysis and luciferase reporter assays that miR-375 has a unique functional binding site in the 3'-UTR of the aryl hydrocarbon receptor (AhR) gene. Furthermore overexpression of miR-375 in LS180 cells demonstrated significant repression of endogenous AhR protein (by 40%) and mRNA (by 10%), as well as enzyme activity and/or mRNA of AhR regulated enzymes including UGT1A1, UGT1A6, and CYP1A2, without affecting UGT2B7, which is not regulated by AhR. Thus miR-375 is identified as a novel repressor of UGT1A-mediated hepatic acetaminophen glucuronidation through reduced AhR expression, which could predispose some individuals to increased risk for acetaminophen-induced ALF.
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Liu Y, Lu Q. Extracellular vesicle microRNAs: biomarker discovery in various diseases based on RT-qPCR. Biomark Med 2016; 9:791-805. [PMID: 26287938 DOI: 10.2217/bmm.15.45] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
In recent years, biomarker discovery based on extracellular microRNAs (miRNAs), especially exosome miRNAs, has drawn wide attention. While exosome isolation and identification technologies are increasingly sophisticated, the preanalytical process of exosome miRNAs seems to be no longer a crucial problem. Though next-generation sequencing, microarray and digital PCR have been recommended as good downstream analytical platforms for exosome miRNA quantification, they are still more constrained in clinical utility compared with RT-qPCR method at present. In this review, we will trace back to the origin and summarize current studies of biomarker discovery based on extracellular vesicle miRNAs, and provide an overview and latest developments of RT-qPCR-based data normalization, in order to further assist the development of translational medicine.
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Affiliation(s)
- Ying Liu
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, Second Xiangya Hospital, Central South University, #139 Renmin Middle Rd, Changsha, Hunan 410011, PR China
| | - Qianjin Lu
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, Second Xiangya Hospital, Central South University, #139 Renmin Middle Rd, Changsha, Hunan 410011, PR China
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Tan Y, Ge G, Pan T, Wen D, Gan J. Serum MiRNA panel as potential biomarkers for chronic hepatitis B with persistently normal alanine aminotransferase. Clin Chim Acta 2015; 451:232-9. [PMID: 26483130 DOI: 10.1016/j.cca.2015.10.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 09/25/2015] [Accepted: 10/02/2015] [Indexed: 02/09/2023]
Abstract
BACKGROUND Circulating miRNAs, a family of miRNAs existing in plasma and serum, have a great potential to serve as novel biomarkers in body fluids for non-invasive diagnosis and prognosis of many diseases. METHODS A multistage, case-control study was designed to establish a panel of serum miRNAs that could be surrogate markers for chronic hepatitis B with persistently normal alanine aminotransferase (ALT). A total of 295 CHB patients presenting persistently normal ALT levels with significant histological features (SPNALT group), 243 CHB patients presenting persistently normal ALT levels with no significant histological features (NSPNALT group), and 178 healthy controls (healthy group) were enrolled in the study. An initial screening of miRNAs was performed by Illumina sequencing using serum samples pooled from SPNALT patients and controls. Quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR) assay was performed to evaluate the expression of selected miRNAs. A logistic regression model was constructed using a training cohort (n=380) and validated using a cohort (n=258). The area under the receiver operating characteristic curve (AUC) was used to evaluate diagnostic accuracy. RESULTS We identified 9 miRNAs (hsa-miR-885-5p, hsa-miR-122-5p, hsa-miR-10a-5p, hsa-miR-511-5p, hsa-miR-574-5p, hsa-miR-98-5p, hsa-miR-26a-5p, hsa-miR-192-5p, hsa-miR-30b-5p) and established 3 miRNA panels that provided high diagnostic accuracy for SPNALT. The AUC of miRNA panels for SPNALT vs. healthy was 0.882 (95% CI=0.839 to 0.925), for SPNALT vs. NSPNALT was 0.894 (95% CI=0.857 to 0.930), and for SPNALT vs. control was 0.860 (95% CI=0.821 to 0.899). CONCLUSIONS We constructed serum miRNA panels with considerable clinical value in diagnosing PNALT.
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Affiliation(s)
- Youwen Tan
- Department of Hepatosis, The Third Hospital of Zhenjiang Affiliated Jiangsu University, Zhenjiang, China.
| | - Guohong Ge
- Department of Hepatosis, The Third Hospital of Zhenjiang Affiliated Jiangsu University, Zhenjiang, China
| | - Tengli Pan
- Department of Hepatosis, The Third Hospital of Zhenjiang Affiliated Jiangsu University, Zhenjiang, China
| | - Danfeng Wen
- Department of Hepatosis, The Third Hospital of Zhenjiang Affiliated Jiangsu University, Zhenjiang, China
| | - Jianhe Gan
- Department of Hepatosis, The Third Hospital of Zhenjiang Affiliated Jiangsu University, Zhenjiang, China
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Schwarzenbach H, da Silva AM, Calin G, Pantel K. Data Normalization Strategies for MicroRNA Quantification. Clin Chem 2015; 61:1333-42. [PMID: 26408530 DOI: 10.1373/clinchem.2015.239459] [Citation(s) in RCA: 346] [Impact Index Per Article: 38.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 08/25/2015] [Indexed: 12/15/2022]
Abstract
BACKGROUND Different technologies, such as quantitative real-time PCR or microarrays, have been developed to measure microRNA (miRNA) expression levels. Quantification of miRNA transcripts implicates data normalization using endogenous and exogenous reference genes for data correction. However, there is no consensus about an optimal normalization strategy. The choice of a reference gene remains problematic and can have a serious impact on the actual available transcript levels and, consequently, on the biological interpretation of data. CONTENT In this review article we discuss the reliability of the use of small RNAs, commonly reported in the literature as miRNA expression normalizers, and compare different strategies used for data normalization. SUMMARY A workflow strategy is proposed for normalization of miRNA expression data in an attempt to provide a basis for the establishment of a global standard procedure that will allow comparison across studies.
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Affiliation(s)
- Heidi Schwarzenbach
- Department of Tumour Biology, Center of Experimental Medicine, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Andreia Machado da Silva
- Department of Experimental Therapeutics and The Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX; Instituto de Investigação em Saúde, Universidade do Porto, Porto, Portugal; INEB, Institute of Biomedical Engineering, Universidade do Porto, Porto, Portugal
| | - George Calin
- Department of Experimental Therapeutics and The Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Klaus Pantel
- Department of Tumour Biology, Center of Experimental Medicine, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany;
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Lou G, Ma N, Xu Y, Jiang L, Yang J, Wang C, Jiao Y, Gao X. Differential distribution of U6 (RNU6-1) expression in human carcinoma tissues demonstrates the requirement for caution in the internal control gene selection for microRNA quantification. Int J Mol Med 2015; 36:1400-8. [PMID: 26352225 DOI: 10.3892/ijmm.2015.2338] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Accepted: 08/24/2015] [Indexed: 11/06/2022] Open
Abstract
Alterations in microRNA (miRNA) expression patterns have been associated with a number of human diseases. Accurate quantitation of miRNA levels is important for their use as biomarkers and in determining their functions. Although the issue of proper miRNA detection was solved with the introduction of standard reverse transcription‑quantitative polymerase chain reaction (RT‑qPCR) assays, numerous issues with the selection of appropriate internal control genes remain. U6 (RNU6‑1) snRNA, the most commonly used internal control gene in miRNA RT‑qPCR assays, was shown to be unstable in clinical samples, particularly cancer tissues. Identification of the distribution of U6 in different tissues is the premise of more accurate quantification of miRNAs. However, the distribution of U6 in human carcinoma tissues and corresponding normal tissues is unknown. In the present study, U6 levels were significantly higher in human breast carcinoma tissues compared with the corresponding normal tissues by RT‑qPCR. In the carcinoma or corresponding adjacent normal tissues, the expression levels of U6 in epithelial cells were higher than those in the mesenchymal cells. Furthermore, the expression levels of U6 in the carcinoma tissues of the liver and intrahepatic bile ducts were higher than those in the adjacent normal tissues. These results suggest that the expression and distribution of U6 exhibits a high degree of variability among several types of human cells. Therefore, caution is required when selecting U6 as an internal control gene for evaluating expression profiles of miRNAs in patients with carcinoma, particularly carcinoma of the liver and intrahepatic bile ducts.
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Affiliation(s)
- Ge Lou
- Department of Pathology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, P.R. China
| | - Ning Ma
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin 150081, P.R. China
| | - Ya Xu
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin 150081, P.R. China
| | - Lei Jiang
- Department of Pathology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, P.R. China
| | - Jing Yang
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin 150081, P.R. China
| | - Chuxuan Wang
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin 150081, P.R. China
| | - Yufei Jiao
- Department of Pathology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, P.R. China
| | - Xu Gao
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin 150081, P.R. China
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Rehbein G, Schmidt B, Fleischhacker M. Extracellular microRNAs in bronchoalveolar lavage samples from patients with lung diseases as predictors for lung cancer. Clin Chim Acta 2015; 450:78-82. [PMID: 26232753 DOI: 10.1016/j.cca.2015.07.027] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 07/21/2015] [Accepted: 07/28/2015] [Indexed: 11/28/2022]
Abstract
OBJECTIVE The detection of tumor-associated microRNA expression in bronchial lavage (BL) samples of lung cancer patients could improve the non-invasive tumor diagnostic. METHODS The profile of extracellular microRNAs in bronchial lavage was evaluated using three pools for lung cancer group (malignant) and three pools for non-cancerous group (benign) of 10 patients each. To confirm the results for the selected microRNAs in a qRT-PCR the BL of 30 different lung cancer and non-cancerous patients was used. We examined total-RNA from cell-free supernatant of BL samples. For normalization we added exogenous cel-miR 39. RESULTS Using microRNA arrays we found a panel of eight microRNAs (hsa-miR 19b-1, 1285, 1289, 1303, 217, 29a-5p, 548-3p, 650) that were differentially expressed between the lung cancer and the non-cancerous group. Further investigation by qPCR revealed five microRNAs (U6 snRNA, hsa-miR 1285, 1303, 29a-5p, 650) that were significantly up-regulated in patients with lung cancer. CONCLUSIONS In bronchial lavage samples the five microRNAs identified in this study have a diagnostic potential for use as noninvasive biomarkers in lung cancer.
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Affiliation(s)
- Grit Rehbein
- Abteilung Pneumologie, Klinik für Innere Medizin 1, Martin-Luther-Universität Halle-Wittenberg, Ernst-Grube-Straße 40, 06120 Halle/Saale, Germany.
| | - Bernd Schmidt
- Abteilung Pneumologie, Klinik für Innere Medizin 1, Martin-Luther-Universität Halle-Wittenberg, Ernst-Grube-Straße 40, 06120 Halle/Saale, Germany.
| | - Michael Fleischhacker
- Abteilung Pneumologie, Klinik für Innere Medizin 1, Martin-Luther-Universität Halle-Wittenberg, Ernst-Grube-Straße 40, 06120 Halle/Saale, Germany.
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Juzėnas S, Saltenienė V, Kupcinskas J, Link A, Kiudelis G, Jonaitis L, Jarmalaite S, Kupcinskas L, Malfertheiner P, Skieceviciene J. Analysis of Deregulated microRNAs and Their Target Genes in Gastric Cancer. PLoS One 2015; 10:e0132327. [PMID: 26172537 PMCID: PMC4501563 DOI: 10.1371/journal.pone.0132327] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 06/13/2015] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are widely studied non-coding RNAs that modulate gene expression. MiRNAs are deregulated in different tumors including gastric cancer (GC) and have potential diagnostic and prognostic implications. The aim of our study was to determine miRNA profile in GC tissues, followed by evaluation of deregulated miRNAs in plasma of GC patients. Using available databases and bioinformatics methods we also aimed to evaluate potential target genes of confirmed differentially expressed miRNA and validate these findings in GC tissues. METHODS The study included 51 GC patients and 51 controls. Initially, we screened miRNA expression profile in 13 tissue samples of GC and 12 normal gastric tissues with TaqMan low density array (TLDA). In the second stage, differentially expressed miRNAs were validated in a replication cohort using qRT-PCR in tissue and plasma samples. Subsequently, we analyzed potential target genes of deregulated miRNAs using bioinformatics approach, determined their expression in GC tissues and performed correlation analysis with targeting miRNAs. RESULTS Profiling with TLDA revealed 15 deregulated miRNAs in GC tissues compared to normal gastric mucosa. Replication analysis confirmed that miR-148a-3p, miR-204-5p, miR-223-3p and miR-375 were consistently deregulated in GC tissues. Analysis of GC patients' plasma samples showed significant down-regulation of miR-148a-3p, miR-375 and up-regulation of miR-223-3p compared to healthy subjects. Further, using bioinformatic tools we identified targets of replicated miRNAs and performed disease-associated gene enrichment analysis. Ultimately, we evaluated potential target gene BCL2 and DNMT3B expression by qRT-PCR in GC tissue, which correlated with targeting miRNA expression. CONCLUSIONS Our study revealed miRNA profile in GC tissues and showed that miR-148a-3p, miR-223-3p and miR-375 are deregulated in GC plasma samples, but these circulating miRNAs showed relatively weak diagnostic performance as sole biomarkers. Target gene analysis demonstrated that BCL2 and DNMT3B expression in GC tissue correlated with their targeting miRNA expression.
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Affiliation(s)
- Simonas Juzėnas
- Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Violeta Saltenienė
- Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Juozas Kupcinskas
- Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
- Department of Gastroenterology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Alexander Link
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto von Guericke University, Magdeburg, Germany
| | - Gediminas Kiudelis
- Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
- Department of Gastroenterology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Laimas Jonaitis
- Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
- Department of Gastroenterology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Sonata Jarmalaite
- Division of Human Genome Research Centre, Faculty of Natural Sciences, Vilnius University, Vilnius, Lithuania
| | - Limas Kupcinskas
- Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
- Department of Gastroenterology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Peter Malfertheiner
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto von Guericke University, Magdeburg, Germany
| | - Jurgita Skieceviciene
- Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
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Stability Assessment of Candidate Reference Genes in Urine Sediment of Prostate Cancer Patients for miRNA Applications. DISEASE MARKERS 2015; 2015:973597. [PMID: 26078486 PMCID: PMC4452852 DOI: 10.1155/2015/973597] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 04/30/2015] [Indexed: 12/19/2022]
Abstract
We aimed at assessing the stability of candidate reference genes in urine sediments of men subjected to digital rectal examination for suspected prostate cancer (PCa). Two microRNAs (miR-191 and miR-25) and 1 small nucleolar RNA (SNORD48) were assayed in 35 post-DRE urine sediments of men with PCa and in 26 subjects with histologically confirmed benign prostatic hyperplasia (BPH). The stability of candidate reference genes was assessed through BestKeeper algorithm and equivalence test. miR-200b and miR-452 were used to test for the effect of normalization on target genes. Our results proved miR-191 to be the most stable gene, showing the lowest degree of variation and the highest stability value. miR-25 and SNORD48 values fell beyond the cutoff of acceptability. In conclusion, we recommend the use of miR-191 for normalization purposes in post-DRE urine sediments.
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Tan Y, Lin B, Ye Y, Wen D, Chen L, Zhou X. Differential expression of serum microRNAs in cirrhosis that evolve into hepatocellular carcinoma related to hepatitis B virus. Oncol Rep 2015; 33:2863-70. [PMID: 25962820 DOI: 10.3892/or.2015.3924] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Accepted: 03/24/2015] [Indexed: 11/06/2022] Open
Abstract
Circulating microRNAs (miRNAs) exist stably in body fluids and are potential biomarkers for hepatocellular carcinoma (HCC). Twenty-five patients with cirrhosis that evolved into HCC, who were treated at The Third Hospital of Zhenjiang Affiliated to Jiangsu University between January 2005 and December 2012, were enrolled. In the discovery stage, 2 serum samples pooled from 3 cirrhosis and 3 HCC samples were subjected to deep sequencing. Subsequently, differential expression of miRNAs was validated by quantitative reverse transcription-polymerase chain reaction (qRT-PCR) in the serum samples from an independent cohort of 22 patients with cirrhosis and HCC. Twenty-two miRNAs showed a >2-fold upregulation (P<0.01), and 2 miRNAs showed a >2-fold downregulation (P<0.01) in the cirrhosis and HCC samples. Using the comparative Ct method, we calculated the 2-(ΔΔCt) for 40 candidate miRNAs in the sample sets. Eight of the 40 miRNAs demonstrated significantly differential expression levels between the disease categories. The miRNAs exhibiting differential expression were hsa-miR-122-5p, has-miR-199a-5p, hsa-miR-486-5p, has-miR-193b-5p, hsa-miR-206, has-miR-141-3p, has-miR-192-5p and has-miR-26a-5p. We identified the miRNAs differentially expressed in cirrhosis that evolved into hepatitis B virus-related HCC.
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Affiliation(s)
- Youwen Tan
- Department of Hepatosis, The Third Hospital of Zhenjiang Affiliated to Jiangsu University, Zhenjiang, Jiangsu, P.R. China
| | - Bin Lin
- Department of Infectious Diseases, Jintan Hospital Affiliated to Jiangsu University, Changzhou, Jiangsu, P.R. China
| | - Yun Ye
- Department of Hepatosis, The Third Hospital of Zhenjiang Affiliated to Jiangsu University, Zhenjiang, Jiangsu, P.R. China
| | - Danfeng Wen
- Department of Hepatosis, The Third Hospital of Zhenjiang Affiliated to Jiangsu University, Zhenjiang, Jiangsu, P.R. China
| | - Li Chen
- Department of Hepatosis, The Third Hospital of Zhenjiang Affiliated to Jiangsu University, Zhenjiang, Jiangsu, P.R. China
| | - Xinbei Zhou
- Department of Hepatosis, The Third Hospital of Zhenjiang Affiliated to Jiangsu University, Zhenjiang, Jiangsu, P.R. China
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Shen Y, Tian F, Chen Z, Li R, Ge Q, Lu Z. Amplification-based method for microRNA detection. Biosens Bioelectron 2015; 71:322-331. [PMID: 25930002 DOI: 10.1016/j.bios.2015.04.057] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 04/17/2015] [Accepted: 04/18/2015] [Indexed: 12/20/2022]
Abstract
Over the last two decades, the study of miRNAs has attracted tremendous attention since they regulate gene expression post-transcriptionally and have been demonstrated to be dysregulated in many diseases. Detection methods with higher sensitivity, specificity and selectivity between precursors and mature microRNAs are urgently needed and widely studied. This review gave an overview of the amplification-based technologies including traditional methods, current modified methods and the cross-platforms of them combined with other techniques. Many progresses were found in the modified amplification-based microRNA detection methods, while traditional platforms could not be replaced until now. Several sample-specific normalizers had been validated, suggesting that the different normalizers should be established for different sample types and the combination of several normalizers might be more appropriate than a single universal normalizer. This systematic overview would be useful to provide comprehensive information for subsequent related studies and could reduce the un-necessary repetition in the future.
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Affiliation(s)
- Yanting Shen
- Research Center for Learning Science, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China.
| | - Fei Tian
- Research Center for Learning Science, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China.
| | - Zhenzhu Chen
- Research Center for Learning Science, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China.
| | - Rui Li
- Research Center for Learning Science, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China.
| | - Qinyu Ge
- Research Center for Learning Science, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China; State Key Laboratory of Bioelectronics, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China.
| | - Zuhong Lu
- Research Center for Learning Science, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China; State Key Laboratory of Bioelectronics, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China.
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Wang H, Wang J, Sun S, Wang Y, Guo J, Ning C, Yang K, Liu JF. Identification of reference microRNAs for quantitative expression analysis in porcine peripheral blood mononuclear cells treated with polyinosinic-polycytidylic acid. Int J Immunogenet 2015; 42:217-25. [PMID: 25817599 DOI: 10.1111/iji.12198] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Revised: 03/02/2015] [Accepted: 03/08/2015] [Indexed: 11/29/2022]
Abstract
Peripheral blood mononuclear cells (PBMCs) are clinically important cells. Detection of microRNAs (miRNAs) expression in PBMCs can be useful for miRNA biomarker discovery for various diseases. Quantitative real-time PCR (qRT-PCR) has become an important method used for measuring miRNAs expression. However, the reliability of qRT-PCR data critically depends on proper selection of reference genes. Here, we performed qRT-PCR to quantify the expression levels of nine miRNAs (Ssc-miR-16, Hsa-miR-25, Ssc-miR-34a, Hsa-miR-93, Bta-miR-92b, Ssc-miR-103, Ssc-miR-106a, Ssc-miR-128 and Ssc-miR-107) and one small nuclear RNA (U6) in PBMCs treated with polyinosinic-polycytidylic acid [poly (I:C)] that widely used for simulating viral infection. We used the four statistical algorithms (GeNorm 3.5, NormFinder, BestKeeper and comparative ∆ Ct method) to evaluate gene expression stability and observed that Ssc-miR-34a was the best single reference gene and the pair of Ssc-miR-107 and Ssc-miR-103 was the best combination of reference miRNAs for porcine PBMCs treated with poly (I:C). Our study shows the first evidence of careful selection of reference miRNAs in porcine PBMCs and maybe helpful for discovering miRNA biomarkers for double-stranded RNA-induced disease.
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Affiliation(s)
- H Wang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - J Wang
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - S Sun
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Y Wang
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - J Guo
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - C Ning
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - K Yang
- College of Animal Science and Technology, Shanxi Agricultural University, Taigu, China
| | - J-F Liu
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
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Zhan C, Yan L, Wang L, Jiang W, Zhang Y, Xi J, Chen L, Jin Y, Qiao Y, Shi Y, Wang Q. Identification of reference miRNAs in human tumors by TCGA miRNA-seq data. Biochem Biophys Res Commun 2014; 453:375-8. [PMID: 25264191 DOI: 10.1016/j.bbrc.2014.09.086] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 09/20/2014] [Indexed: 01/22/2023]
Abstract
Although the accuracy of detecting the expression of miRNAs by quantitative real-time polymerase chain reaction (qRT-PCR) is highly dependent on reliable reference miRNAs, many commonly used reference miRNAs are not stably expressed and as such are not suitable for quantification and normalization of qRT-PCR data. To solve this problem, we analyzed the global expression profiles of thousands of samples in 14 types of common human tumors released by The Cancer Genome Atlas (TCGA), and identified the most stably and highly expressed miRNAs as candidate reference miRNAs in each type of tumor. We found that miR-361-5p and let-7i-5p were the most recommended candidate reference miRNAs in nine and eight types of tumors, respectively, followed by let-7a-5p, mir-28-5p and miR-99b-5p. Our results are of important value to those researchers focused on miRNA; however, these candidate reference miRNAs still need to be validated prior to their use in qRT-PCR studies.
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Affiliation(s)
- Cheng Zhan
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Li Yan
- Department of Radiation Oncology, Eye and ENT Hospital, Fudan University, Shanghai 200031, China
| | - Lin Wang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Wei Jiang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yongxing Zhang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Junjie Xi
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Li Chen
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yulin Jin
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yulei Qiao
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China.
| | - Yu Shi
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China.
| | - Qun Wang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China
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