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Bustin SA. Improving the quality of quantitative polymerase chain reaction experiments: 15 years of MIQE. Mol Aspects Med 2024; 96:101249. [PMID: 38290180 DOI: 10.1016/j.mam.2024.101249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/02/2024] [Accepted: 01/15/2024] [Indexed: 02/01/2024]
Abstract
The quantitative polymerase chain reaction (qPCR) is fundamental to molecular biology. It is not just a laboratory technique, qPCR is a bridge between research and clinical practice. Its theoretical foundations guide the design of experiments, while its practical implications extend to diagnostics, treatment, and research advancements in the life sciences, human and veterinary medicine, agriculture, and forensics. However, the accuracy, reliability and reproducibility of qPCR data face challenges arising from various factors associated with experimental design, execution, data analysis and inadequate reporting details. Addressing these concerns, the Minimum Information for the Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines have emerged as a cohesive framework offering a standardised set of recommendations that describe the essential information required for assessing qPCR experiments. By emphasising the importance of methodological rigour, the MIQE guidelines have made a major contribution to improving the trustworthiness, consistency, and transparency of many published qPCR results. However, major challenges related to awareness, resources, and publication pressures continue to affect their consistent application.
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Affiliation(s)
- Stephen A Bustin
- Medical Technology Research Centre, Anglia Ruskin University, Chelmsford, Essex, CM1 1SQ, UK.
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2
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Rhodes C, Lewis C, Price K, Valentine A, Creighton MRA, Boone E, Seashols-Williams S. Evaluation and Verification of a microRNA Panel Using Quadratic Discriminant Analysis for the Classification of Human Body Fluids in DNA Extracts. Genes (Basel) 2023; 14:genes14050968. [PMID: 37239328 DOI: 10.3390/genes14050968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/20/2023] [Accepted: 04/22/2023] [Indexed: 05/28/2023] Open
Abstract
There is significant interest in the use of miRNA analysis for forensic body fluid identification. Demonstrated co-extraction and detection in DNA extracts could make the use of miRNAs a more streamlined molecular body fluid identification method than other RNA-based methods. We previously reported a reverse transcription-quantitative PCR (RT-qPCR) panel of eight miRNAs that classified venous and menstrual blood, feces, urine, saliva, semen, and vaginal secretions using a quadratic discriminant analysis (QDA) model with 93% accuracy in RNA extracts. Herein, miRNA expression in DNA extracts from 50 donors of each body fluid were tested using the model. Initially, a classification rate of 87% was obtained, which increased to 92% when three additional miRNAs were added. Body fluid identification was found to be reliable across population samples of mixed ages, ethnicities, and sex, with 72-98% of the unknown samples classifying correctly. The model was then tested against compromised samples and over biological cycles, where classification accuracy varied, depending on the body fluid. In conclusion, we demonstrated the ability to classify body fluids using miRNA expression from DNA extracts, eliminating the need for RNA extraction, greatly reducing evidentiary sample consumption and processing time in forensic laboratories, but acknowledge that compromised semen and saliva samples can fail to classify properly, and mixed sample classification remains untested and may have limitations.
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Affiliation(s)
- Ciara Rhodes
- Department of Forensic Science, Virginia Commonwealth University, P.O. Box 843079, 1015 Floyd Ave., Richmond, VA 23284-3079, USA
- Integrative Life Sciences Program, Virginia Commonwealth University, P.O. Box 842030, 1000 West Cary St., Richmond, VA 23284-2030, USA
| | - Carolyn Lewis
- Department of Forensic Science, Virginia Commonwealth University, P.O. Box 843079, 1015 Floyd Ave., Richmond, VA 23284-3079, USA
- Integrative Life Sciences Program, Virginia Commonwealth University, P.O. Box 842030, 1000 West Cary St., Richmond, VA 23284-2030, USA
| | - Kelsey Price
- Department of Forensic Science, Virginia Commonwealth University, P.O. Box 843079, 1015 Floyd Ave., Richmond, VA 23284-3079, USA
| | - Anaya Valentine
- Department of Forensic Science, Virginia Commonwealth University, P.O. Box 843079, 1015 Floyd Ave., Richmond, VA 23284-3079, USA
| | - Mary-Randall A Creighton
- Center for Biological Data Science, Virginia Commonwealth University, P.O. Box 842030, 1015 Floyd Ave., Richmond, VA 23284-2030, USA
| | - Edward Boone
- Department of Statistical Sciences and Operations Research, Virginia Commonwealth University, P.O. Box 843083, 1015 Floyd Ave., Richmond, VA 23284-3083, USA
| | - Sarah Seashols-Williams
- Department of Forensic Science, Virginia Commonwealth University, P.O. Box 843079, 1015 Floyd Ave., Richmond, VA 23284-3079, USA
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3
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Shi M, Han W, Loudig O, Shah CD, Dobkin JB, Keller S, Sadoughi A, Zhu C, Siegel RE, Fernandez MK, DeLaRosa L, Patel D, Desai A, Siddiqui T, Gombar S, Suh Y, Wang T, Hosgood HD, Pradhan K, Ye K, Spivack SD. Initial development and testing of an exhaled microRNA detection strategy for lung cancer case-control discrimination. Sci Rep 2023; 13:6620. [PMID: 37095155 PMCID: PMC10126132 DOI: 10.1038/s41598-023-33698-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 04/18/2023] [Indexed: 04/26/2023] Open
Abstract
For detecting field carcinogenesis non-invasively, early technical development and case-control testing of exhaled breath condensate microRNAs was performed. In design, human lung tissue microRNA-seq discovery was reconciled with TCGA and published tumor-discriminant microRNAs, yielding a panel of 24 upregulated microRNAs. The airway origin of exhaled microRNAs was topographically "fingerprinted", using paired EBC, upper and lower airway donor sample sets. A clinic-based case-control study (166 NSCLC cases, 185 controls) was interrogated with the microRNA panel by qualitative RT-PCR. Data were analyzed by logistic regression (LR), and by random-forest (RF) models. Feasibility testing of exhaled microRNA detection, including optimized whole EBC extraction, and RT and qualitative PCR method evaluation, was performed. For sensitivity in this low template setting, intercalating dye-based URT-PCR was superior to fluorescent probe-based PCR (TaqMan). In application, adjusted logistic regression models identified exhaled miR-21, 33b, 212 as overall case-control discriminant. RF analysis of combined clinical + microRNA models showed modest added discrimination capacity (1.1-2.5%) beyond clinical models alone: all subjects 1.1% (p = 8.7e-04)); former smokers 2.5% (p = 3.6e-05); early stage 1.2% (p = 9.0e-03), yielding combined ROC AUC ranging from 0.74 to 0.83. We conclude that exhaled microRNAs are qualitatively measureable, reflect in part lower airway signatures; and when further refined/quantitated, can potentially help to improve lung cancer risk assessment.
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Affiliation(s)
- Miao Shi
- Pulmonary Medicine, Albert Einstein College of Medicine, Bronx, NY, USA.
| | - Weiguo Han
- Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ, USA
| | | | - Chirag D Shah
- Pulmonary Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jay B Dobkin
- Pulmonary Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | | | - Ali Sadoughi
- Pulmonary Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Changcheng Zhu
- Pathology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Robert E Siegel
- Pulmonary Medicine, Icahn School of Medicine at Mount Sinai, James J. Peters Veterans Affairs Medical Center, New York, USA
| | | | - Lizett DeLaRosa
- Pulmonary Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | | | | | - Taha Siddiqui
- Pulmonary Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Saurabh Gombar
- Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Yousin Suh
- Reproductive Sciences (in Obstetrics and Gynecology), Columbia University, New York, USA
- Genetics and Development, Columbia University, New York, USA
| | - Tao Wang
- Biostatistics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - H Dean Hosgood
- Epidemiology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Kith Pradhan
- Biostatistics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Kenny Ye
- Biostatistics, Albert Einstein College of Medicine, Bronx, NY, USA
- Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Simon D Spivack
- Pulmonary Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
- Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
- Epidemiology, Albert Einstein College of Medicine, Bronx, NY, USA
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4
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Wenzlow N, Mills D, Byrd J, Warren M, Long MT. Review of the current and potential use of biological and molecular methods for the estimation of the postmortem interval in animals and humans. J Vet Diagn Invest 2023; 35:97-108. [PMID: 36744749 PMCID: PMC9999395 DOI: 10.1177/10406387231153930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
We provide here an overview of the state of applied techniques in the estimation of the early period of the postmortem interval (PMI). The biological methods included consist of body cooling, CSF potassium, body cooling combined with CSF potassium, and tissue autolysis. For each method, we present its application in human and veterinary medicine and provide current methodology, strengths, and weaknesses, as well as target areas for improvement. We examine current and future molecular methods as they pertain to DNA and primarily to messenger RNA degradation for the estimation of the PMI, as well as the use of RNA in aging wounds, aging blood stains, and the identification of body fluids. Various types of RNA have different lengths, structures, and functions in cells. These differences in RNAs determine various intrinsic properties, such as their half-lives in cells, and, hence, their decay rate as well as their unique use for specific forensic tests. Future applications and refinements of RNA-based techniques provide opportunities for the use of molecular methods in the estimation of PMI and other general forensic applications.
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Affiliation(s)
- Nanny Wenzlow
- Louisiana Animal Disease Diagnostic Laboratory, Louisiana State University, Baton Rouge, LA, USA
| | - DeEtta Mills
- Department of Biological Sciences and International Forensic Research Institute, Florida International University, Miami, FL, USA
| | - Jason Byrd
- Maples Center for Forensic Medicine, University of Florida, Gainesville, FL, USA
| | - Mike Warren
- Maples Center for Forensic Medicine, University of Florida, Gainesville, FL, USA
| | - Maureen T. Long
- Department of Comparative, Diagnostic, and Population Medicine, University of Florida, Gainesville, FL, USA
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5
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De los Santos Funes JA, Andrade JPN, Berndtson J, Parrish J. Short communication: profiling the expression of Let-7d-5p microRNA in circulating blood of pregnant and nonpregnant cows. J Anim Sci 2023; 101:skad054. [PMID: 36850045 PMCID: PMC10079811 DOI: 10.1093/jas/skad054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 02/14/2023] [Indexed: 03/01/2023] Open
Abstract
The objective of this work was to determine if specific circulating microRNA (miRNA) differed due to pregnancy status in heifers. Blood samples were collected from heifers 21 d after receiving an in vitro-produced embryo. Pregnancy status was diagnosed 21 d after embryo transfer, equivalent to day 28 of gestation, with rectal ultrasonography. Blood samples from 10 pregnant and 10 nonpregnant heifers were then evaluated for miRNA expression. There were five different miRNAs quantified using delta-delta Ct and qPCR methodology. These miRNAs had previously been associated with early pregnancy in cattle. The miRNA Let-7d-5p was decreased in nonpregnant as compared to pregnant females (P < 0.05). There were no changes in 16-5p, 16-1-3p, 16-2-3p, and 26a-5p associated with pregnancy (P > 0.05). Results demonstrate an opportunity to identify and study the differential expression of miRNAs from the blood of pregnant cows. The Let-7d-5p miRNA is a potential early pregnancy marker and is critical to better understand the early relationships of the cellular and molecular interactions of the cow and embryo.
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Affiliation(s)
| | - João Paulo N Andrade
- Department of Animal and Dairy Sciences, University of Wisconsin Madison, WI 53706-1205, USA
| | - Jodi Berndtson
- Department of Animal and Dairy Sciences, University of Wisconsin Madison, WI 53706-1205, USA
| | - John Parrish
- Department of Animal and Dairy Sciences, University of Wisconsin Madison, WI 53706-1205, USA
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6
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Identification of the vaginal secretion donor in mixture stains using polymorphic cSNPs on mRNA biomarkers. Forensic Sci Int Genet 2022; 59:102703. [DOI: 10.1016/j.fsigen.2022.102703] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 03/27/2022] [Accepted: 03/28/2022] [Indexed: 01/27/2023]
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7
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Rhodes C, Lewis C, Szekely J, Campbell A, Creighton MRA, Boone E, Seashols-Williams S. Developmental validation of a microRNA panel using quadratic discriminant analysis for the classification of seven forensically relevant body fluids. Forensic Sci Int Genet 2022; 59:102692. [DOI: 10.1016/j.fsigen.2022.102692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 03/09/2022] [Accepted: 03/21/2022] [Indexed: 11/30/2022]
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8
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Błaszczyk M, Gajewska M, Dymowska M, Majewska A, Domoradzki T, Prostek A, Pingwara R, Hulanicka M, Grzelkowska-Kowalczyk K. Interleukin-6 mimics insulin-dependent cellular distribution of some cytoskeletal proteins and Glut4 transporter without effect on glucose uptake in 3T3-L1 adipocytes. Histochem Cell Biol 2022; 157:525-546. [PMID: 35230485 DOI: 10.1007/s00418-022-02091-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2022] [Indexed: 11/04/2022]
Abstract
Interleukin (IL)-6, a known proinflammatory cytokine, is released in both visceral adipose tissue and contracting skeletal muscle. In this study, we used microRNA profiling as a screening method to identify miRNA species modified by IL-6 treatment in mouse 3T3-L1 adipocytes. miRNA microarray analysis and qRT-PCR revealed increased expression of miR-146b-3p in adipocytes exposed to IL-6 (1 ng/ml) during 8-day differentiation. On the basis of ontological analysis of potential targets, selected proteins associated with cytoskeleton and transport were examined in the context of adipocyte response to insulin, using immunofluorescence and confocal microscopy. We concluded that IL-6: (i) does not affect insulin action on actin cellular distribution; (ii) modulates the effect of insulin on myosin light chain kinase (Mylk) distribution by preventing its shift toward cytoplasm; (iii) mimics the effect of insulin on dynein distribution by increasing its near-nuclear accumulation; (iv) mimics the effect of insulin on glucose transporter Glut4 distribution, especially by increasing its near-nuclear accumulation; (v) supports insulin action on early endosome marker Rab4A near-nuclear accumulation. Moreover, as IL-6 did not disturb insulin-dependent glucose uptake, our results do not confirm the IL-6-induced impairment of insulin action observed in some in vitro studies, suggesting that the effect of IL-6 is dose dependent.
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Affiliation(s)
- Maciej Błaszczyk
- Department of Physiological Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Małgorzata Gajewska
- Department of Physiological Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Marta Dymowska
- Department of Physiological Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Alicja Majewska
- Department of Physiological Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Tomasz Domoradzki
- Department of Physiological Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Adam Prostek
- Department of Physiological Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Rafał Pingwara
- Department of Physiological Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Magdalena Hulanicka
- Department of Physiological Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Katarzyna Grzelkowska-Kowalczyk
- Department of Physiological Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776, Warsaw, Poland.
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9
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miR-9 Does Not Regulate Lamin A Expression in Metastatic Cells from Lung Adenocarcinoma. Int J Mol Sci 2020; 21:ijms21051599. [PMID: 32111074 PMCID: PMC7084260 DOI: 10.3390/ijms21051599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/20/2020] [Accepted: 02/22/2020] [Indexed: 11/17/2022] Open
Abstract
In lung adenocarcinoma, low lamin A expression in pleural metastatic cells has been proposed as a pejorative factor. miR-9 physiologically inhibits the expression of lamin A in neural cells and seems to be a central actor in the carcinogenesis and the metastatic process in lung cancer. Thus, it could be a good candidate to explain the reduction of lamin A expression in lung adenocarcinoma cells. miR-9 expression was analyzed in 16 pleural effusions containing metastatic cells from lung adenocarcinoma and was significantly reduced in patients from the 'Low lamin A expression' group compared to patients from the 'High lamin A expression' group. Then, carcinoma cells selection by fluorescence-activated cell sorting (FACS) was performed according to epithelial membrane antigen (EMA) expression, reflecting lamin A expression. miR-9 was underexpressed in lamin A- carcinoma cells compared to lamin A+ carcinoma cells in patients from the 'Low lamin A expression' group, whereas there was no difference of miR-9 expression between lamin A+ and lamin A- carcinoma cells in patients from the 'High lamin A expression' group. These results suggest that miR-9 does not regulate lamin A expression in metastatic cells from lung adenocarcinoma. On the contrary, miR-9 expression was shown to be reduced in lamin A-negative carcinoma cells.
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10
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Milewska M, Domoradzki T, Majewska A, Błaszczyk M, Gajewska M, Hulanicka M, Grzelkowska-Kowalczyk K. Interleukin-6 affects pacsin3, ephrinA4 expression and cytoskeletal proteins in differentiating primary skeletal myoblasts through transcriptional and post-transcriptional mechanisms. Cell Tissue Res 2019; 380:155-172. [PMID: 31820147 DOI: 10.1007/s00441-019-03133-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 10/29/2019] [Indexed: 12/18/2022]
Abstract
Interleukin (IL)-6 is a proinflammatory cytokine released in injured and contracting skeletal muscles. In this study, we examined cellular expression of proteins associated with cytoskeleton organization and cell migration, chosen on the basis of microRNA profiling, in rat primary skeletal muscle cells (RSkMC) treated with IL-6 (1 ng/ml) for 11 days. MiRNA microarray analysis and qRT-PCR revealed increased expression of miR-154-3p and miR-338-3p in muscle cells treated with IL-6. Pacsin3 was downregulated post-transcriptionally by IL-6, but not by IGF-I. Ephrin4A protein was increased both in IL-6- and IGF-I-treated myocytes. IL-6, but not IGF-I, stimulated migratory ability of RSkMC, examined in wound healing assay. Alpha-actinin protein was slightly augmented in RSKMC treated with IL-6, similarly to IGF-I. IL-6, but not IGF-I, upregulated desmin in differentiating RSkMC. IL-6 supplementation caused accumulation of alpha-actinin and desmin in near-nuclear area of muscle cells, which was manifested by increased ratio: mean near-nuclear fluorescence/mean peripheral cytoplasm fluorescence of these proteins. We concluded that IL-6, a known proinflammatory cytokine and a physical activity-associated myokine, acting during differentiation of primary skeletal muscle cells, alters expression of nonmuscle-specific miRNAs. This cytokine causes differential effects on pacsin-3 and ephrinA4, through post-transcriptional inhibition and stimulation, respectively. IL-6-exerted modifications of cytoskeletal proteins in muscle cells include both transcriptional (desmin and dynein heavy chain 5) and post-transcriptional activation (alpha-actinin). Moreover, IL-6 augments near-nuclear distribution of cytoskeletal proteins, alpha-actinin and desmin and promotes migration of myocytes. Such effects suggest that IL-6 plays a role during skeletal muscle regeneration, acting through mechanisms independent of regulation of myogenic program.
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Affiliation(s)
- Marta Milewska
- Institute of Veterinary Medicine, Department of Physiological Sciences, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Tomasz Domoradzki
- Institute of Veterinary Medicine, Department of Physiological Sciences, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Alicja Majewska
- Institute of Veterinary Medicine, Department of Physiological Sciences, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Maciej Błaszczyk
- Institute of Veterinary Medicine, Department of Physiological Sciences, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Małgorzata Gajewska
- Institute of Veterinary Medicine, Department of Physiological Sciences, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Magdalena Hulanicka
- Institute of Veterinary Medicine, Department of Physiological Sciences, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Katarzyna Grzelkowska-Kowalczyk
- Institute of Veterinary Medicine, Department of Physiological Sciences, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776, Warsaw, Poland.
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11
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Lv Y, Li S, Li Z, Tao R, Shao Y, Chen Y. Quantitative analysis of noncoding RNA from paired fresh and formalin-fixed paraffin-embedded brain tissues. Int J Legal Med 2019; 134:873-884. [PMID: 31788707 DOI: 10.1007/s00414-019-02210-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 11/13/2019] [Indexed: 12/30/2022]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues are commonly used both clinically and in forensic pathology. Recently, noncoding RNA (ncRNA) has attracted interest among molecular medical researchers. However, it remains unclear whether newly identified ncRNAs, such as long noncoding RNA (lncRNA) and circular RNA (circRNA), remain stable for downstream molecular analysis in FFPE tissues. Here, we assessed the feasibility of using autoptic FFPE brain tissues from eight individuals to perform quantitative molecular analyses. Selected RNA targets (9 mRNAs and 15 ncRNAs) with different amplicon lengths were studied by RT-qPCR in paired fresh and FFPE specimens. For RNA quality assessment, RNA purity and yield were comparable between the two sample cohorts; however, the RNA integrity number decreased significantly during FFPE sampling. Amplification efficiency also displayed certain variability related with amplicon length and RNA species. We found molecular evidence that short amplicons of mRNA, lncRNA, and circRNA were amplified more efficiently than long amplicons. With the assistance of RefFinder, 5S, SNORD48, miR-103a, and miR-125b were selected as reference genes given their high stability. After normalization, we found that short amplicon markers (e.g., ACTB mRNA and MALAT1 lncRNA) exhibited high consistency of quantification in paired fresh/FFPE samples. In particular, circRNAs (XPO1, HIPK3, and TMEM56) presented relatively consistent and stable expression profiles in FFPE tissues compared with their corresponding linear transcripts. Additionally, we evaluated the influence of prolonged storage time on the amplification of gene transcripts and found that short amplicons still work effectively in archived FFPE biospecimens. In conclusion, our findings demonstrate the possibility of performing accurate quantitative analysis of ncRNAs using short amplicons and standardized RT-qPCR assays in autopsy-derived FFPE samples.
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Affiliation(s)
- Yehui Lv
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610065, China. .,Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, 200063, China. .,School of basic medical sciences, Shanghai University of Medicine & Health Science, Shanghai, 201318, China.
| | - Shiying Li
- Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, 200063, China
| | - Zhihong Li
- School of basic medical sciences, Shanghai University of Medicine & Health Science, Shanghai, 201318, China
| | - Ruiyang Tao
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610065, China.,Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, 200063, China
| | - Yu Shao
- Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, 200063, China
| | - Yijiu Chen
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610065, China. .,Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, 200063, China.
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12
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Carrasco‐Rozas A, Fernández‐Simón E, Lleixà MC, Belmonte I, Pedrosa-Hernandez I, Montiel-Morillo E, Nuñez‐Peralta C, Llauger Rossello J, Segovia S, De Luna N, Suarez‐Calvet X, Illa I, Díaz‐Manera J, Gallardo E. Identification of serum microRNAs as potential biomarkers in Pompe disease. Ann Clin Transl Neurol 2019; 6:1214-1224. [PMID: 31353854 PMCID: PMC6649638 DOI: 10.1002/acn3.50800] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 05/03/2019] [Accepted: 05/04/2019] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVE To analyze the microRNA profile in serum of patients with Adult Onset Pompe disease (AOPD). METHODS We analyzed the expression of 185 microRNAs in serum of 15 AOPD patients and five controls using microRNA PCR Panels. The expression levels of microRNAs that were deregulated were further studied in 35 AOPD patients and 10 controls using Real-Time PCR. Additionally, the skeletal muscle expression of microRNAs which showed significant increase levels in serum samples was also studied. Correlations between microRNA serum levels and muscle function test, spirometry, and quantitative muscle MRI were performed (these data correspond to the study NCT01914536 at ClinicalTrials.gov). RESULTS We identified 14 microRNAs that showed different expression levels in serum samples of AOPD patients compared to controls. We validated these results in a larger cohort of patients and we found increased levels of three microRNAs, the so called dystromirs: miR-1-3p, miR-133a-3p, and miR-206. These microRNAs are involved in muscle regeneration and the expression of these was increased in patients' muscle biopsies. Significant correlations between microRNA levels and muscle function test were found. INTERPRETATION Serum expression levels of dystromirs may represent additional biomarkers for the follow-up of AOPD patients.
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Affiliation(s)
- Ana Carrasco‐Rozas
- Neuromuscular Disorders Unit, Neurology DepartmentHospital de la Santa Creu i Sant Pau, Universitat Autònoma de BarcelonaBarcelonaSpain
| | - Esther Fernández‐Simón
- Neuromuscular Disorders Unit, Neurology DepartmentHospital de la Santa Creu i Sant Pau, Universitat Autònoma de BarcelonaBarcelonaSpain
| | - Maria Cinta Lleixà
- Neuromuscular Disorders Unit, Neurology DepartmentHospital de la Santa Creu i Sant Pau, Universitat Autònoma de BarcelonaBarcelonaSpain
| | - Izaskun Belmonte
- Rehabilitation and Physiotherapy DepartmentHospital de la Santa Creu i Sant Pau, Universitat Autònoma de BarcelonaBarcelonaSpain
| | - Irene Pedrosa-Hernandez
- Rehabilitation and Physiotherapy DepartmentHospital de la Santa Creu i Sant Pau, Universitat Autònoma de BarcelonaBarcelonaSpain
| | - Elena Montiel-Morillo
- Rehabilitation and Physiotherapy DepartmentHospital de la Santa Creu i Sant Pau, Universitat Autònoma de BarcelonaBarcelonaSpain
| | - Claudia Nuñez‐Peralta
- Radiology DepartmentHospital de la Santa Creu I Sant Pau, Universitat Autònoma de BarcelonaBarcelonaSpain
| | - Jaume Llauger Rossello
- Radiology DepartmentHospital de la Santa Creu I Sant Pau, Universitat Autònoma de BarcelonaBarcelonaSpain
| | - Sonia Segovia
- Neuromuscular Disorders Unit, Neurology DepartmentHospital de la Santa Creu i Sant Pau, Universitat Autònoma de BarcelonaBarcelonaSpain
- Centro de Investigación Biomédica en Red en Enfermedades RarasValenciaSpain
| | - Noemí De Luna
- Neuromuscular Disorders Unit, Neurology DepartmentHospital de la Santa Creu i Sant Pau, Universitat Autònoma de BarcelonaBarcelonaSpain
- Centro de Investigación Biomédica en Red en Enfermedades RarasValenciaSpain
| | - Xavier Suarez‐Calvet
- Neuromuscular Disorders Unit, Neurology DepartmentHospital de la Santa Creu i Sant Pau, Universitat Autònoma de BarcelonaBarcelonaSpain
- Centro de Investigación Biomédica en Red en Enfermedades RarasValenciaSpain
| | - Isabel Illa
- Neuromuscular Disorders Unit, Neurology DepartmentHospital de la Santa Creu i Sant Pau, Universitat Autònoma de BarcelonaBarcelonaSpain
- Centro de Investigación Biomédica en Red en Enfermedades RarasValenciaSpain
| | - Jordi Díaz‐Manera
- Neuromuscular Disorders Unit, Neurology DepartmentHospital de la Santa Creu i Sant Pau, Universitat Autònoma de BarcelonaBarcelonaSpain
- Centro de Investigación Biomédica en Red en Enfermedades RarasValenciaSpain
| | - Eduard Gallardo
- Neuromuscular Disorders Unit, Neurology DepartmentHospital de la Santa Creu i Sant Pau, Universitat Autònoma de BarcelonaBarcelonaSpain
- Centro de Investigación Biomédica en Red en Enfermedades RarasValenciaSpain
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13
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Courts C, Pfaffl MW, Sauer E, Parson W. Pleading for adherence to the MIQE-Guidelines when reporting quantitative PCR data in forensic genetic research. Forensic Sci Int Genet 2019; 42:e21-e24. [PMID: 31270013 DOI: 10.1016/j.fsigen.2019.06.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/25/2019] [Accepted: 06/25/2019] [Indexed: 01/13/2023]
Affiliation(s)
- Cornelius Courts
- University Hospital of Schleswig-Holstein, Institute of Forensic Medicine, Kiel, Germany.
| | - Michael W Pfaffl
- Technical University of Munich, Animal Physiology and Immunology, Freising, Germany
| | - Eva Sauer
- State Office of Criminal Investigation of Rhineland-Palatinate, Mainz, Germany
| | - Walther Parson
- Innsbruck Medical University, Institute of Legal Medicine, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, University Park, Pennsylvania, USA
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14
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Layne TR, Green RA, Lewis CA, Nogales F, Dawson Cruz TC, Zehner ZE, Seashols-Williams SJ. microRNA Detection in Blood, Urine, Semen, and Saliva Stains After Compromising Treatments. J Forensic Sci 2019; 64:1831-1837. [PMID: 31184791 DOI: 10.1111/1556-4029.14113] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 05/22/2019] [Accepted: 05/24/2019] [Indexed: 02/06/2023]
Abstract
Evaluation of microRNA (miRNA) expression as a potential method for forensic body fluid identification has been the subject of investigation over the past several years. Because of their size and encapsulation within proteins and lipids, miRNAs are inherently less susceptible to degradation than other RNAs. In this work, blood, urine, semen, and saliva were exposed to environmental and chemical conditions mimicking sample compromise at the crime scene. For many treated samples, including 100% of blood samples, miRNAs remained detectable, comparable to the untreated control. Sample degradation varied by body fluid and treatment, with blood remarkably resistant, while semen and saliva are more susceptible to environmental insult. Body fluid identification using relative miRNA expression of blood and semen of the exposed samples was 100% and 94%, respectively. Given the overall robust results herein, the case is strengthened for the use of miRNAs as a molecular method for body fluid identification.
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Affiliation(s)
- Tiffany R Layne
- Department of Forensic Science, Virginia Commonwealth University, Box 843079, Richmond, Virginia, 23284-3079
| | - Raquel A Green
- Department of Forensic Science, Virginia Commonwealth University, Box 843079, Richmond, Virginia, 23284-3079
| | - Carolyn A Lewis
- Department of Forensic Science, Virginia Commonwealth University, Box 843079, Richmond, Virginia, 23284-3079
| | - Francy Nogales
- Department of Forensic Science, Virginia Commonwealth University, Box 843079, Richmond, Virginia, 23284-3079
| | - Tracey C Dawson Cruz
- Department of Forensic Science, Virginia Commonwealth University, Box 843079, Richmond, Virginia, 23284-3079
| | - Zendra E Zehner
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Box 980614, Richmond, Virginia, 23298-0614
| | - Sarah J Seashols-Williams
- Department of Forensic Science, Virginia Commonwealth University, Box 843079, Richmond, Virginia, 23284-3079
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15
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Milewska M, Domoradzki T, Majewska A, Błaszczyk M, Gajewska M, Hulanicka M, Ciecierska A, Grzelkowska-Kowalczyk K. Interleukin-8 enhances myocilin expression, Akt-FoxO3 signaling and myogenic differentiation in rat skeletal muscle cells. J Cell Physiol 2019; 234:19675-19690. [PMID: 30945300 DOI: 10.1002/jcp.28568] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 03/04/2019] [Accepted: 03/06/2019] [Indexed: 01/01/2023]
Abstract
Interleukin (IL)-8 is released both in visceral adipose tissue and in contracting skeletal muscles. In this study, we examined cellular pathways associated with muscle hypertrophy, chosen on the basis of microRNA profiling, in differentiating rat primary skeletal muscle cells (RSkMC) treated with IL-8 (1 ng/ml) for 11 days. IL-8 increased myocilin expression, Akt phosphorylation, FoxO3 dispersion throughout the cytoplasm, and reduced FoxO3 level. IL-8 decreased the expression of atrogin and MuRF1 and increased myotube length and diameter. We concluded that IL-8 present in extracellular environment of myoblasts induced to differentiation stimulates expression of myocilin, a protein important for skeletal muscle hypertrophy. This phenomenon was associated with: (a) activation of myogenic transcription, (b) increased phosphorylation and activation of PKB/Akt, leading to (c) cytoplasm distribution and degradation of a transcription factor FoxO3, (d) decreased expression of gene markers of proteolysis, atrogin and Murf1, and (e) increased myotube length and diameter. In this regard, IL-8 affects skeletal muscle cells similarly to IGF-I and can be considered as a potent anticatabolic factor for skeletal muscle.
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Affiliation(s)
- Marta Milewska
- Department of Physiological Sciences, Faculty of Veterinary Medicine, Warsaw University of Life Sciences (SGGW), Warsaw, Poland
| | - Tomasz Domoradzki
- Department of Physiological Sciences, Faculty of Veterinary Medicine, Warsaw University of Life Sciences (SGGW), Warsaw, Poland
| | - Alicja Majewska
- Department of Physiological Sciences, Faculty of Veterinary Medicine, Warsaw University of Life Sciences (SGGW), Warsaw, Poland
| | - Maciej Błaszczyk
- Department of Physiological Sciences, Faculty of Veterinary Medicine, Warsaw University of Life Sciences (SGGW), Warsaw, Poland
| | - Małgorzata Gajewska
- Department of Physiological Sciences, Faculty of Veterinary Medicine, Warsaw University of Life Sciences (SGGW), Warsaw, Poland
| | - Magdalena Hulanicka
- Department of Physiological Sciences, Faculty of Veterinary Medicine, Warsaw University of Life Sciences (SGGW), Warsaw, Poland
| | - Anna Ciecierska
- Department of Physiological Sciences, Faculty of Veterinary Medicine, Warsaw University of Life Sciences (SGGW), Warsaw, Poland
| | - Katarzyna Grzelkowska-Kowalczyk
- Department of Physiological Sciences, Faculty of Veterinary Medicine, Warsaw University of Life Sciences (SGGW), Warsaw, Poland
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16
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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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17
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Characterization of tissue-specific biomarkers with the expression of circRNAs in forensically relevant body fluids. Int J Legal Med 2019; 133:1321-1331. [PMID: 30810820 DOI: 10.1007/s00414-019-02027-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 02/14/2019] [Indexed: 10/27/2022]
Abstract
Messenger RNA (mRNA) markers have been extensively investigated for the identification of forensically relevant body fluids and tissues based on their expression profiles among cell types. As products of the backsplicing of pre-mRNAs, circular RNAs (circRNAs) share exonic sequences with their linear counterparts. The inclusion of circRNAs in mRNA profiling is shown to facilitate the detection of biomarkers in the identification of body fluids. In this study, we identified the expression of circRNAs of 14 out of 45 biomarkers from five body fluid types using outward-facing primer sets and revealed the ratio of circular to total transcripts of biomarkers by RNase R treatment. Furthermore, our results of qPCR analysis show that the inclusion of circRNAs in the detection of biomarkers, including HBA and ALAS2 for blood; MMP7 and MMP10 for menstrual blood; HTN3 for saliva; SPINK5, SERPINB3, ESR1, and CYP2B7P1 for vaginal secretions; TGM4, KLK3, and PRM2 for semen; and SLC22A6 and MIOX for urine, does not impair the specificity of these biomarkers. Additionally, a high copy number of targets from linear transcripts could be employed to increase the detection sensitivity of TGM4 and KLK3 with a low expression level of circRNAs in urine samples. Altogether, these results will help with the development of robust multiplex assays for body fluid identification.
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18
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Inada K, Okoshi Y, Cho-Isoda Y, Ishiguro S, Suzuki H, Oki A, Tamaki Y, Shimazui T, Saito H, Hori M, Iijima T, Kojima H. Endogenous reference RNAs for microRNA quantitation in formalin-fixed, paraffin-embedded lymph node tissue. Sci Rep 2018; 8:5918. [PMID: 29651113 PMCID: PMC5897550 DOI: 10.1038/s41598-018-24338-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 03/28/2018] [Indexed: 12/18/2022] Open
Abstract
Lymph node metastasis is one of the most important factors for tumor dissemination. Quantifying microRNA (miRNA) expression using real-time PCR in formalin-fixed, paraffin-embedded (FFPE) lymph node can provide valuable information regarding the biological research for cancer metastasis. However, a universal endogenous reference gene has not been identified in FFPE lymph node. This study aimed to identify suitable endogenous reference genes for miRNA expression analysis in FFPE lymph node. FFPE lymph nodes were obtained from 41 metastatic cancer and from 16 non-cancerous tissues. We selected 10 miRNAs as endogenous reference gene candidates using the global mean method. The stability of candidate genes was assessed by the following four statistical tools: BestKeeper, geNorm, NormFinder, and the comparative ΔCt method. miR-103a was the most stable gene among candidate genes. However, the use of a single miR-103a was not recommended because its stability value exceeded the reference value. Thus, we combined stable genes and investigated the stability and the effect of gene normalization. The combination of miR-24, miR-103a, and let-7a was identified as one of the most stable sets of endogenous reference genes for normalization in FFPE lymph node. This study may provide a basis for miRNA expression analysis in FFPE lymph node tissue.
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Affiliation(s)
- Katsushige Inada
- Department of Hematology, Ibaraki Prefectural Central Hospital, Ibaraki, Japan.
| | - Yasushi Okoshi
- Department of Hematology, Ibaraki Prefectural Central Hospital, Ibaraki, Japan.,Ibaraki Clinical Education and Training Center, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Yukiko Cho-Isoda
- Department of Medical Oncology, Ibaraki Prefectural Central Hospital, Ibaraki, Japan
| | - Shingo Ishiguro
- Department of Medical Oncology, Ibaraki Prefectural Central Hospital, Ibaraki, Japan
| | - Hisashi Suzuki
- Ibaraki Clinical Education and Training Center, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan.,Department of Thoracic Surgery, Ibaraki Prefectural Central Hospital, Ibaraki, Japan
| | - Akinori Oki
- Ibaraki Clinical Education and Training Center, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan.,Department of Obstetrics and Gynecology, Ibaraki Prefectural Central Hospital, Ibaraki, Japan
| | - Yoshio Tamaki
- Ibaraki Clinical Education and Training Center, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan.,Department of Radiation Oncology, Ibaraki Prefectural Central Hospital, Ibaraki, Japan
| | - Toru Shimazui
- Ibaraki Clinical Education and Training Center, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan.,Department of Urology, Ibaraki Prefectural Central Hospital, Ibaraki, Japan
| | - Hitoaki Saito
- Department of Pathology, Ibaraki Prefectural Central Hospital, Ibaraki, Japan
| | - Mitsuo Hori
- Department of Hematology, Ibaraki Prefectural Central Hospital, Ibaraki, Japan
| | - Tatsuo Iijima
- Department of Pathology, Ibaraki Prefectural Central Hospital, Ibaraki, Japan
| | - Hiroshi Kojima
- Ibaraki Clinical Education and Training Center, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan.,Department of Medical Oncology, Ibaraki Prefectural Central Hospital, Ibaraki, Japan
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19
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Semen-specific miRNAs: Suitable for the distinction of infertile semen in the body fluid identification? Forensic Sci Int Genet 2018; 33:161-167. [DOI: 10.1016/j.fsigen.2017.12.010] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 11/02/2017] [Accepted: 12/19/2017] [Indexed: 11/24/2022]
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20
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Wilczynski M, Danielska J, Domanska-Senderowska D, Dzieniecka M, Szymanska B, Malinowski A. Association of microRNA-200c expression levels with clinicopathological factors and prognosis in endometrioid endometrial cancer. Acta Obstet Gynecol Scand 2018; 97:560-569. [PMID: 29355888 DOI: 10.1111/aogs.13306] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 01/13/2018] [Indexed: 12/16/2022]
Abstract
INTRODUCTION MicroRNAs (miRNAs) are regulators of gene expression, which play an important role in many critical cellular processes including apoptosis, proliferation and cell differentiation. Aberrant miRNA expression has been reported in a variety of human malignancies. Therefore, miRNAs may be potentially used as cancer biomarkers. miRNA-200c, which is a member of the miRNA-200 family, might play an essential role in tumor progression. The purpose of this study was to evaluate the prognostic and clinical significance of miRNA-200c in women with endometrioid endometrial cancer. MATERIAL AND METHODS Total RNA extraction from 90 archival formalin-fixed paraffin-embedded tissue samples of endometri-oid endometrial cancer and 10 normal endometrium samples was performed. After cDNA synthesis, real-time polymerase chain reaction was conducted and relative expression of miRNA-200c was assessed. Then, miRNA-200c expression levels were evaluated with regard to clinicopathological characteristics. RESULTS The expression levels of miRNA-200c were significantly increased in endometrioid endometrial cancer samples. Expression of miRNA-200c maintained at significantly higher levels in the early stage endometrioid endometrial cancer compared with more advanced stages. In the Kaplan-Meier analysis, lower levels of miRNA-200c expression were associated with inferior survival. CONCLUSIONS Expression levels of miRNA-200c might be associated with clinicopathological factors and survival in endometrioid endometrial cancer.
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Affiliation(s)
- Milosz Wilczynski
- Endoscopy and Gynecologic Oncology, Department of Operative Gynecology, Polish Mother's Memorial Hospital Research Institute, Lodz, Poland
| | | | | | - Monika Dzieniecka
- Department of Pathology, Polish Mother's Memorial Hospital Research Institute, Lodz, Poland
| | | | - Andrzej Malinowski
- Department of Surgical and Endoscopic Gynecology, Medical University in Lodz, Lodz, Poland
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21
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Mayes C, Seashols-Williams S, Hughes-Stamm S. A capillary electrophoresis method for identifying forensically relevant body fluids using miRNAs. Leg Med (Tokyo) 2017; 30:1-4. [PMID: 29125963 DOI: 10.1016/j.legalmed.2017.10.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 10/25/2017] [Accepted: 10/30/2017] [Indexed: 12/20/2022]
Abstract
Body fluid identification (BFID) can provide crucial information during the course of an investigation. In recent years, microRNAs (miRNAs) have shown considerable body fluid specificity, are able to be co-extracted with DNA, and their small size (18-25 nucleotides) make them ideal for analyzing highly degraded forensic samples. In this study, we designed a preliminary 8-marker system for BFID including an endogenous reference gene (let-7g) to differentiate between venous blood (miR-451a and miR-142-3p), menstrual blood (miR-141-3p and miR-412-3p), semen (miR-891a and miR-10b), and saliva (miR-205) using a capillary electrophoresis approach. This panel uses a linear primer system in order to incorporate additional miRNA markers by forming a multiplex system. The miRNA system was able to distinguish between venous blood, menstrual blood, semen, and saliva using a rudimentary data interpretation strategy. All STR amplifications from co-extracted DNA yielded complete profiles from human identification purposes.
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Affiliation(s)
- Carrie Mayes
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, 1003 Bowers Blvd., Huntsville, TX 77340-2525, United States.
| | - Sarah Seashols-Williams
- Department of Forensic Science, Virginia Commonwealth University, Box 843079, Richmond, VA 23284, United States
| | - Sheree Hughes-Stamm
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, 1003 Bowers Blvd., Huntsville, TX 77340-2525, United States
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22
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RNA/DNA co-analysis from bloodstains on aged polyvinyl-alcohol gloves prepared for securing evidence from the hands of victims of fatal gunshot injuries. Int J Legal Med 2017; 132:53-66. [PMID: 28956148 DOI: 10.1007/s00414-017-1687-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 08/30/2017] [Indexed: 12/22/2022]
Abstract
In contrast to cumulative techniques (e.g., tape-lift) for qualitative gunshot residues (GSR) analysis, topographic methods are commonly applied to preserve the integrity of evidence from a shooter's or victim's hand in cases of gun-related crimes. Topographic sampling techniques employing adhesive foils, latex, or the polyvinyl alcohol (PVAL) method enable unambiguous sampling of biological and non-biological trace material while preserving its spatial distribution and relation to each other. The PVAL method in particular allows for a topographically veridic and quantitative conservation of traces of GSR and biological stains that are embedded in the PVAL glove, because it completely removes these traces from the hand. The present study investigated the success rates of STR profiling and the detection of blood and brain-specific gene expression from minimal traces of blood splatter as well as parallel to the positive detection of gunshot residues embedded in 17 PVAL gloves taken from the hands of deceased persons in the context of homicide cases in the period between 1996 and 2003. The water-soluble PVAL matrix is shown to be fully compatible with successful STR profiling and the detection of blood- and brain-specific miRNA expression, even after up to 20 years of storage, demonstrating that this sampling technique offers advantages compared to other more simplistic sampling methods like taping.
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23
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DNA methylation variations are required for epithelial-to-mesenchymal transition induced by cancer-associated fibroblasts in prostate cancer cells. Oncogene 2017; 36:5551-5566. [PMID: 28581528 DOI: 10.1038/onc.2017.159] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 04/08/2017] [Accepted: 04/14/2017] [Indexed: 12/26/2022]
Abstract
Widespread genome hypo-methylation and promoter hyper-methylation of epithelium-specific genes are hallmarks of stable epithelial-to-mesenchymal transition (EMT), which in prostate cancer (PCa) correlates with castration resistance, cancer stem cells generation, chemoresistance and worst prognosis. Exploiting our consolidated 'ex-vivo' system, we show that cancer-associated fibroblasts (CAFs) released factors have pivotal roles in inducing genome methylation changes required for EMT and stemness in EMT-prone PCa cells. By global DNA methylation analysis and RNA-Seq, we provide compelling evidence that conditioned media from CAFs explanted from two unrelated patients with advanced PCa, stimulates concurrent DNA hypo- and hyper-methylation required for EMT and stemness in PC3 and DU145, but not in LN-CaP and its derivative C4-2B, PCa cells. CpG island (CGI) hyper-methylation associates with repression of genes required for epithelial maintenance and invasion antagonism, whereas activation of EMT markers and stemness genes correlate with CGI hypo-methylation. Remarkably, methylation variations and EMT-regulated transcripts almost completely reverse qualitatively and quantitatively during MET. Unsupervised clustering analysis of the PRAD TCGA data set with the differentially expressed (DE) and methylated EMT signature, identified a gene cluster of DE genes defined by a CAF+ and AR- phenotype and worst diagnosis. This gene cluster includes the relevant factors for EMT and stemness, which display DNA methylation variations in regulatory regions inversely correlated to their expression changes, thus strongly sustaining the ex-vivo data. DNMT3A-dependent methylation is essential for silencing epithelial maintenance and EMT counteracting genes, such as CDH1 and GRHL2, that is, the direct repressor of ZEB1, the key transcriptional factor for EMT and stemness. Accordingly, DNMT3A knock-down prevents EMT entry. These results shed light on the mechanisms of establishment and maintenance of coexisting DNA hypo- and hyper-methylation patterns during cancer progression, the generation of EMT and cell stemness in advanced PCa, and may pave the way to new therapeutic implications.
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24
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Identification of organ tissue types and skin from forensic samples by microRNA expression analysis. Forensic Sci Int Genet 2017; 28:99-110. [DOI: 10.1016/j.fsigen.2017.02.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 01/26/2017] [Accepted: 02/03/2017] [Indexed: 01/19/2023]
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25
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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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26
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Morata-Tarifa C, Picon-Ruiz M, Griñan-Lison C, Boulaiz H, Perán M, Garcia MA, Marchal JA. Validation of suitable normalizers for miR expression patterns analysis covering tumour heterogeneity. Sci Rep 2017; 7:39782. [PMID: 28051134 PMCID: PMC5209713 DOI: 10.1038/srep39782] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 11/28/2016] [Indexed: 12/12/2022] Open
Abstract
Oncogenic microRNAs (miRs) have emerged as diagnostic biomarkers and novel molecular targets for anti-cancer drug therapies. Real-time quantitative PCR (qPCR) is one of the most powerful techniques for analyzing miRs; however, the use of unsuitable normalizers might bias the results. Tumour heterogeneity makes even more difficult the selection of an adequate endogenous normalizer control. Here, we have evaluated five potential referenced small RNAs (U6, rRNA5s, SNORD44, SNORD24 and hsa-miR-24c-3p) using RedFinder algorisms to perform a stability expression analysis in i) normal colon cells, ii) colon and breast cancer cell lines and iii) cancer stem-like cell subpopulations. We identified SNORD44 as a suitable housekeeping gene for qPCR analysis comparing normal and cancer cells. However, this small nucleolar RNA was not a useful normalizer for cancer stem-like cell subpopulations versus subpopulations without stemness properties. In addition, we show for the first time that hsa-miR-24c-3p is the most stable normalizer for comparing these two subpopulations. Also, we have identified by bioinformatic and qPCR analysis, different miR expression patterns in colon cancer versus non tumour cells using the previously selected suitable normalizers. Our results emphasize the importance of select suitable normalizers to ensure the robustness and reliability of qPCR data for analyzing miR expression.
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Affiliation(s)
- C Morata-Tarifa
- Biopathology and Medicine Regenerative Institute (IBIMER), University of Granada, Granada, Spain.,Biosanitary Institute of Granada (ibs.GRANADA), University Hospitals of Granada-University of Granada, Granada, Spain.,Braman Family Breast Cancer Institute, Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, Florida, USA
| | - M Picon-Ruiz
- Biopathology and Medicine Regenerative Institute (IBIMER), University of Granada, Granada, Spain.,Biosanitary Institute of Granada (ibs.GRANADA), University Hospitals of Granada-University of Granada, Granada, Spain.,Braman Family Breast Cancer Institute, Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, Florida, USA
| | - C Griñan-Lison
- Biopathology and Medicine Regenerative Institute (IBIMER), University of Granada, Granada, Spain.,Biosanitary Institute of Granada (ibs.GRANADA), University Hospitals of Granada-University of Granada, Granada, Spain
| | - H Boulaiz
- Biopathology and Medicine Regenerative Institute (IBIMER), University of Granada, Granada, Spain.,Biosanitary Institute of Granada (ibs.GRANADA), University Hospitals of Granada-University of Granada, Granada, Spain.,Department of Human Anatomy and Embryology, University of Granada, Granada, Spain
| | - M Perán
- Biopathology and Medicine Regenerative Institute (IBIMER), University of Granada, Granada, Spain.,Department of Health Sciences, University of Jaén, Jaén, Spain
| | - M A Garcia
- Biopathology and Medicine Regenerative Institute (IBIMER), University of Granada, Granada, Spain.,Biosanitary Institute of Granada (ibs.GRANADA), University Hospitals of Granada-University of Granada, Granada, Spain.,Virgen de las Nieves University Hospital, Oncology Department, Oncology Unit, Granada, Spain
| | - J A Marchal
- Biopathology and Medicine Regenerative Institute (IBIMER), University of Granada, Granada, Spain.,Biosanitary Institute of Granada (ibs.GRANADA), University Hospitals of Granada-University of Granada, Granada, Spain.,Department of Human Anatomy and Embryology, University of Granada, Granada, Spain
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27
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Wilczynski M, Danielska J, Dzieniecka M, Szymanska B, Wojciechowski M, Malinowski A. Prognostic and Clinical Significance of miRNA-205 in Endometrioid Endometrial Cancer. PLoS One 2016; 11:e0164687. [PMID: 27737015 PMCID: PMC5063284 DOI: 10.1371/journal.pone.0164687] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 09/29/2016] [Indexed: 01/09/2023] Open
Abstract
Endometrial cancer is one of the most common malignancies of the reproductive female tract, with endometrioid endometrial cancer being the most frequent type. Despite the relatively favourable prognosis in cases of endometrial cancer, there is a necessity to evaluate clinical and prognostic utility of new molecular markers. MiRNAs are small, non-coding RNA molecules that take part in RNA silencing and post-transcriptional regulation of gene expression. Altered expression of miRNAs may be associated with cancer initiation, progression and metastatic capabilities. MiRNA-205 seems to be one of the key regulators of gene expression in endometrial cancer. In this study, we investigated clinical and prognostic role of miRNA-205 in endometrioid endometrial cancer. After total RNA extraction from 100 archival formalin-fixed paraffin-embedded tissues, real-time quantitative RT-PCR was used to define miRNA-205 expression levels. The aim of the study was to evaluate miRNA-205 expression levels in regard to patients' clinical and histopathological features, such as: survival rate, recurrence rate, staging, myometrial invasion, grading and lymph nodes involvement. Higher levels of miRNA-205 expression were observed in tumours with less than half of myometrial invasion and non-advanced cancers. Kaplan-Maier analysis revealed that higher levels of miRNA-205 were associated with better overall survival (p = 0,034). These results indicate potential clinical utility of miRNA-205 as a prognostic marker.
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Affiliation(s)
- Milosz Wilczynski
- Department of Operative Gynecology, Endoscopy and Gynecologic Oncology, Polish Mother’s Memorial Hospital Research Institute, Lodz, Poland
| | | | - Monika Dzieniecka
- Department of Pathology, Polish Mother’s Memorial Hospital Research Institute, Lodz, Poland
| | - Bozena Szymanska
- The Central Laboratory of Medical University in Lodz, Lodz, Poland
| | - Michal Wojciechowski
- Department of Operative Gynecology, Endoscopy and Gynecologic Oncology, Polish Mother’s Memorial Hospital Research Institute, Lodz, Poland
| | - Andrzej Malinowski
- Department of Surgical and Endoscopic Gynecology, Medical University in Lodz, Lodz, Poland
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28
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Peng D, Li Z, Wang L, Su Q, Jiang Y, Zhu J, Wang H, Mao J, Liang W, Zhang L. The species specific of 3 microRNA markers in saliva. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2015. [DOI: 10.1016/j.fsigss.2015.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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29
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On the effect of shooting distance, ballistic model construction, doping and weapon type on the simultaneous analysis of DNA and RNA from backspatter recovered from inside surfaces of firearms. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2015. [DOI: 10.1016/j.fsigss.2015.10.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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30
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Grabmüller M, Cachée P, Madea B, Courts C. How far does it get?--The effect of shooting distance and type of firearm on the simultaneous analysis of DNA and RNA from backspatter recovered from inside and outside surfaces of firearms. Forensic Sci Int 2015; 258:11-8. [PMID: 26625183 DOI: 10.1016/j.forsciint.2015.10.030] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 09/24/2015] [Accepted: 10/29/2015] [Indexed: 10/22/2022]
Abstract
When a firearm projectile hits a biological target a spray of biological material (e.g. blood and tissue) is ejected from the entrance wound and propelled back into the direction of the firearm. This phenomenon has been termed 'backspatter' and if backspattered biological material reaches the firearm on its backward trajectory it may persist on and be recovered from the firearm's inside surfaces. Molecular genetic analysis of backspatter generated by contact shots and shots from very short distances has already been demonstrated to critically contribute to victim identification and the reconstruction of firearm-related crimes. It is not known, however, up to what shooting distance can backspatter be found on firearms' inside surfaces and what influence the weapon's type and caliber has on backspatter attributes (e.g. reach, amount and distribution). Therefore, the present pilot study investigated the effect of serval combinations of shooting distances and types of firearms and ammunitions on the analyzability of co-extracted DNA and micro-RNA in samples of backspatter collected from interior and exterior surfaces of the firearms after experimental shootings employing standardized ballistic models. We demonstrate the limiting effect of shooting distance and the type of firearm on the yield of nucleic acids recovered from backspatter and the success rates of forensic DNA profiling and RNA based body-fluid and organ tissue identification in experimental shootings.
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Affiliation(s)
- Melanie Grabmüller
- Institute of Legal Medicine, University of Bonn, Stiftsplatz 12, 53111 Bonn, Germany
| | - Philipp Cachée
- Firearms and Ballistic Expert Witness P. Cachée, Birkenweg 6, 14554 Neuseddin, Germany
| | - Burkhard Madea
- Institute of Legal Medicine, University of Bonn, Stiftsplatz 12, 53111 Bonn, Germany
| | - Cornelius Courts
- Institute of Legal Medicine, University of Bonn, Stiftsplatz 12, 53111 Bonn, Germany.
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31
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Tong YS, Wang XW, Zhou XL, Liu ZH, Yang TX, Shi WH, Xie HW, Lv J, Wu QQ, Cao XF. Identification of the long non-coding RNA POU3F3 in plasma as a novel biomarker for diagnosis of esophageal squamous cell carcinoma. Mol Cancer 2015; 14:3. [PMID: 25608466 PMCID: PMC4631113 DOI: 10.1186/1476-4598-14-3] [Citation(s) in RCA: 238] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 12/09/2014] [Indexed: 12/15/2022] Open
Abstract
Background Recent studies have demonstrated that long non-coding RNAs (lncRNAs) were present in the blood of cancer patients and have shown great potential as powerful and non-invasive tumor markers. However, little is known about the value of lncRNAs in the diagnosis of esophageal squamous cell carcinoma (ESCC). We hypothesized that ESCC-related lncRNAs might be released into the circulation during tumor initiation and could be utilized to detect and monitor ESCC. Methods Ten lncRNAs (HOTAIR, AFAP1-AS1, POU3F3, HNF1A-AS1, 91H, PlncRNA1, SPRY4-IT1, ENST00000435885.1, XLOC_013104 and ENST00000547963.1) which previously found to be differently expressed in esophageal cancer were selected as candidate targets for subsequent circulating lncRNA assay. A four-stage exploratory study was conducted to test the hypothesis: (1) optimization of detected method to accurately and reproducibly measure ESCC-related lncRNAs in plasma and serum; (2) evaluation of the stability of circulating lncRNAs in human plasma or serum; (3) exploration the origin of ESCC-related lncRNAs in vitro and in vivo; (4) evaluation the diagnostic power of circulating lncRNAs for ESCC. Results ESCC-related lncRNAs were detectable and stable in plasma of cancer patients, and derived largely from ESCC tumor cells. Furthermore, plasma levels of POU3F3, HNF1A-AS1 and SPRY4-IT1 were significantly higher in ESCC patients compared with normal controls. By receiver operating characteristic curve (ROC) analysis, among the three lncRNAs investigated, plasma POU3F3 provided the highest diagnostic performance for detection of ESCC (the area under the ROC curve (AUC), 0.842; p < 0.001; sensitivity, 72.8%; specificity, 89.4%). Moreover, use of POU3F3 and SCCA in combination could provide a more effective diagnosis performance (AUC, 0.926, p < 0.001, sensitivity, 85.7%; specificity, 81.4%). Most importantly, this combination was effective to detect ESCC at an early stage (80.8%). Conclusions Plasma POU3F3 could serve as a potential biomarker for diagnosis of ESCC, and the combination of POU3F3 and SCCA was more efficient for ESCC detection, in particular for early tumor screening. Electronic supplementary material The online version of this article (doi:10.1186/1476-4598-14-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yu-Suo Tong
- Department of Surgical Oncology, Nanjing Frist Hospital, Nanjing Medical University, Nanjing, Jiangsu, China.
| | - Xiao-Wei Wang
- Department of Medical Oncology, Huai'an First People's Hospital Affiliated to Nanjing Medical University, Huai'an, Jiangsu, China.
| | - Xi-Lei Zhou
- Department of Radiation Oncology, Huai'an First People's Hospital Affiliated to Nanjing Medical University, Huai'an, Jiangsu, China.
| | - Zi-Hao Liu
- Department of Surgical Oncology, Nanjing Frist Hospital, Nanjing Medical University, Nanjing, Jiangsu, China.
| | - Tong-Xin Yang
- Department of Surgical Oncology, Nanjing Frist Hospital, Nanjing Medical University, Nanjing, Jiangsu, China.
| | - Wei-Hong Shi
- Department of Surgical Oncology, Nanjing Frist Hospital, Nanjing Medical University, Nanjing, Jiangsu, China.
| | - Hai-Wei Xie
- Department of Surgical Oncology, Nanjing Frist Hospital, Nanjing Medical University, Nanjing, Jiangsu, China.
| | - Jin Lv
- Department of Surgical Oncology, Nanjing Frist Hospital, Nanjing Medical University, Nanjing, Jiangsu, China.
| | - Qing-Quan Wu
- Department of Thoracic Surgery, Huai'an First People's Hospital Affiliated to Nanjing Medical University, Huai'an, Jiangsu, China.
| | - Xiu-Feng Cao
- Department of Surgical Oncology, Nanjing Frist Hospital, Nanjing Medical University, Nanjing, Jiangsu, China.
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