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Fazzina M, Bergonzoni M, Massenzio F, Monti B, Frabetti F, Casadei R. Selection of suitable reference genes for gene expression studies in HMC3 cell line by quantitative real-time RT-PCR. Sci Rep 2024; 14:2431. [PMID: 38287074 PMCID: PMC10825209 DOI: 10.1038/s41598-024-52415-7] [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: 03/30/2023] [Accepted: 01/18/2024] [Indexed: 01/31/2024] Open
Abstract
Microglia represent the primary immune defense system within the central nervous system and play a role in the inflammatory processes occurring in numerous disorders, such as Parkinson's disease (PD). PD onset and progression are associated with factors considered possible causes of neuroinflammation, i.e. genetic mutations. In vitro models of microglial cells were established to identify specific molecular targets in PD through the analysis of gene expression data. Recently, the Human Microglial Clone 3 cell line (HMC3) has been characterized and a new human microglia model has emerged. Here we perform RT-qPCR analyses to evaluate the expression of ten reference genes in HMC3, untreated or stimulated to a pro-inflammatory status. The comparative ∆CT method, BestKeeper, Normfinder, geNorm and RefFinder algorithms were used to assess the stability of the candidate genes. The results showed that the most suitable internal controls are HPRT1, RPS18 and B2M genes. In addition, the most stable and unstable reference genes were used to normalize the expression of a gene of interest in HMC3, resulting in a difference in the statistical significance in cells treated with Rotenone. This is the first reference gene validation study in HMC3 cell line in pro-inflammatory status and can contribute to more reliable gene expression analysis in the field of neurodegenerative and neuroinflammatory research.
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Affiliation(s)
- Martina Fazzina
- Department for Life Quality Studies - QUVI, University of Bologna, Rimini, Italy
| | - Matteo Bergonzoni
- Department of Pharmacy and Biotechnology - FABIT, University of Bologna, Bologna, Italy
| | - Francesca Massenzio
- Department of Pharmacy and Biotechnology - FABIT, University of Bologna, Bologna, Italy
| | - Barbara Monti
- Department of Pharmacy and Biotechnology - FABIT, University of Bologna, Bologna, Italy
| | - Flavia Frabetti
- Department of Medical and Surgical Sciences - DIMEC, University of Bologna, Bologna, Italy
| | - Raffaella Casadei
- Department for Life Quality Studies - QUVI, University of Bologna, Rimini, Italy.
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Wilmes V, Mildeberger L, Verhoff MA, Kauferstein S. Influence of microRNAs on iNOS expression in postmortem human infarction hearts. Forensic Sci Int 2024; 354:111892. [PMID: 38150896 DOI: 10.1016/j.forsciint.2023.111892] [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: 10/09/2023] [Revised: 11/14/2023] [Accepted: 11/21/2023] [Indexed: 12/29/2023]
Abstract
MicroRNAs (miRNAs) are important post-transcriptional regulators in several diseases, including cancer, immunologic and cardiovascular diseases. A growing list of miRNAs are dysregulated in cardiac arrhythmias, contractility diseases, myocardial infarction (MI), sudden cardiac death (SCD), chronic heart failure and hypertrophy. However, the exact regulatory pathways, through which miRNAs exert their effects are often unclear. In this study, we measured the expression patterns of miR-21, miR-939 and miR-30e in postmortem human MI. The aim of the study was to examine the influence of these miRNAs on cardiac inducible nitric oxide synthase (iNOS) mRNA levels. We measured iNOS mRNA and miRNA expression patterns by means of qPCR. Further we used correlation analyses to determine causality between miRNA expression and cardiac iNOS levels. iNOS mRNA, miR-21, miR-939 and miR-30e were significantly upregulated in infarcted and non-infarcted regions of postmortem human MI hearts in comparison to healthy controls. While miR-21 and miR-939 showed their strongest expression in infarcted regions, miR-30e peaked in the non-infarcted myocardium. Further, we found a significant correlation between miR-939 and iNOS expression levels in controls and infarcted regions. The results indicate, that miR-939 is a regulator of cardiac iNOS expression. However, a massive iNOS activation might exceed the capability of miR-939 to keep its expression in balance. miR-21 and miR-30e do not seem to influence cardiac iNOS levels in MI. Further studies are needed to evaluate downstream targets of these miRNAs and their signaling pathways to clarify their role in human MI.
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Affiliation(s)
- Verena Wilmes
- Institute of Legal Medicine, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany.
| | - Luise Mildeberger
- Institute of Legal Medicine, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Marcel A Verhoff
- Institute of Legal Medicine, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Silke Kauferstein
- Institute of Legal Medicine, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
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Nevone A, Lattarulo F, Russo M, Panno G, Milani P, Basset M, Avanzini MA, Merlini G, Palladini G, Nuvolone M. A Strategy for the Selection of RT-qPCR Reference Genes Based on Publicly Available Transcriptomic Datasets. Biomedicines 2023; 11:biomedicines11041079. [PMID: 37189697 DOI: 10.3390/biomedicines11041079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/23/2023] [Accepted: 03/27/2023] [Indexed: 04/05/2023] Open
Abstract
In the next-generation sequencing era, RT-qPCR is still widely employed to quantify levels of nucleic acids of interest due to its popularity, versatility, and limited costs. The measurement of transcriptional levels through RT-qPCR critically depends on reference genes used for normalization. Here, we devised a strategy to select appropriate reference genes for a specific clinical/experimental setting based on publicly available transcriptomic datasets and a pipeline for RT-qPCR assay design and validation. As a proof-of-principle, we applied this strategy to identify and validate reference genes for transcriptional studies of bone-marrow plasma cells from patients with AL amyloidosis. We performed a systematic review of published literature to compile a list of 163 candidate reference genes for RT-qPCR experiments employing human samples. Next, we interrogated the Gene Expression Omnibus to assess expression levels of these genes in published transcriptomic studies on bone-marrow plasma cells from patients with different plasma cell dyscrasias and identified the most stably expressed genes as candidate normalizing genes. Experimental validation on bone-marrow plasma cells showed the superiority of candidate reference genes identified through this strategy over commonly employed “housekeeping” genes. The strategy presented here may apply to other clinical and experimental settings for which publicly available transcriptomic datasets are available.
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Affiliation(s)
- Alice Nevone
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Francesca Lattarulo
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Monica Russo
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Giada Panno
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Paolo Milani
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Marco Basset
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Maria Antonietta Avanzini
- Pediatric Hematology Oncology, Cell Factory, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Giampaolo Merlini
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Giovanni Palladini
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Mario Nuvolone
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
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Wilmes V, Kur IM, Weigert A, Verhoff MA, Gradhand E, Kauferstein S. iNOS expressing macrophages co-localize with nitrotyrosine staining after myocardial infarction in humans. Front Cardiovasc Med 2023; 10:1104019. [PMID: 37063955 PMCID: PMC10098457 DOI: 10.3389/fcvm.2023.1104019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 03/15/2023] [Indexed: 04/03/2023] Open
Abstract
IntroductionInducible nitric oxide synthase (iNOS) produces micromolar amounts of nitric oxide (NO) upon the right stimuli, whose further reactions can lead to oxidative stress. In murine models of myocardial infarction (MI), iNOS is known to be expressed in infiltrating macrophages, which at early onset enter the infarcted zone and are associated with inflammation. In contrast cardiac tissue resident macrophages are thought to enhance regeneration of tissue injury and re-establish homeostasis. Both detrimental and beneficial effects of iNOS have been described, still the role of iNOS in MI is not fully understood. Our aim was to examine cell expression patterns of iNOS and nitrotyrosine (NT) production in human MI.Material and MethodsWe examined in postmortem human MI hearts the iNOS mRNA expression by means of qPCR. Further we performed immunohistochemical stainings for cell type identification. Afterwards a distance analysis between iNOS and NT was carried out to determine causality between iNOS and NT production.ResultsiNOS mRNA expression was significantly increased in infarcted regions of human MI hearts and iNOS protein expression was detected in resident macrophages in infarcted human hearts as well as in controls hearts, being higher in resident macrophages in MI hearts compared to control. Furthermore in MI and in healthy human hearts cells showing signs of NT production peaked within 10–15 µm proximity of iNOS+ cells.DiscussionThese results indicate that, unexpectedly, resident macrophages are the main source of iNOS expression in postmortem human MI hearts. The peak of NT positive cells within 10–15 µm of iNOS+ cells suggest an iNOS dependent level of NT and therefore iNOS dependent oxidative stress. Our results contribute to understanding the role of iNOS in human MI.
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Affiliation(s)
- Verena Wilmes
- Institute of Legal Medicine, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
- Correspondence: Verena Wilmes
| | - Ivan M. Kur
- Institute of Biochemistry I, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
| | - Andreas Weigert
- Institute of Biochemistry I, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
- Cardio-Pulmonary Institute (CPI), Goethe University, Frankfurt am Main, Germany
| | - Marcel A. Verhoff
- Institute of Legal Medicine, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Elise Gradhand
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Silke Kauferstein
- Institute of Legal Medicine, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
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Cheng TY, Zimmerman JJ, Giménez-Lirola LG. Internal reference genes with the potential for normalizing quantitative PCR results for oral fluid specimens. Anim Health Res Rev 2022; 23:147-156. [PMID: 36330795 DOI: 10.1017/s1466252322000044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In basic research, testing of oral fluid specimens by real-time quantitative polymerase chain reaction (qPCR) has been used to evaluate changes in gene expression levels following experimental treatments. In diagnostic medicine, qPCR has been used to detect DNA/RNA transcripts indicative of bacterial or viral infections. Normalization of qPCR using endogenous and exogenous reference genes is a well-established strategy for ensuring result comparability by controlling sample-to-sample variation introduced during sampling, storage, and qPCR testing. In this review, the majority of recent publications in human (n = 136) and veterinary (n = 179) medicine did not describe the use of internal reference genes in qPCRs for oral fluid specimens (52.9% animal studies; 57.0% human studies). However, the use of endogenous reference genes has not been fully explored or validated for oral fluid specimens. The lack of valid internal reference genes inherent to the oral fluid matrix will continue to hamper the reliability, reproducibility, and generalizability of oral fluid qPCR assays until this issue is addressed.
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Affiliation(s)
- Ting-Yu Cheng
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Jeffrey J Zimmerman
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Luis G Giménez-Lirola
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
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Normalization strategy for selection of reference genes for RT-qPCR analysis in left ventricles of failing human hearts. BMC Cardiovasc Disord 2022; 22:180. [PMID: 35439923 PMCID: PMC9019989 DOI: 10.1186/s12872-022-02614-9] [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: 08/27/2021] [Accepted: 03/11/2022] [Indexed: 11/10/2022] Open
Abstract
Background Quantitative RT-PCR is a valuable tool for assessing the gene expression in different human tissues, particularly due to its exceptional sensitivity, accuracy and reliability. However, the choice of adequate control for normalization is a crucial step, greatly affecting the results of all subsequent analyses. So far, only a few studies were focused on the selection of optimal reference genes in left ventricles of failing human hearts, leading to several disparities in experimental results focused on differential gene expression in this area. Therefore, the main objective of this study was to identify a set of suitable reference genes in normal and failing left ventricle tissues, which could increase the reliability of RT-qPCR-based studies in the future. Methods We analyzed the expression of 15 commonly used housekeeping genes (ACTB, B2M, GAPDH, GUSB, HMBS, HPRT1, IPO8, PGK1, POLR2A, PPIA, RPLP0, TBP, TFRC, UBC and YWHAZ) in left ventricles of normal and failed hearts with two-step approach. In the first step, we excluded genes which are variantly expressed using ANOVA-based statistical method. Afterwards, the remaining genes were analyzed using geNorm, NormFinder and BestKeeper algorithms, together with delta Cq method. Finally, the geometric mean of gene rankings across all methods was calculated. Results Our analysis identified IPO8 and POLR2A as the most stably expressed genes, whereas ACTB and B2M were found to be expressed variantly, suggesting a potential role of these genes in the pathophysiological processes in failing human hearts. Discussion/conclusion Using our two-step approach, we identified and validated two reference genes expressed invariantly in left ventricles of both healthy and failing human hearts, as well as provided a guideline for the selection of reference genes in studies comparing gene expression in these types of tissues. Supplementary Information The online version contains supplementary material available at 10.1186/s12872-022-02614-9.
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Ros AC, Bacci S, Luna A, Legaz I. Forensic Impact of the Omics Science Involved in the Wound: A Systematic Review. Front Med (Lausanne) 2022; 8:786798. [PMID: 35071269 PMCID: PMC8770859 DOI: 10.3389/fmed.2021.786798] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/14/2021] [Indexed: 12/28/2022] Open
Abstract
Background: In forensic autopsies, examining the wounds is one of the most critical aspects to clarify the causal relationship between the cause of death and the wounds observed on the corpse. However, on many occasions, it is difficult to differentiate antemortem injuries from post-mortem injuries, mainly when they occur very close to the moment of death. At present, various studies try to find biomarkers and clarify the molecular mechanisms involved in a wound due to the high variability of conditions in which they occur, thus being one of the most challenging problems in forensic pathology. This review aimed to study the omics data to determine the main lines of investigation emerging in the diagnosis of vital injuries, time of appearance, estimation of the age and vitality of the wound, and its possible contributions to the forensic field. Methods: A systematic review of the human wound concerning forensic science was carried out by following PRISMA guidelines. Results: This study sheds light on the role of omics research during the process of wounding, identifying different cytokines and other inflammatory mediators, as well as cells involved in the specific stage of the wound healing process, show great use in estimating the age of a wound. On the other hand, the expression levels of skin enzymes, proteins, metal ions, and other biomarkers play an essential role in differentiating vital and post-mortem wounds. More recent studies have begun to analyze and quantify mRNA from different genes that encode proteins that participate in the inflammation phase of a wound and miRNAs related to various cellular processes. Conclusions: This study sheds light on the role of research in the molecular characterization of vital wounds, heralding a promising future for molecular characterization of wounds in the field of forensic pathology, opening up an important new area of research. Systematic Review Registration: URL: https://www.crd.york.ac.uk/prospero/#myprospero, Identifier: CRD42021286623.
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Affiliation(s)
- Aurelia Collados Ros
- Department of Legal and Forensic Medicine, Biomedical Research Institute (IMIB), Regional Campus of International Excellence "Campus Mare Nostrum", Faculty of Medicine, University of Murcia, Murcia, Spain
| | - Stefano Bacci
- Department of Biology, Research Unit of Histology and Embriology, University of Florence, Florence, Italy
| | - Aurelio Luna
- Department of Legal and Forensic Medicine, Biomedical Research Institute (IMIB), Regional Campus of International Excellence "Campus Mare Nostrum", Faculty of Medicine, University of Murcia, Murcia, Spain
| | - Isabel Legaz
- Department of Legal and Forensic Medicine, Biomedical Research Institute (IMIB), Regional Campus of International Excellence "Campus Mare Nostrum", Faculty of Medicine, University of Murcia, Murcia, Spain
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Sangwan A, Singh SP, Singh P, Gupta OP, Manas A, Gupta S. Role of molecular techniques in PMI estimation: An update. J Forensic Leg Med 2021; 83:102251. [PMID: 34592482 DOI: 10.1016/j.jflm.2021.102251] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 08/19/2021] [Accepted: 09/12/2021] [Indexed: 10/20/2022]
Abstract
The time frames between death and reporting of the cadaver, known as post Mortem interval (PMI), is essential in investigation of homicide deaths, suspicious deaths, or other untimely deaths as well as natural deaths. Such information helps to connect the missing links in homicide or other relevant cases. Over the time several methods are developed which depends upon factors as several methods physiological, biochemical, entomological, and archaeological for the estimation of degradation of body with time. These methods lack precision, require expertise to achieve worthy results or authentic estimate. Although these methods are currently in use but, these evaluations are still unreliable and imprecise. Hence, we still need new methods for better estimation of PMI. Initially, the predictable morphological and chemical changes in cadaver are used as PMI indicators but, as the time since death increases, the above methods become less useful for as they can't pin point the time of death rather give a ballpark idea. With the advent of the field of molecular biology, the estimation of PMI is proposed to be executed by evaluating the degradation pattern of the biological markers (DNA, RNA, and Proteins). It is now proved that the DNA is fairly unwavering over long post-mortem phases, RNA is much more labile in nature, and sensitive to degradation in a tissue-specific manner. Thus, the main purpose (aim, agenda) of this document is to provide review that mainly focuses on potential use of RNA markers in estimation of PMI. For this Critical Review, the systematic evaluation of 47 studies is executed according to the chosen inclusion and exclusion criteria.
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Affiliation(s)
- Amita Sangwan
- Department of Oral Pathology & Microbiology, King George's Medical University, Lucknow, India
| | - Saurabh Pratap Singh
- Department of Oral Pathology & Microbiology, King George's Medical University, Lucknow, India
| | - Prerna Singh
- Department of Oral Pathology & Microbiology, King George's Medical University, Lucknow, India
| | - O P Gupta
- Department of General Surgery, Career Institute of Medical Sciences, Lucknow, India
| | - Abhigyan Manas
- Department of General Surgery, Career Institute of Medical Sciences, Lucknow, India
| | - Shalini Gupta
- Department of Oral Pathology & Microbiology, King George's Medical University, Lucknow, India.
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Nguyen TYT, Cacciottola L, Camboni A, Ravau J, De Vos M, Demeestere I, Donnez J, Dolmans MM. Ovarian tissue cryopreservation and transplantation in patients with central nervous system tumours. Hum Reprod 2021; 36:1296-1309. [PMID: 33394011 DOI: 10.1093/humrep/deaa353] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 11/24/2020] [Indexed: 11/12/2022] Open
Abstract
STUDY QUESTION Is there a possibility of reseeding cancer cells potentially present in frozen ovarian tissue from patients with central nervous system (CNS) tumours? SUMMARY ANSWER Malignancy reseeding in cryopreserved ovarian tissue from 20 patients with CNS tumours was not detected by histology, immunohistochemistry (IHC), molecular biology or xenotransplantation. WHAT IS KNOWN ALREADY Ovarian metastasis potential has been documented in patients with leukaemia, borderline ovarian tumours, advanced breast cancer and Ewing sarcoma. However, data on the safety of transplanting frozen-thawed ovarian tissue from cancer patients with CNS tumours are still lacking. STUDY DESIGN, SIZE, DURATION This prospective experimental study was conducted in an academic gynaecology research laboratory using cryopreserved ovarian cortex from 20 patients suffering from CNS tumours. Long-term (5 months) xenografting was performed in immunodeficient mice. PARTICIPANTS/MATERIALS, SETTING, METHODS Subjects enrolled in the study were suffering from one of six types of CNS tumours including medulloblastoma, ependymoma, primitive neuroectodermal tumours, astrocytoma, glioblastoma and germinoma. The presence of malignant cells was investigated with disease-specific markers for each patient in cryopreserved and xenografted ovarian tissue by histology, IHC via expression of neuron-specific enolase (NSE) and glial fibrillary acidic protein (GFAP), and reverse transcription droplet digital polymerase chain reaction (RT-ddPCR) for quantification of GFAP and ENO2 gene amplification. MAIN RESULTS AND THE ROLE OF CHANCE Serial sections of cryopreserved and xenografted ovarian tissue from 20 patients showed no malignant cells by histology. All samples were negative for NSE and GFAP, although these neural markers were expressed extensively in the patients' primary tumours. Analysis by RT-ddPCR revealed no cancer cells detected in cryopreserved and xenografted ovarian fragments from subjects with astrocytoma, ependymoma, glioblastoma or medulloblastoma. Taken together, the study found no evidence of malignancy seeding in frozen-thawed and xenotransplanted ovarian tissue from patients affected by CNS cancers. LIMITATIONS, REASONS FOR CAUTION This analysis cannot guarantee complete elimination of disseminated disease from all cryopreserved ovarian cortex, since we are unable to examine the fragments used for transplantation. WIDER IMPLICATIONS OF THE FINDINGS This is the first study to be conducted in patients with CNS cancers undergoing ovarian tissue cryopreservation and transplantation, and clearly demonstrates no tumour seeding in their frozen-thawed and xenografted tissue. This information is vital for doctors to provide patients with meaningful and accurate advice on the possibilities and risks of ovarian tissue reimplantation. STUDY FUNDING/COMPETING INTEREST(S) This study was supported by grants from the Fonds National de la Recherche Scientifique de Belgique-the Excellence of Science (FNRS-EOS), number 30443682 awarded to M.-M.D. and T.Y.T.N., FNRS grant number 5/4/150/5 and FNRS-PDR Convention grant number T.0077.14 awarded to M.-M.D., grant 2018-042 from the Foundation Against Cancer awarded to A.C., and private donations (Ferrero, de Spoelberch). The authors declare no competing financial interests. TRIAL REGISTRATION NUMBER N/A.
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Affiliation(s)
- Thu Yen Thi Nguyen
- Pôle de Gynécologie, Institut de Recherche Expérimentale et Clinique (IREC), Université Catholique de Louvain, Brussels, Belgium
| | - Luciana Cacciottola
- Pôle de Gynécologie, Institut de Recherche Expérimentale et Clinique (IREC), Université Catholique de Louvain, Brussels, Belgium
| | - Alessandra Camboni
- Pôle de Gynécologie, Institut de Recherche Expérimentale et Clinique (IREC), Université Catholique de Louvain, Brussels, Belgium.,Service d'Anatomie Pathologique, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - Joachim Ravau
- Laboratory of Pediatric Hepatology and Cell Therapy, Institut de Recherche Expérimentale et Clinique (IREC), Université Catholique de Louvain, Brussels, Belgium
| | - Michel De Vos
- Centre for Reproductive Medicine, Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium.,Follicle Biology Laboratory (FOBI), UZ Brussel, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Isabelle Demeestere
- Research Laboratory in Human Reproduction, Faculty of Medicine, Université Libre de Bruxelles, Brussels, Belgium
| | - Jacques Donnez
- Société de Recherche pour l'Infertilité (SRI), Brussels, Belgium
| | - Marie-Madeleine Dolmans
- Pôle de Gynécologie, Institut de Recherche Expérimentale et Clinique (IREC), Université Catholique de Louvain, Brussels, Belgium.,Gynecology Department, Cliniques Universitaires Saint-Luc, Brussels, Belgium
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MicroRNAs as Useful Tools to Estimate Time Since Death. A Systematic Review of Current Literature. Diagnostics (Basel) 2021; 11:diagnostics11010064. [PMID: 33401603 PMCID: PMC7823686 DOI: 10.3390/diagnostics11010064] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/28/2020] [Accepted: 12/29/2020] [Indexed: 12/12/2022] Open
Abstract
Estimating the time of death remains the most challenging question in forensic medicine, because post-mortem interval (PMI) estimation can be a remarkably difficult goal to achieve. The aim of this review is to analyze the potential of microRNAs (miRNAs) to evaluate PMI. MiRNAs have been studied as hallmarks and biomarkers in several pathologies and have also showed interesting applications in forensic science, such as high sensible biomarkers in body fluid and tissue, for wound age determination and PMI evaluation due to their low molecular weight and tissue-specific expression. The present systematic review was carried out according to the Preferred Reporting Items for Systematic Review (PRISMA) standards. We performed an electronic search of PubMed, Science Direct Scopus, and Excerpta Medica Database (EMBASE) from the inception of these databases to 12 August 2020. The search terms were (“PMI miRNA” or “PMI micro RNA”) and (“miRNA” and “time of death”) in the title, abstract and keywords. Through analysis of scientific literature regarding forensic uses of miRNAs, has emerged that the intrinsic characteristics of such molecules, and their subsequent resistance to degradation, make them suitable as endogenous markers in order to determine PMI. However, further and larger studies with human samples and standardized protocols are still needed.
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Noshy PA. Postmortem expression of apoptosis-related genes in the liver of mice and their use for estimation of the time of death. Int J Legal Med 2020; 135:539-545. [PMID: 32914226 DOI: 10.1007/s00414-020-02419-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 09/02/2020] [Indexed: 12/11/2022]
Abstract
PURPOSE A major challenge in forensic medicine is to estimate the postmortem interval (PMI). Several approaches had been tried to determine the time of death, including physical and chemical changes. This study aims to explore the postmortem changes in the expression of apoptosis-related genes in the liver of mice and to use these changes for estimation of the PMI. METHODS Hepatic tissue was collected from sacrificed mice immediately after death (the control group) and at 3, 6, 9, 12, 18, and 24 hours after death. Four apoptosisrelated genes were selected as target genes, which are Caspase 3 (Casp3), B cell leukemia/ lymphoma 2 (Bcl2), BCL2-associated X protein (Bax), and Transformation related protein 53 (Trp53), and their relative expression was measured using quantitative PCR. miR-122 was used as a reference gene for normalization of the Ct (threshold cycle) values of the target genes. RESULTS The results revealed that the postmortem expression of Casp3 increased in a time-dependent manner; the expression of Bax increased from 3 to 18 hours followed by a decrease at 24 hours after death; the expression of Bcl2 decreased in a time-dependent manner after death; the expression of Trp53 increased from 3 to 6 hours and then started to decrease from 9 to 24 hours after death. CONCLUSION Based on the observed changes in the expression level of these genes, mathematical models were established to estimate the PMI. Further research is needed to investigate these markers and mathematical models in human tissues.
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Affiliation(s)
- Peter A Noshy
- Department of Toxicology and Forensic Medicine, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt.
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Comparative Evaluation of RNAlater Solution and Snap Frozen Methods for Gene Expression Studies in Different Tissues. REV ROMANA MED LAB 2020. [DOI: 10.2478/rrlm-2020-0024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Abstract
Introduction: Freezing of tissues with liquid nitrogen is the most common method in studies performed at the RNA level. However, the use of RNA stabilization solutions has become a popular alternative method. The aim of this study is to investigate the effectiveness of RNAlater on RNA stabilization in different tissues.
Material and Methods: In this study, RNA were isolated from the lung, heart, liver and skeletal muscle tissues of rats that were frozen with liquid nitrogen (snap frozen, SF group) or stored in RNAlater solution (RL group), and the changes in concentration, purity, reference genes expression, and fold-change levels between groups were analyzed.
Results: In the RL group, the concentration of RNA isolated from the liver tissues was higher (P<0.05), whereas the A260/280 ratio was lower in the heart and liver tissues (P<0.05). PPIA and SRP72 genes were found to have lower Ct values in the heart tissues of rats in the RL group (P<0.05 and P<0.001, respectively) than the SF group. Expression levels of PPIA, ACTB, and SRP72 genes across the tissues were found to be different between the groups (P<0.05). The gene expression level examined in terms of fold-change was significantly different in the RL group (upregulated up to 4 folds and downregulated about 0.5 fold) (P< 0.05).
Conclusions: The results showed that RNAlater can maintain the RNA integrity and can also change the results of gene expression because it does not inhibit biological activity. The snap freezing method is more reliable because gene expression is more stable in tissues frozen with liquid nitrogen.
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13
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Wilmes V, Lux C, Niess C, Gradhand E, Verhoff MA, Kauferstein S. Changes in gene expression patterns in postmortem human myocardial infarction. Int J Legal Med 2020; 134:1753-1763. [PMID: 32399898 PMCID: PMC7417407 DOI: 10.1007/s00414-020-02311-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 04/28/2020] [Indexed: 01/22/2023]
Abstract
In murine models, the expression of inducible nitric oxide synthase (iNOS) in myocardial infarction (MI) has been reported to be the result of tissue injury and inflammation. In the present study, mRNA expression of iNOS, hypoxia-inducible factor-1α (HIF-1α), and vascular endothelial growth factor (VEGF) was investigated in postmortem human infarction hearts. Since HIF-1α is the inducible subunit of the transcription factor HIF-1, which regulates transcription of iNOS and VEGF, the interrelation between the three genes was observed, to examine the molecular processes during the emergence of MI. iNOS and VEGF mRNAs were found to be significantly upregulated in the affected regions of MI hearts in comparison to healthy controls. Upregulation of HIF-1α was also present but not significant. Correlation analysis of the three genes indicated a stronger and significant correlation between HIF-1α and iNOS mRNAs than between HIF-1α and VEGF. The results of the study revealed differences in the expression patterns of HIF-1 downstream targets. The stronger transcription of iNOS by HIF-1 in the affected regions of MI hearts may represent a pathological process, since no correlation of iNOS and HIF-1α mRNA was found in non-affected areas of MI hearts. Oxidative stress is considered to cause molecular changes in MI, leading to increased iNOS expression. Therefore, it may also represent a forensic marker for detection of early changes in heart tissue.
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Affiliation(s)
- Verena Wilmes
- Institute of Legal Medicine, Johann Wolfgang Goethe University, Frankfurt, Germany.
| | - Constantin Lux
- Institute of Legal Medicine, Johann Wolfgang Goethe University, Frankfurt, Germany
| | - Constanze Niess
- Institute of Legal Medicine, Johann Wolfgang Goethe University, Frankfurt, Germany
| | - Elise Gradhand
- Institute of Pathology, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Marcel A Verhoff
- Institute of Legal Medicine, Johann Wolfgang Goethe University, Frankfurt, Germany
| | - Silke Kauferstein
- Institute of Legal Medicine, Johann Wolfgang Goethe University, Frankfurt, Germany
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14
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Life and death: A systematic comparison of antemortem and postmortem gene expression. Gene 2020; 731:144349. [PMID: 31935499 DOI: 10.1016/j.gene.2020.144349] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 01/06/2020] [Accepted: 01/07/2020] [Indexed: 12/30/2022]
Abstract
Gene expression is the process by which DNA is decoded to produce a functional transcript. The collection of all transcripts is referred to as the transcriptome and has extensively been used to evaluate differentially expressed genes in a certain cell or tissue type. In response to internal or external stimuli, the transcriptome is greatly regulated by epigenetic changes. Many studies have elucidated that antemortem gene expression (transcriptome) may be linked to an array of disease etiologies as well as potential targets for drug discovery; on the other hand, a number of studies have utilized postmortem gene expression (thanatotranscriptome) patterns to determine cause and time of death. The "transcriptome after death" involves the study of mRNA transcripts occurring in human tissues after death (thanatos, Greek for death). While antemortem gene expression can provide a wide range of important information about the host, the determination of the communication of genes after a human dies has recently been explored. After death a plethora of genes are regulated via activation versus repression as well as diverse regulatory factors such as the absence or presence of stimulated feedback. Even postmortem transcriptional regulation contains many more cellular constituents and is massively more complicated. The rates of degradation of mRNA transcripts vary depending on the types of postmortem tissues and their combinatorial gene expression signatures. mRNA molecules have been shown to persist for extended time frames; nevertheless, they are highly susceptible to degradation, with half-lives of selected mRNAs varying between minutes to weeks for specifically induced genes. Furthermore, postmortem genetic studies may be used to improve organ transplantation techniques. This review is the first of its kind to fully explore both gene expression and mRNA stability after death and the trove of information that can be provided about phenotypical characteristics of specific genes postmortem.
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15
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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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16
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Analysis of RNA in the estimation of post-mortem interval: a review of current evidence. Int J Legal Med 2019; 133:1629-1640. [DOI: 10.1007/s00414-019-02125-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 07/10/2019] [Indexed: 10/26/2022]
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17
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Molina CE, Jacquet E, Ponien P, Muñoz-Guijosa C, Baczkó I, Maier LS, Donzeau-Gouge P, Dobrev D, Fischmeister R, Garnier A. Identification of optimal reference genes for transcriptomic analyses in normal and diseased human heart. Cardiovasc Res 2019; 114:247-258. [PMID: 29036603 DOI: 10.1093/cvr/cvx182] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 09/20/2017] [Indexed: 11/13/2022] Open
Abstract
Aims Quantitative real-time RT-PCR (RT-qPCR) has become the method of choice for mRNA quantification, but requires an accurate normalization based on the use of reference genes showing invariant expression across various pathological conditions. Only few data exist on appropriate reference genes for the human heart. The objective of this study was to determine a set of suitable reference genes in human atrial and ventricular tissues, from right and left cavities in control and in cardiac diseases. Methods and results We assessed the expression of 16 reference genes (ACTB, B2M, GAPDH, GUSB, HMBS, HPRT1, IPO8, PGK1, POLR2A, PPIA, RPLP0, TBP, TFRC, UBC, YWHAZ, 18S) in tissues from: right and left ventricles from healthy controls and heart failure (HF) patients; right-atrial tissue from patients in sinus rhythm with (SRd) or without (SRnd) atrial dilatation, patients with paroxysmal (pAF) or chronic (cAF) atrial fibrillation or with HF; and left-atrial tissue from patients in SR or cAF. Consensual analysis (by geNorm and Normfinder algorithms, BestKeeper software tool and comparative delta-Ct method) of the variability scores obtained for each reference gene expression shows that the most stably expressed genes are: GAPDH, GUSB, IPO8, POLR2A, and YWHAZ when comparing either right and left ventricle or ventricle from healthy controls and HF patients; GAPDH, IPO8, POLR2A, PPIA, and RPLP0 when comparing either right and left atrium or right atria from all pathological groups. ACTB, TBP, TFRC, and 18S genes were identified as the least stable. Conclusions The overall most stable reference genes across different heart cavities and disease conditions were GAPDH, IPO8, POLR2A and PPIA. YWHAZ or GUSB could be added to this set for some specific experiments. This study should provide useful guidelines for reference gene selection in RT-qPCR studies in human heart.
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Affiliation(s)
- Cristina E Molina
- Inserm, UMR-S 1180, University of Paris-Sud, Université Paris-Saclay, Châtenay-Malabry, France.,Institute of Pharmacology and Toxicology, Heart Research Center Göttingen, University Medical Center, Georg-August University Göttingen, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Göttingen, Germany
| | - Eric Jacquet
- Institut de Chimie des Substances Naturelles, UPR 2301, CNRS, University of Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Prishila Ponien
- Institut de Chimie des Substances Naturelles, UPR 2301, CNRS, University of Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | | | - Istvan Baczkó
- Department Pharmacology and Pharmacotherapy, University of Szeged, Hungary
| | - Lars S Maier
- Department Internal Medicine II, University Heart Center, University Hospital Regensburg, Regensburg, Germany
| | | | - Dobromir Dobrev
- West German Heart and Vascular Center, Institute of Pharmacology, University Duisburg-Essen, Essen, Germany
| | - Rodolphe Fischmeister
- Inserm, UMR-S 1180, University of Paris-Sud, Université Paris-Saclay, Châtenay-Malabry, France
| | - Anne Garnier
- Inserm, UMR-S 1180, University of Paris-Sud, Université Paris-Saclay, Châtenay-Malabry, France
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18
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Wang H, Ma J, Xu H, Lyu Y, Tao L, Li W, Zeng Y, Ma K, Xiao B, Chen L. Early postmortem interval (EPMI) estimation using differentially expressed gene transcripts. Leg Med (Tokyo) 2019; 38:83-91. [PMID: 31108272 DOI: 10.1016/j.legalmed.2019.04.008] [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: 01/07/2019] [Revised: 04/07/2019] [Accepted: 04/30/2019] [Indexed: 10/26/2022]
Abstract
Genes differentially expressed after death were selected to construct a mathematical model for early postmortem interval estimation. Sprague Dawley rats were sacrificed and placed at temperatures of 4 °C, 15 °C, 25 °C, and 35 °C. Brain tissues were collected at 0, 6, 12, 18, and 24 h after death and total RNA was extracted. Changes in gene transcript levels after death were detected using microarray expression profiling and differentially expressed genes was screened. Expanded experiments were performed to validate gene transcript levels at different temperatures using the reverse transcription real-time quantitative polymerase chain reaction. Six genes with high coefficients of determination were chosen for construction of mathematical models. Optimal ternary cubic equations were built using R software with temperature, postmortem interval and ΔCq defined as the independent variable x, y and z, respectively. Equations were converted into a three-dimensional visual statistical model using MATLAB. Animal samples were used to validate the mathematical models. Results showed that the 5srRNA showed best stability at four temperatures. The genes Ninj2, Grifin, Arpp19, and Hopx showed high coefficients of determination (>80%) and low error (<3h) in verification experiments which indicate that they are potential markers for early postmortem interval estimation.
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Affiliation(s)
- Hui Wang
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, 131 Dongan Road, Shanghai 200032, PR China
| | - Jianlong Ma
- Shenzhen Institute of Criminal Science and Technology, Investigation Department of Shenzhen Public Security Bureau, Key Laboratory of Forensic Pathology, Ministry of Public Security, Shenzhen 518000, PR China
| | - Hongmei Xu
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, 131 Dongan Road, Shanghai 200032, PR China
| | - Yehui Lyu
- Shanghai University of Medicine & Health Sciences, 279 ZhouzhuHwy, Shanghai 201318, PR China
| | - Li Tao
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, 131 Dongan Road, Shanghai 200032, PR China
| | - Wencan Li
- Forensic Lab, Criminal Science and Technology Institute, Pudong Branch, Shanghai Public Security Bureau, 255 Yanzhong Road, Shanghai 200125, PR China
| | - Yan Zeng
- Children's Hospital, Fudan University, 399 Wanyuan Road, Shanghai 201102, PR China
| | - Kaijun Ma
- Forensic Lab, Criminal Science and Technology Institute, Shanghai Public Security Bureau, 803 North Zhongshan Road, Shanghai 200082, PR China
| | - Bi Xiao
- Forensic Lab, Criminal Science and Technology Institute, Shanghai Public Security Bureau, 803 North Zhongshan Road, Shanghai 200082, PR China.
| | - Long Chen
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, 131 Dongan Road, Shanghai 200032, PR China.
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19
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Wilmes V, Scheiper S, Roehr W, Niess C, Kippenberger S, Steinhorst K, Verhoff MA, Kauferstein S. Increased inducible nitric oxide synthase (iNOS) expression in human myocardial infarction. Int J Legal Med 2019; 134:575-581. [DOI: 10.1007/s00414-019-02051-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 03/21/2019] [Indexed: 01/06/2023]
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20
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Cipriani S, Phan V, Médard JJ, Horvath R, Lochmüller H, Chrast R, Roos A, Spendiff S. Neuromuscular Junction Changes in a Mouse Model of Charcot-Marie-Tooth Disease Type 4C. Int J Mol Sci 2018; 19:ijms19124072. [PMID: 30562927 PMCID: PMC6320960 DOI: 10.3390/ijms19124072] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 12/06/2018] [Accepted: 12/14/2018] [Indexed: 01/08/2023] Open
Abstract
The neuromuscular junction (NMJ) appears to be a site of pathology in a number of peripheral nerve diseases. Charcot-Marie-Tooth (CMT) 4C is an autosomal recessive, early onset, demyelinating neuropathy. Numerous mutations in the SH3TC2 gene have been shown to underlie the condition often associated with scoliosis, foot deformities, and reduced nerve conduction velocities. Mice with exon 1 of the Sh3tc2 gene knocked out demonstrate many of the features seen in patients. To determine if NMJ pathology is contributory to the pathomechanisms of CMT4C we examined NMJs in the gastrocnemius muscle of SH3TC2-deficient mice. In addition, we performed proteomic assessment of the sciatic nerve to identify protein factors contributing to the NMJ alterations and the survival of demyelinated axons. Morphological and gene expression analysis of NMJs revealed a lack of continuity between the pre- and post-synaptic apparatus, increases in post-synaptic fragmentation and dispersal, and an increase in expression of the gamma subunit of the acetylcholine receptor. There were no changes in axonal width or the number of axonal inputs to the NMJ. Proteome investigations of the sciatic nerve revealed altered expression of extracellular matrix proteins important for NMJ integrity. Together these observations suggest that CMT4C pathology includes a compromised NMJ even in the absence of changes to the innervating axon.
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Affiliation(s)
- Silvia Cipriani
- John Walton Muscular Dystrophy Research Centre, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK.
- INSPE-Institute of Experimental Neurology, San Raffaele Scientific Institute, 20132 Milan, Italy.
- Division of Neuroscience, San Raffaele Scientific Institute, 20132 Milan, Italy.
| | - Vietxuan Phan
- Leibniz-Institut für Analytische Wissenschaften -ISAS- e.V.; Otto-Hahn-Strasse 6b, 44227 Dortmund, Germany.
| | - Jean-Jacques Médard
- Department of Neuroscience, Karolinska Institutet, 171 65 Stockholm, Sweden.
- Department of Clinical Neuroscience, Karolinska Institutet, 171 65 Stockholm, Sweden.
| | - Rita Horvath
- Department of Clinical Neurosciences, University of Cambridge, John Van Geest Cambridge Centre for Brain Repair, Forvie, Robinson way, Cambridge Biomedical Campus, Cambridge CB2 0PY, UK.
| | - Hanns Lochmüller
- Department of Neuropediatrics and Muscle Disorders, Medical Center-University of Freiburg, Mathildenstrasse 1, 79106 Freiburg, Germany.
- Centro Nacional de Análisis Genómico, Center for Genomic Regulation, Barcelona Institute of Science and Technology, Baldri I reixac 4, 08028 Barcelona, Spain.
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada.
- Division of Neurology, Department of Medicine, The Ottawa Hospital, Riverside Drive, Ottawa, ON K1H 7X5, Canada.
| | - Roman Chrast
- Department of Neuroscience, Karolinska Institutet, 171 65 Stockholm, Sweden.
- Department of Clinical Neuroscience, Karolinska Institutet, 171 65 Stockholm, Sweden.
| | - Andreas Roos
- Leibniz-Institut für Analytische Wissenschaften -ISAS- e.V.; Otto-Hahn-Strasse 6b, 44227 Dortmund, Germany.
- Department of Neuropediatrics, Developmental Neurology and Social Pediatrics, Centre for Neuromuscular Disorders in Children, University Children's Hospital Essen, University of Duisburg-Essen, 45122 Essen, Germany.
| | - Sally Spendiff
- John Walton Muscular Dystrophy Research Centre, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK.
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada.
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21
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Evaluating the potential of housekeeping genes, rRNAs, snRNAs, microRNAs and circRNAs as reference genes for the estimation of PMI. Forensic Sci Med Pathol 2018; 14:194-201. [DOI: 10.1007/s12024-018-9973-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2018] [Indexed: 12/18/2022]
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22
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Using Skin Gene Markers for Estimating Early Postmortem Interval at Different Temperatures. Am J Forensic Med Pathol 2017; 38:323-325. [PMID: 28796650 DOI: 10.1097/paf.0000000000000337] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Many researches document long-term RNA persistence in a variety of tissues and its applicability in estimating the postmortem interval (PMI). Skin-specific mRNA marker, late cornified envelope 1C (LCE1C), was used to identified skin samples. Before using the LCE1C in criminal casework, its persistence and applicability for estimating PMI in different temperatures were tested. Twelve skin samples were collected from 6 patients, and 6 samples were kept at 24°C and others were kept at 40°C for 5 days. The expression levels of LCE1C mRNA are serially detected and quantified using real-time polymerase chain reaction. The expression levels of LCE1C were decreased with increasing the time interval in time-dependent manner, whereas changing the surrounding temperatures did not show any statistical significance. These results could suggest using LCE1C in estimation of PMI. Moreover, these encourage investigators and crime laboratories to know environmental conditions before interpreting the results.
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23
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Warden CH, Bettaieb A, Min E, Fisler JS, Haj FG, Stern JS. Chow fed UC Davis strain female Lepr fatty Zucker rats exhibit mild glucose intolerance, hypertriglyceridemia, and increased urine volume, all reduced by a Brown Norway strain chromosome 1 congenic donor region. PLoS One 2017; 12:e0188175. [PMID: 29211750 PMCID: PMC5718614 DOI: 10.1371/journal.pone.0188175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 10/23/2017] [Indexed: 12/01/2022] Open
Abstract
Our objective is to identify genes that influence the development of any phenotypes of type 2 diabetes (T2D) or kidney disease in obese animals. We use the reproductively isolated UC Davis fatty Zucker strain rat model in which the defective chromosome 4 leptin receptor (LeprfaSte/faSte) results in fatty obesity. We previously produced a congenic strain with the distal half of chromosome 1 from the Brown Norway strain (BN) on a Zucker (ZUC) background (BN.ZUC-D1Rat183–D1Rat90). Previously published studies in males showed that the BN congenic donor region protects from some phenotypes of renal dysfunction and T2D. We now expand our studies to include females and expand phenotyping to gene expression. We performed diabetes and kidney disease phenotyping in chow-fed females of the BN.ZUC-D1Rat183-D1Rat90 congenic strain to determine the specific characteristics of the UC Davis model. Fatty LeprfaSte/faSte animals of both BN and ZUC genotype in the congenic donor region had prediabetic levels of fasting blood glucose and blood glucose 2 hours after a glucose tolerance test. We observed significant congenic strain chromosome 1 genotype effects of the BN donor region in fatty females that resulted in decreased food intake, urine volume, glucose area under the curve during glucose tolerance test, plasma triglyceride levels, and urine glucose excretion per day. In fatty females, there were significant congenic strain BN genotype effects on non-fasted plasma urea nitrogen, triglyceride, and creatinine. Congenic region genotype effects were observed by quantitative PCR of mRNA from the kidney for six genes, all located in the chromosome 1 BN donor region, with potential effects on T2D or kidney function. The results are consistent with the hypothesis that the BN genotype chromosome 1 congenic region influences traits of both type 2 diabetes and kidney function in fatty UC Davis ZUC females and that there are many positional candidate genes.
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Affiliation(s)
- Craig H. Warden
- Departments of Pediatrics, Neurobiology Physiology and Behavior, University of California, Davis, Davis, CA, United States of America
- * E-mail:
| | - Ahmed Bettaieb
- Department of Nutrition, University of Tennessee, Knoxville, TN, United States of America
| | - Esther Min
- Department of Nutrition, University of California, Davis, Davis, CA, United States of America
| | - Janis S. Fisler
- Department of Nutrition, University of California, Davis, Davis, CA, United States of America
| | - Fawaz G. Haj
- Department of Nutrition, University of California, Davis, Davis, CA, United States of America
| | - Judith S. Stern
- Department of Nutrition, University of California, Davis, Davis, CA, United States of America
- Internal Medicine, University of California, Davis, Davis, CA, United States of America
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24
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Kim JY, Kim Y, Cha HK, Lim HY, Kim H, Chung S, Hwang JJ, Park SH, Son GH. Cell Death-Associated Ribosomal RNA Cleavage in Postmortem Tissues and Its Forensic Applications. Mol Cells 2017; 40:410-417. [PMID: 28614917 PMCID: PMC5523017 DOI: 10.14348/molcells.2017.0039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 04/24/2017] [Accepted: 05/12/2017] [Indexed: 12/21/2022] Open
Abstract
Estimation of postmortem interval (PMI) is a key issue in the field of forensic pathology. With the availability of quantitative analysis of RNA levels in postmortem tissues, several studies have assessed the postmortem degradation of constitutively expressed RNA species to estimate PMI. However, conventional RNA quantification as well as biochemical and physiological changes employed thus far have limitations related to standardization or normalization. The present study focuses on an interesting feature of the subdomains of certain RNA species, in which they are site-specifically cleaved during apoptotic cell death. We found that the D8 divergent domain of ribosomal RNA (rRNA) bearing cell death-related cleavage sites was rapidly removed during postmortem RNA degradation. In contrast to the fragile domain, the 5' terminal region of 28S rRNA was remarkably stable during the postmortem period. Importantly, the differences in the degradation rates between the two domains in mammalian 28S rRNA were highly proportional to increasing PMI with a significant linear correlation observed in mice as well as human autopsy tissues. In conclusion, we demonstrate that comparison of the degradation rates between domains of a single RNA species provides quantitative information on postmortem degradation states, which can be applied for the estimation of PMI.
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Affiliation(s)
- Ji Yeon Kim
- Department of Legal Medicine, College of Medicine, Korea University, Seoul 02841,
Korea
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul 02841,
Korea
| | - Yunmi Kim
- Department of Legal Medicine, College of Medicine, Korea University, Seoul 02841,
Korea
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul 02841,
Korea
| | - Hyo Kyeong Cha
- Department of Legal Medicine, College of Medicine, Korea University, Seoul 02841,
Korea
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul 02841,
Korea
| | - Hye Young Lim
- Department of Legal Medicine, College of Medicine, Korea University, Seoul 02841,
Korea
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul 02841,
Korea
| | - Hyungsub Kim
- Department of Legal Medicine, College of Medicine, Korea University, Seoul 02841,
Korea
| | - Sooyoung Chung
- Department of Brain and Cognitive Sciences, Scranton College, Ewha Womans University, Seoul 03760,
Korea
| | - Juck-Joon Hwang
- Department of Legal Medicine, College of Medicine, Korea University, Seoul 02841,
Korea
| | - Seong Hwan Park
- Department of Legal Medicine, College of Medicine, Korea University, Seoul 02841,
Korea
| | - Gi Hoon Son
- Department of Legal Medicine, College of Medicine, Korea University, Seoul 02841,
Korea
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul 02841,
Korea
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Increased cerebral expressions of MMPs, CLDN5, OCLN, ZO1 and AQPs are associated with brain edema following fatal heat stroke. Sci Rep 2017; 7:1691. [PMID: 28490769 PMCID: PMC5431794 DOI: 10.1038/s41598-017-01923-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 04/06/2017] [Indexed: 01/19/2023] Open
Abstract
Human brain samples were collected from 46 autopsy cases, including 23 fatal heat stroke cases and 23 age-matched controls. Nine candidate reference genes (PES1, POLR2A, IPO8, HMBS, SDHA, GAPDH, UBC, B2M, ACTB) were evaluated in the cerebral cortex of 10 forensic autopsy cases (5 heat stroke and 5 controls), using the geNorm module in qBaseplus software. SDHA, POLR2A, IPO8 and HMBS were identified as the most stable reference genes. Using these validated reference genes, mRNA expressions of Matrix metalloproteinases (MMPs, MMP2 and MMP9), Claudin5 (CLDN5), Occludin (OCLN), Zona occludens protein-1 (ZO1) and Aquaporins (AQPs, AQP1 and AQP4) in the cerebral cortex were examined. Relative mRNA quantification using Taqman real-time PCR assay demonstrated increased calibrated normalized relative quantity (CNRQ) values of MMP9, CLDN5, OCLN, ZO1 and AQP4 in heat stroke cases. Heat stroke cases showed an increase in brain water content, which was found to be positively correlated with MMP9, OCLN, ZO1 and CLDN5 mRNA. When using one conventional reference gene (GAPDH or ACTB) for normalization, no difference was detected between heat stroke and controls. In immunostaining, only AQP4 showed more intense staining in most heat stroke cases. The present study, for the first time, reports increased cerebral MMP9, CLDN5, OCLN, ZO1 and AQP4 in heat stroke and suggest a crucial role of reference gene selection when using postmortem human tissues.
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Lv YH, Ma JL, Pan H, Zeng Y, Tao L, Zhang H, Li WC, Ma KJ, Chen L. Estimation of the human postmortem interval using an established rat mathematical model and multi-RNA markers. Forensic Sci Med Pathol 2016; 13:20-27. [PMID: 28032211 DOI: 10.1007/s12024-016-9827-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2016] [Indexed: 10/20/2022]
Abstract
In our previous study, a R code-based mathematical model using RNA degradation patterns was developed for PMI determination in rat brain specimens. However, the postmortem changes of RNA are much more complicated in real cases, and there is still a huge challenge in efficiently applying information in animal data to real cases. In the present study, different RNA markers in both rat and human tissues were collected to screen valid biomarkers and the corresponding mathematical models were established and validated. With the same methodology, multi-RNA markers of myocardium and liver tissues were detected by qPCR and the Ct values of ten biomarkers generally increased with prolonged PMIs. 5S, miR-1 and miR-133a were shown to be optimum reference biomarkers that were not affected by a PMI of up to 5 or more days; however, liver-specific miR-122 began to degrade under higher temperatures and only 5S was selected as an endogenous control in the liver. Among the tested target RNAs, similar to our previous study in brain tissue, β-actin (ΔCt) was found to exhibit the best correlation coefficient with PMI and was employed to build mathematical models using R software. Following validation, the relatively low estimated error demonstrated that PMIs can be accurately predicted in human cases through comprehensive consideration of various factors and using effective biomarkers.
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Affiliation(s)
- Ye-Hui Lv
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, 131 Dongan Road, Shanghai, 200032, People's Republic of China.,Shanghai University of Medicine & Health Sciences, 21 Meilong Road, Shanghai, 200030, People's Republic of China
| | - Jian-Long Ma
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, 131 Dongan Road, Shanghai, 200032, People's Republic of China
| | - Hui Pan
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, 131 Dongan Road, Shanghai, 200032, People's Republic of China
| | - Yan Zeng
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, 131 Dongan Road, Shanghai, 200032, People's Republic of China
| | - Li Tao
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, 131 Dongan Road, Shanghai, 200032, People's Republic of China
| | - Heng Zhang
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, 131 Dongan Road, Shanghai, 200032, People's Republic of China
| | - Wen-Can Li
- Shanghai Public Security Bureau, Pudong Branch, 655 Dingxiang Road, Shanghai, 200032, People's Republic of China
| | - Kai-Jun Ma
- Forensic Lab, Criminal Science and Technology Institute, Shanghai Public Security Bureau, 803 North Zhongshan Road, Shanghai, 200082, People's Republic of China
| | - Long Chen
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, 131 Dongan Road, Shanghai, 200032, People's Republic of China.
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Meira-Strejevitch CS, Pereira-Chioccola VL, Maia MM, Carnietto de Hipólito DD, Wang HTL, Motoie G, de Souza Gomes AH, Kanamura CT, Martines RB, de Mattos CCB, Frederico FB, de Mattos LC, de Mattos CCB, Frederico FB, Siqueira RC, Previato M, Barbosa AP, Murata FHA. WITHDRAWN: Selection of reference genes in five types of human tissues for normalization of gene expression studies in infectious diseases. Gene 2016:S0378-1119(16)30816-2. [PMID: 27743995 DOI: 10.1016/j.gene.2016.10.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 10/09/2016] [Indexed: 11/23/2022]
Abstract
This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicy.
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Affiliation(s)
| | | | - Marta Marques Maia
- Centro de Parasitologia e Micologia, Instituto Adolfo Lutz, Sao Paulo Brazil
| | | | - Hui-Tzu Lin Wang
- Laboratório de Investigação Molecular em Cardiologia, Instituto Dante Pazzanese de Cardiologia, Sao Paulo Brazil
| | - Gabriela Motoie
- Centro de Parasitologia e Micologia, Instituto Adolfo Lutz, Sao Paulo Brazil
| | | | | | | | - Cinara Cássia Brandão de Mattos
- Laboratório de Imunogenética, Departamento de Biologia Molecular, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, Brazil
| | - Fábio Batista Frederico
- Ambulatório de Oftalmologia, Fundação Faculdade Regional de Medicina-Hospital de Base, São José do Rio Preto, Brazil
| | - Luiz Carlos de Mattos
- Laboratório de Imunogenética, Departamento de Biologia Molecular, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, Brazil
| | - Cinara Cássia Brandão de Mattos
- Laboratório de Imunogenética, Departamento de Biologia Molecular, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, Brazil
| | - Fábio Batista Frederico
- Ambulatório de Oftalmologia, Fundação Faculdade Regional de Medicina-Hospital de Base, São José do Rio Preto, Brazil
| | - Rubens Camargo Siqueira
- Laboratório de Imunogenética, Departamento de Biologia Molecular, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, Brazil
| | - Mariana Previato
- Laboratório de Imunogenética, Departamento de Biologia Molecular, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, Brazil
| | - Amanda Pires Barbosa
- Ambulatório de Oftalmologia, Fundação Faculdade Regional de Medicina-Hospital de Base, São José do Rio Preto, Brazil
| | - Fernando Henrique Antunes Murata
- Laboratório de Imunogenética, Departamento de Biologia Molecular, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, Brazil
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Du Y, Jin HN, Zhao R, Zhao D, Xue Y, Zhu BL, Guan DW, Xie XL, Wang Q. Molecular Pathology of Pulmonary Edema in Forensic Autopsy Cases with Special Regard to Fatal Methamphetamine Intoxication. J Forensic Sci 2016; 61:1531-1537. [DOI: 10.1111/1556-4029.13199] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 01/12/2016] [Accepted: 01/16/2016] [Indexed: 12/17/2022]
Affiliation(s)
- Yu Du
- Department of Forensic Medicine; National Police University of China, No. 83, Tawan Street, Huangpu District, 110035; Shenyang China
| | - Hong-Nian Jin
- Forensic Science Centre of Guangdong Provincial Public Security Department; No. 3 Beijiaochang Cross Road Yuexiu District 510050 Guangzhou China
| | - Rui Zhao
- Department of Forensic Pathology; China Medical University; School of Forensic Medicine; No. 77 Puhe Road, Shenyang North New Area Shenyang Liaoning Province China
| | - Dong Zhao
- Collaborative Innovation Center of Judicial Civilization, China; Key Laboratory of Evidence Science (China University of Political Science and Law); Ministry of Education; No. 25 West Tucheng Road Haidian District Beijing 100088 China
| | - Ye Xue
- Department of Forensic Pathology; School of Forensic Medicine; Southern Medical University; No. 1838 510515 Guangzhou China
| | - Bao-Li Zhu
- Department of Forensic Pathology; China Medical University; School of Forensic Medicine; No. 77 Puhe Road, Shenyang North New Area Shenyang Liaoning Province China
| | - Da-Wei Guan
- Department of Forensic Pathology; China Medical University; School of Forensic Medicine; No. 77 Puhe Road, Shenyang North New Area Shenyang Liaoning Province China
| | - Xiao-Li Xie
- Department of Toxicology, School of Public Health; Southern Medical University, (Guangdong Provincial Key Laboratory of Tropical Disease Research); No. 1838 Guangzhou 510515 China
| | - Qi Wang
- Department of Forensic Pathology; School of Forensic Medicine; Southern Medical University; No. 1838 510515 Guangzhou China
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DNA and RNA profiling of excavated human remains with varying postmortem intervals. Int J Legal Med 2016; 130:1471-1480. [PMID: 27627902 DOI: 10.1007/s00414-016-1438-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 08/09/2016] [Indexed: 01/03/2023]
Abstract
When postmortem intervals (PMIs) increase such as with longer burial times, human remains suffer increasingly from the taphonomic effects of decomposition processes such as autolysis and putrefaction. In this study, various DNA analysis techniques and a messenger RNA (mRNA) profiling method were applied to examine for trends in nucleic acid degradation and the postmortem interval. The DNA analysis techniques include highly sensitive DNA quantitation (with and without degradation index), standard and low template STR profiling, insertion and null alleles (INNUL) of retrotransposable elements typing and mitochondrial DNA profiling. The used mRNA profiling system targets genes with tissue specific expression for seven human organs as reported by Lindenbergh et al. (Int J Legal Med 127:891-900, 27) and has been applied to forensic evidentiary traces but not to excavated tissues. The techniques were applied to a total of 81 brain, lung, liver, skeletal muscle, heart, kidney and skin samples obtained from 19 excavated graves with burial times ranging from 4 to 42 years. Results show that brain and heart are the organs in which both DNA and RNA remain remarkably stable, notwithstanding long PMIs. The other organ tissues either show poor overall profiling results or vary for DNA and RNA profiling success, with sometimes DNA and other times RNA profiling being more successful. No straightforward relations were observed between nucleic acid profiling results and the PMI. This study shows that not only DNA but also RNA molecules can be remarkably stable and used for profiling of long-buried human remains, which corroborate forensic applications. The insight that the brain and heart tissues tend to provide the best profiling results may change sampling policies in identification cases of degrading cadavers.
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Lv YH, Ma JL, Pan H, Zhang H, Li WC, Xue AM, Wang HJ, Ma KJ, Chen L. RNA degradation as described by a mathematical model for postmortem interval determination. J Forensic Leg Med 2016; 44:43-52. [PMID: 27598868 DOI: 10.1016/j.jflm.2016.08.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 08/16/2016] [Accepted: 08/28/2016] [Indexed: 10/21/2022]
Abstract
Precisely determining the postmortem interval (PMI) is crucial to civil, criminal and forensic cases. A technique to exploit the postmortem RNA transcript level was developed to increase the accuracy and practicality of PMI estimation. For this purpose, lung tissues and muscle tissues were removed at twelve time points (0-144 h) from rat corpses that had been stored at three different temperatures (10, 20 and 30 °C). Human tissues were collected at autopsy from twelve real cases with known PMI values and other parameters. After the RNA was extracted from all these samples, the transcript levels of nine biomarkers were analyzed by real-time quantitative PCR (RT-qPCR). With the assistance of geNorm, miR-195, miR-200c, 5S, U6 and RPS29 were selected as reference biomarkers for lung specimens; miR-1, miR-206, 5S and RPS29 were chosen as control markers for muscle tissues. On the contrary, ACTB and GAPDH were significantly correlated with the PMI. The mathematical models using these target biomarkers were constructed to describe the characteristic relationship between △Ct values (normalized to reference biomarkers) and the observed PMI for each temperature group. Following validation, the relatively low error rates (7.4% and 12.5% for rat and human samples, respectively) demonstrated the accuracy and reliability of the mathematical model. We believe these results indicate that the multi-parametric mathematical model can become a practical tool for PMI estimation.
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Affiliation(s)
- Ye-Hui Lv
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, 131 Dongan Road, Shanghai, 200032, People's Republic of China; Department of Physiology & Pathophysiology, School of Basic Medical Sciences, Fudan University, 130 Dongan Road, Shanghai, 200032, People's Republic of China; Shanghai University of Medicine & Health Sciences, 21 Meilong Road, Shanghai, 200030, People's Republic of China
| | - Jian-Long Ma
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, 131 Dongan Road, Shanghai, 200032, People's Republic of China
| | - Hui Pan
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, 131 Dongan Road, Shanghai, 200032, People's Republic of China
| | - Heng Zhang
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, 131 Dongan Road, Shanghai, 200032, People's Republic of China; Department of Physiology & Pathophysiology, School of Basic Medical Sciences, Fudan University, 130 Dongan Road, Shanghai, 200032, People's Republic of China
| | - Wen-Can Li
- Shanghai Public Security Bureau, Pudong Branch, 655 Dingxiang Road, Shanghai, 200032, People's Republic of China
| | - Ai-Min Xue
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, 131 Dongan Road, Shanghai, 200032, People's Republic of China
| | - Hui-Jun Wang
- Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, People's Republic of China
| | - Kai-Jun Ma
- Forensic Lab, Criminal Science and Technology Institute, Shanghai Public Security Bureau, 803 North Zhongshan Road, Shanghai, 200082, People's Republic of China
| | - Long Chen
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, 131 Dongan Road, Shanghai, 200032, People's Republic of China.
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Morales MA, Mendoza BM, Lavine LC, Lavine MD, Walsh DB, Zhu F. Selection of Reference Genes for Expression Studies of Xenobiotic Adaptation in Tetranychus urticae. Int J Biol Sci 2016; 12:1129-39. [PMID: 27570487 PMCID: PMC4997057 DOI: 10.7150/ijbs.16319] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Accepted: 07/08/2016] [Indexed: 11/25/2022] Open
Abstract
Quantitative real-time PCR (qRT-PCR) is an extensively used, high-throughput method to analyze transcriptional expression of genes of interest. An appropriate normalization strategy with reliable reference genes is required for calculating gene expression across diverse experimental conditions. In this study, we aim to identify the most stable reference genes for expression studies of xenobiotic adaptation in Tetranychus urticae, an extremely polyphagous herbivore causing significant yield reduction of agriculture. We chose eight commonly used housekeeping genes as candidates. The qRT-PCR expression data for these genes were evaluated from seven populations: a susceptible and three acaricide resistant populations feeding on lima beans, and three other susceptible populations which had been shifted host from lima beans to three other plant species. The stability of the candidate reference genes was then assessed using four different algorithms (comparative ΔCt method, geNorm, NormFinder, and BestKeeper). Additionally, we used an online web-based tool (RefFinder) to assign an overall final rank for each candidate gene. Our study found that CycA and Rp49 are best for investigating gene expression in acaricide susceptible and resistant populations. GAPDH, Rp49, and Rpl18 are best for host plant shift studies. And GAPDH and Rp49 were the most stable reference genes when investigating gene expression under changes in both experimental conditions. These results will facilitate research in revealing molecular mechanisms underlying the xenobiotic adaptation of this notorious agricultural pest.
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Affiliation(s)
- Mariany Ashanty Morales
- Department of Entomology, Washington State University, Pullman, WA 99164, USA
- Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA 99350, USA
| | | | - Laura Corley Lavine
- Department of Entomology, Washington State University, Pullman, WA 99164, USA
| | - Mark Daniel Lavine
- Department of Entomology, Washington State University, Pullman, WA 99164, USA
| | - Douglas Bruce Walsh
- Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA 99350, USA
| | - Fang Zhu
- Department of Entomology, Washington State University, Pullman, WA 99164, USA
- Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA 99350, USA
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Liu G, Qiu X, Cao L, Zhang Y, Zhan Z, Han R. Evaluation of Reference Genes for Reverse Transcription Quantitative PCR Studies of Physiological Responses in the Ghost Moth, Thitarodes armoricanus (Lepidoptera, Hepialidae). PLoS One 2016; 11:e0159060. [PMID: 27392023 PMCID: PMC4938418 DOI: 10.1371/journal.pone.0159060] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 06/27/2016] [Indexed: 12/18/2022] Open
Abstract
Reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) is the sensitive method to quantify the expression levels of target genes on the basis of endogenous control. An appropriate reference gene set for normalization is essential for reliable results. The ghost moth, Thitarodes armoricanus, a host species of a medicinal fungus, Ophiocordyceps sinensis, is an economically important member of the Lepidoptera. Recent studies have focused on the mechanism of adaptation of this species to its high-altitude environment and host immune response to O. sinensis infection and RT-qPCR is commonly used in these studies to decipher the genetic basis of physiological functions. However, a thorough assessment of candidate reference genes in the genus Thitarodes is lacking. Here, the expression levels of eight candidate reference genes (ACT, EF, EIF4A, GAPDH, G6PDH, RPL13A, TUB and 18S) in T. armoricanus at different developmental stages and in different body parts of the seventh instar larvae were analyzed, along with larvae kept under low temperatures, larvae exposed to two fungal infections and larvae fed different diets. Three established software programs–Bestkeeper, geNorm and NormFinder–were employed to calculate variation among the treatments. The results revealed that the best-suited reference genes differed across the treatments, with EF, EIF4A and GAPDH found to be the best suited for the different developmental stages and larvae body parts; EF, EIF4A and RPL13A found to be the best suited for low-temperature challenge; and EF, EIF4A and TUB found to be the best suited for the fungal infections and dietary treatments. This study thus further contributes to the establishment of an accurate method for normalizing RT-qPCR results for T. armoricanus and serves as a reference for gene expression studies of related insect species.
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Affiliation(s)
- Guiqing Liu
- Guangdong Key Laboratory of IPM in Agriculture and Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
| | - Xuehong Qiu
- Guangdong Key Laboratory of IPM in Agriculture and Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
| | - Li Cao
- Guangdong Key Laboratory of IPM in Agriculture and Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
| | - Yi Zhang
- Guangdong Key Laboratory of IPM in Agriculture and Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
| | - Zubing Zhan
- Guangdong Key Laboratory of IPM in Agriculture and Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
| | - Richou Han
- Guangdong Key Laboratory of IPM in Agriculture and Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
- * E-mail:
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Xue Y, Zhao R, Du SH, Zhao D, Li DR, Xu JT, Xie XL, Wang Q. Decreased mRNA levels of cardiac Cx43 and ZO1 in sudden cardiac death related to coronary atherosclerosis: a pilot study. Int J Legal Med 2016; 130:915-922. [PMID: 26972693 DOI: 10.1007/s00414-016-1353-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 02/25/2016] [Indexed: 02/07/2023]
Abstract
Sudden cardiac death (SCD) is the most frequent cause of sudden unexplained death in forensic practice. The most common cause of SCD is coronary artery disease related to coronary atherosclerosis. Previous study suggested the possible application of connexin 43 (Cx43) and zonula occludens-1 (ZO1) immunostaining in the early diagnosis of myocardial ischemia. However, there appears to be insufficient data with regard to their mRNA levels. The present study investigated the cardiac mRNA levels of Cx43 and ZO1, using forensic autopsy materials consisting of 41 control cases without any disease or structural abnormality of the heart (group 1), 32 deaths due to acute ischemic heart disease related to coronary atherosclerosis without apparent myocardial necrosis (group 2), and 29 traumatic deaths with coronary atherosclerosis (group 3). Ten candidate reference genes were evaluated in the left ventricles of 10 forensic autopsy cases. EEF1A1, PPIA, TPT1, and RPL13A were identified as the most stable reference genes. Using these validated reference genes, mRNA levels of Cx43 and ZO1 were examined in the bilateral ventricles and atria of the heart. Relative mRNA quantification demonstrated decreased calibrated normalized relative quantity (CNRQ) values of Cx43 and ZO1 in bilateral ventricles of group 2. When using one conventional reference gene (GAPDH or ACTB) for normalization, nearly no difference was detected among the three groups. These findings indicate that ventricular gap junction remodeling may be a key contributor to rhythm disturbances. Analysis of cardiac Cx43 and ZO1 using real-time PCR is useful in diagnosis of SCD, and validation of reference genes is crucial.
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Affiliation(s)
- Ye Xue
- Department of Forensic Medicine, School of Basic Medical Science, Southern Medical University, No. 1838, Guangzhou, 510515, Guangdong Province, China
| | - Rui Zhao
- Department of Forensic Pathology, China Medical University School of Forensic Medicine, Shenyang, China
| | - Si-Hao Du
- Department of Forensic Medicine, School of Basic Medical Science, Southern Medical University, No. 1838, Guangzhou, 510515, Guangdong Province, China
| | - Dong Zhao
- Collaborative Innovation Center of Judicial Civilization, Beijing, China
- Ministry of Education, Key Laboratory of Evidence Science (China University of Political Science and Law), Beijing, China
| | - Dong-Ri Li
- Department of Forensic Medicine, School of Basic Medical Science, Southern Medical University, No. 1838, Guangzhou, 510515, Guangdong Province, China
| | - Jing-Tao Xu
- Department of Forensic Medicine, School of Basic Medical Science, Southern Medical University, No. 1838, Guangzhou, 510515, Guangdong Province, China
| | - Xiao-Li Xie
- Department of Toxicology, School of Public Health and Tropical Medicine, Southern Medical University, No. 1838, Guangzhou, 510515, Guangdong Province, China.
| | - Qi Wang
- Department of Forensic Medicine, School of Basic Medical Science, Southern Medical University, No. 1838, Guangzhou, 510515, Guangdong Province, China.
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Dean B, Udawela M, Scarr E. Validating reference genes using minimally transformed qpcr data: findings in human cortex and outcomes in schizophrenia. BMC Psychiatry 2016; 16:154. [PMID: 27206773 PMCID: PMC4875643 DOI: 10.1186/s12888-016-0855-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 05/09/2016] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND It is common practice, when using quantitative real time polymerase chain reaction (qPCR), to normalise levels of mRNA to reference gene mRNA which, by definition, should not vary between tissue, with any disease aetiology or after drug treatments. The complexity of human CNS means it unlikely that any gene could fulfil these criteria. METHODS To address this issue we measured levels of mRNA for six potential reference genes (GAPDH, PPIA, SNCA, NOL9, TFB1M and SKP1) in three cortical regions (Brodmann's areas (BA) 8, 9 and 44) from 30 subjects with schizophrenia and 30 age and sex matched controls. We used a structured statistical approach to examine the characteristics of these data to determine their suitability as reference genes. We also analysed our data using reference genes selected by rank as defined using the average of the standard deviation of pair-gene ΔCt and the BestKeeper, NormFinder and geNorm algorithms to determine if they suggested the same reference genes. RESULTS Our minimally derived data showed that levels of mRNA for all of the six genes varied between cortical regions and therefore no gene fulfilled the absolute requirements for use as reference genes. As levels of some mRNA for some genes did not vary with diagnoses within a cortical region from subjects with schizophrenia compared to controls, we normalised levels of mRNA for all the other genes to mRNA for one, two or three reference genes in each cortical region. This showed that using the geometric mean of at least two reference genes gave more reproducible results. Finally, using the reference gene ranking protocols the average of the standard deviation of pair-gene ΔCt, BestKeeper, NormFinder and geNorm we showed that these approaches ranked potential reference genes differently. We then showed that outcomes of comparing data from subjects with schizophrenia and controls varied depending on the reference genes chosen. CONCLUSIONS Our data shows that the selection of reference genes is a significant component of qPCR study design and therefore the process by which reference genes are selected must be clearly listed as a potential confound in studying gene expression in human CNS. This should include showing that, using minimally derived qPCR data, levels of mRNA for proposed reference genes does not vary with variables such as diagnoses and CNS region.
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Affiliation(s)
- Brian Dean
- The Florey Institute for Neuroscience and Mental Health, Parkville, VIC, Australia. .,The Division of Biological Psychiatry and Mental Health and the Molecular Psychiatry Laboratory, The Florey Institute for Neuroscience and Mental Health, 30 Royal Parade, Parkville, VIC, 3052, Australia.
| | - Madhara Udawela
- The Florey Institute for Neuroscience and Mental Health, Parkville, VIC Australia
| | - Elizabeth Scarr
- The Florey Institute for Neuroscience and Mental Health, Parkville, VIC Australia ,The Department of Psychiatry, the University of Melbourne, Victoria, Australia
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Characterization of gene expression profiling of mouse tissues obtained during the postmortem interval. Exp Mol Pathol 2016; 100:482-92. [PMID: 27185020 DOI: 10.1016/j.yexmp.2016.05.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 05/13/2016] [Indexed: 12/27/2022]
Abstract
Attempts to establish a tissue bank from autopsy samples have led to uncovering of the secrets of many diseases. Here, we examined the length of time that the RNA from postmortem tissues is available for microarray analysis and reported the gene expression profile for up- and down-regulated genes during the postmortem interval. We extracted RNA from fresh-frozen (FF) and formalin-fixed paraffin-embedded (FFPE) brains and livers of three different groups of mice: 1) mice immediately after death, 2) mice that were stored at room temperature for 3h after death, and 3) mice that were stored at 4°C for 18h after death, as this storage resembles the human autopsy process in Japan. The RNA quality of the brain and the liver was maintained up to 18h during the postmortem interval. Based on the microarray analysis, we selected genes that were altered by >1.3-fold or <0.77-fold and classified these genes using hierarchical cluster analysis following DAVID gene ontology analysis. These studies revealed that cytoskeleton-related genes were enriched in the set of up-regulated genes, while serine protease inhibitors were enriched in the set of down-regulated genes. Interestingly, although the RNA quality was maintained due to high RNA integrity number (RIN) values, up-regulated genes were not validated by quantitative PCR, suggesting that these genes may become fragmented or modified by an unknown mechanism. Taken together, our findings suggest that under typical autopsy conditions, gene expression profiles that reflect disease pathology can be examined by understanding comprehensive recognition of postmortem fluctuation of gene expression.
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El-Kashef N, Gomes I, Mercer-Chalmers-Bender K, Schneider PM, Rothschild MA, Juebner M. Validation of adequate endogenous reference genes for reverse transcription-qPCR studies in human post-mortem brain tissue of SIDS cases. Forensic Sci Med Pathol 2015; 11:517-29. [DOI: 10.1007/s12024-015-9717-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2015] [Indexed: 01/04/2023]
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Javan GT, Can I, Finley SJ, Soni S. The apoptotic thanatotranscriptome associated with the liver of cadavers. Forensic Sci Med Pathol 2015; 11:509-16. [PMID: 26318598 DOI: 10.1007/s12024-015-9704-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2015] [Indexed: 01/08/2023]
Abstract
Gene expression investigations are well-established components of ante mortem studies with broad applications ranging from elucidating basic mechanisms responsible for normal physiological processes to discovering therapeutic targets in pathophysiological conditions. However, gene expression studies and their application in the medico-legal field are still in their infancy. Therefore, the present study focuses on RNA using PCR array in the analysis of gene expression associated with tissues taken from actual criminal cases. RNA was extracted from the liver tissues of bodies with PMIs between 6 and 48 h. The results demonstrated that mRNA was stable up to 48 h postmortem. Further, as cell death is an indispensable and necessary part of the biological life cycle, apoptotic gene expression profiles were investigated. The gene expression related to the programmed cell death found in body tissues after death is defined as the apoptotic thanatotranscriptome (thanatos-, Greek for death). On comparison of control and decaying tissues, the results show that with time, pro-apoptotic genes such as caspases are up-regulated and the expression of genes responsible for anti-apoptosis such as BCL2 and BAG3 were down-regulated. Thus, this current work gives a unique perspective of the apoptotic thanatotranscriptome that is affected after death. Up to the present time, gene expression in bodies from criminal cases has not been reported in literature using PCR array techniques. Thus, this thanatotranscriptome study provides insight into postmortem gene activity with potential applications in medico-legal investigations.
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Affiliation(s)
- Gulnaz T Javan
- Forensic Science Program, Alabama State University, Montgomery, AL, 36104, USA.
| | - Ismail Can
- Forensic Science Program, Alabama State University, Montgomery, AL, 36104, USA.
| | | | - Shivani Soni
- Department of Biological Sciences, Alabama State University, Montgomery, AL, 36101, USA.
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Akutsu T, Kitayama T, Watanabe K, Sakurada K. Comparison of automated and manual purification of total RNA for mRNA-based identification of body fluids. Forensic Sci Int Genet 2015; 14:11-7. [DOI: 10.1016/j.fsigen.2014.09.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 07/10/2014] [Accepted: 09/08/2014] [Indexed: 01/21/2023]
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Li WC, Ma KJ, Lv YH, Zhang P, Pan H, Zhang H, Wang HJ, Ma D, Chen L. Postmortem interval determination using 18S-rRNA and microRNA. Sci Justice 2014; 54:307-10. [PMID: 25002049 DOI: 10.1016/j.scijus.2014.03.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 02/20/2014] [Accepted: 03/13/2014] [Indexed: 10/25/2022]
Abstract
The importance of determining postmortem interval (PMI) is crucial to criminal, civil and forensic cases. The precise estimation of PMI is a critical step in many death investigations. A technique exploiting the level of RNA, 18S rRNA and microRNA to estimate PMI was investigated. 18S-rRNA is a main ribosomal RNA presented as part of the ribosomal protein complex, while microRNA is a class of small non-coding single-stranded RNA, only 21-25 nucleotides, which has a strong conservation between different species. In this study, heart tissues were removed from adult rats at various postmortem intervals. An efficient extraction and detection protocol to analyze the level of 18S-rRNA and microRNA in postmortem tissue was carried out. The process consists of total RNA extraction, transcription and visualization by quantitative real time PCR. The result indicates a characteristic parabola relationship between postmortem period and Ct values for 18S-rRNA in dead rat hearts. The result indicates that the degradation pattern of tissue 18S-rRNA and microRNA is useful in the determination of the postmortem interval within seven days.
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Affiliation(s)
- Wen-Can Li
- Forensic Department, Shanghai Medical College, Fudan University, Shanghai 200032, China; Shanghai City Public Security Bureau, Shanghai 200032, China
| | - Kai-Jun Ma
- Forensic Lab, Criminal Science and Technology Institute, Shanghai Public Security Bureau, Shanghai 200032, China
| | - Ye-Hui Lv
- Forensic Department, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Ping Zhang
- Forensic Department, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Hui Pan
- Forensic Department, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Heng Zhang
- Forensic Department, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Hui-Jun Wang
- Children's Hospital, Fudan University, Shanghai 201102, China
| | - Duan Ma
- Key Laboratory of Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, Fudan University, Shanghai 200032, China
| | - Long Chen
- Forensic Department, Shanghai Medical College, Fudan University, Shanghai 200032, China
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Lv YH, Ma KJ, Zhang H, He M, Zhang P, Shen YW, Jiang N, Ma D, Chen L. A time course study demonstrating mRNA, microRNA, 18S rRNA, and U6 snRNA changes to estimate PMI in deceased rat's spleen. J Forensic Sci 2014; 59:1286-94. [PMID: 24611529 DOI: 10.1111/1556-4029.12447] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Revised: 05/26/2013] [Accepted: 06/13/2013] [Indexed: 11/28/2022]
Abstract
Determining the postmortem interval (PMI) is important in criminal, civil, and forensic cases. We examined the feasibility of using the transcript abundances of mRNAs, 18S rRNA, U6 snRNA, and microRNAs as a means to estimate the PMI. We removed spleen tissues from rats at different PMIs under 4°C or 25°C and examined gene transcript abundances in these samples by RT-qPCR. Using the algorithm geNorm, we found that microRNAs to be appropriate control markers because they were less affected by PMI and temperature. We also characterized relationships between observed PMI and the transcript levels of the above-mentioned RNAs. GAPDH1 and ACTB1 fluctuated slightly like cubic curves, while GAPDH2 and ACTB2 decreased rapidly. 18S rRNA transcript level exhibited a parabolic-like trend at 25°C and exponential growth at 4°C, while U6 transcript level exhibited exponential decay at 25°C and a parabolic-like trend at 4°C. Following validation, we conclude that GAPDH2, ACTB2, and 18S rRNA are suitable makers in the accurate determination of PMI.
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Affiliation(s)
- Ye-hui Lv
- Department of Forensic Medicine, Shanghai Medical School of Fudan University, 200032, Shanghai, China
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Wang Q, Ishikawa T, Michiue T, Zhu BL, Guan DW, Maeda H. Molecular pathology of brain matrix metalloproteases, claudin5, and aquaporins in forensic autopsy cases with special regard to methamphetamine intoxication. Int J Legal Med 2014; 128:469-74. [DOI: 10.1007/s00414-014-0972-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 01/21/2014] [Indexed: 01/27/2023]
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Schildberg T, Rauh J, Bretschneider H, Stiehler M. Identification of suitable reference genes in bone marrow stromal cells from osteoarthritic donors. Stem Cell Res 2013; 11:1288-98. [PMID: 24080205 DOI: 10.1016/j.scr.2013.08.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 08/20/2013] [Accepted: 08/31/2013] [Indexed: 12/28/2022] Open
Abstract
Bone marrow stromal cells (BMSCs) are key cellular components for musculoskeletal tissue engineering strategies. Furthermore, recent data suggest that BMSCs are involved in the development of Osteoarthritis (OA) being a frequently occurring degenerative joint disease. Reliable reference genes for the molecular evaluation of BMSCs derived from donors exhibiting OA as a primary co-morbidity have not been reported on yet. Hence, the aim of the study was to identify reference genes suitable for comparative gene expression analyses using OA-BMSCs. Passage 1 bone marrow derived BMSCs were isolated from n=13 patients with advanced stage idiopathic hip osteoarthritis and n=15 age-matched healthy donors. The expression of 31 putative reference genes was analyzed by quantitative reverse transcription polymerase chain reaction (qRT-PCR) using a commercially available TaqMan(®) assay. Calculating the coefficient of variation (CV), mRNA expression stability was determined and afterwards validated using geNorm and NormFinder algorithms. Importin 8 (IPO8), TATA box binding protein (TBP), and cancer susceptibility candidate 3 (CASC3) were identified as the most stable reference genes. Notably, commonly used reference genes, e.g. beta-actin (ACTB) and beta-2-microglobulin (B2M) were among the most unstable genes. For normalization of gene expression data of OA-BMSCs the combined use of IPO8, TBP, and CASC3 gene is recommended.
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Affiliation(s)
- Theresa Schildberg
- University Centre for Orthopaedics & Trauma Surgery and Centre for Translational Bone, Joint & Soft Tissue Research, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany.
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González-Herrera L, Valenzuela A, Marchal JA, Lorente JA, Villanueva E. Studies on RNA integrity and gene expression in human myocardial tissue, pericardial fluid and blood, and its postmortem stability. Forensic Sci Int 2013; 232:218-28. [PMID: 24053884 DOI: 10.1016/j.forsciint.2013.08.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 06/24/2013] [Accepted: 08/03/2013] [Indexed: 11/30/2022]
Abstract
Analyses of gene expression of ischemic myocardial injury and repair related proteins has been carried out for the first time in samples from five specific sites of the myocardium, pericardial fluid and blood from thirty cadavers in relation to post-mortem interval (PMI). RNA integrity was evaluated by RNA integrity number (RIN), with values ranging from 6.57 to 8.11; sufficiently high levels of integrity to permit further gene amplification. No significant correlations between RIN and PMI in any samples were detected. Prior to target gene expression analysis, a normalization strategy was carried out to assess candidate reference gene stability, involving the analysis and comparison of four common housekeeping genes (Glyceraldehide-3-phosphate dehydrogenase, beta-actin, TATA box binding protein and Cyclophilin A). Gene expression of cardiac troponin I (TNNI3), myosin light chain 3 (MYL3), matrix metalloprotease 9 (MMP9), transforming growth factor beta 1 (TGFB1), and vascular endothelial growth factor A (VEGFA) in myocardial zones and body fluids were subsequently studied by real-time quantitative PCR. Expression levels of all the proteins studied in cardiac zone samples were similar. No statistical differences for expression were detected among proteins taken from any myocardial area. No significant differences were detected for TNNI3 and TGFB1 gene expressions when compared with samples at or under 12h-PMI or over 12h-PMI. However, differences in MYL3, MMP9, and VEGFA gene expression in body fluids were found at PMI periods of over 12h. These interesting results may contribute to the refinement of current knowledge regarding cardiac metabolism and improve understanding of the underlying mechanisms involved in myocardium ischemia and its repair.
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Affiliation(s)
- Lucas González-Herrera
- Department of Forensic Medicine, Faculty of Medicine, University of Granada, Av. de Madrid 11, 18071 Granada, Spain.
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Molecular pathology of brain edema after severe burns in forensic autopsy cases with special regard to the importance of reference gene selection. Int J Legal Med 2013; 127:881-9. [DOI: 10.1007/s00414-013-0868-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 04/26/2013] [Indexed: 12/13/2022]
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Wang Q, Ishikawa T, Michiue T, Zhu BL, Guan DW, Maeda H. Molecular pathology of pulmonary edema in forensic autopsy cases with special regard to fatal hyperthermia and hypothermia. Forensic Sci Int 2013; 228:137-41. [DOI: 10.1016/j.forsciint.2013.03.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Revised: 08/07/2012] [Accepted: 03/04/2013] [Indexed: 10/27/2022]
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Sampaio-Silva F, Magalhães T, Carvalho F, Dinis-Oliveira RJ, Silvestre R. Profiling of RNA degradation for estimation of post mortem [corrected] interval. PLoS One 2013; 8:e56507. [PMID: 23437149 PMCID: PMC3577908 DOI: 10.1371/journal.pone.0056507] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 01/10/2013] [Indexed: 11/22/2022] Open
Abstract
An estimation of the post mortem interval (PMI) is frequently touted as the Holy Grail of forensic pathology. During the first hours after death, PMI estimation is dependent on the rate of physical observable modifications including algor, rigor and livor mortis. However, these assessment methods are still largely unreliable and inaccurate. Alternatively, RNA has been put forward as a valuable tool in forensic pathology, namely to identify body fluids, estimate the age of biological stains and to study the mechanism of death. Nevertheless, the attempts to find correlation between RNA degradation and PMI have been unsuccessful. The aim of this study was to characterize the RNA degradation in different post mortem tissues in order to develop a mathematical model that can be used as coadjuvant method for a more accurate PMI determination. For this purpose, we performed an eleven-hour kinetic analysis of total extracted RNA from murine's visceral and muscle tissues. The degradation profile of total RNA and the expression levels of several reference genes were analyzed by quantitative real-time PCR. A quantitative analysis of normalized transcript levels on the former tissues allowed the identification of four quadriceps muscle genes (Actb, Gapdh, Ppia and Srp72) that were found to significantly correlate with PMI. These results allowed us to develop a mathematical model with predictive value for estimation of the PMI (confidence interval of ±51 minutes at 95%) that can become an important complementary tool for traditional methods.
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Affiliation(s)
- Fernanda Sampaio-Silva
- Institute for Molecular and Cell Biology - IBMC, University of Porto, Porto, Portugal
- Department of Sciences, Advanced Institute of Health Sciences North, CESPU, CRL, Gandra, Portugal
| | - Teresa Magalhães
- Department of Legal Medicine and Forensic Sciences, Faculty of Medicine, University of Porto, Porto, Portugal
- Center of Forensic Sciences (CENCIFOR), Portugal
- National Institute of Legal Medicine and Forensic Sciences, North Branch, Porto, Portugal
- Biomedical Sciences Institute “Abel Salazar”, University of Porto, Porto, Portugal
| | - Félix Carvalho
- REQUIMTE, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Ricardo Jorge Dinis-Oliveira
- Department of Sciences, Advanced Institute of Health Sciences North, CESPU, CRL, Gandra, Portugal
- Department of Legal Medicine and Forensic Sciences, Faculty of Medicine, University of Porto, Porto, Portugal
- Center of Forensic Sciences (CENCIFOR), Portugal
- REQUIMTE, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Department of Diagnostic and Therapeutic Technologies, Polytechnic Health Institute North, CESPU, CRL, Vila Nova de Famalicão, Portugal
| | - Ricardo Silvestre
- Institute for Molecular and Cell Biology - IBMC, University of Porto, Porto, Portugal
- Department of Sciences, Advanced Institute of Health Sciences North, CESPU, CRL, Gandra, Portugal
- * E-mail:
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Abstract
The elucidation of epigenetic alterations in the autism brain has potential to provide new insights into the molecular mechanisms underlying abnormal gene expression in this disorder. Given strong evidence that engrailed-2 (EN-2) is a developmentally expressed gene relevant to cerebellar abnormalities and autism, the epigenetic evaluation of this candidate gene was undertaken in 26 case and control post-mortem cerebellar samples. Assessments included global DNA methylation, EN-2 promoter methylation, EN-2 gene expression and EN-2 protein levels. Chromatin immunoprecipitation was used to evaluate trimethylation status of histone H3 lysine 27 (H3K27) associated with gene downregulation and histone H3 lysine 4 (H3K4) associated with gene activation. The results revealed an unusual pattern of global and EN-2 promoter region DNA hypermethylation accompanied by significant increases in EN-2 gene expression and protein levels. Consistent with EN-2 overexpression, histone H3K27 trimethylation mark in the EN-2 promoter was significantly decreased in the autism samples relative to matched controls. Supporting a link between reduced histone H3K27 trimethylation and increased EN-2 gene expression, the mean level of histone H3K4 trimethylation was elevated in the autism cerebellar samples. Together, these results suggest that the normal EN-2 downregulation that signals Purkinje cell maturation during late prenatal and early-postnatal development may not have occurred in some individuals with autism and that the postnatal persistence of EN-2 overexpression may contribute to autism cerebellar abnormalities.
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Validation study of endogenous reference genes for normalization of quantitative real time PCR data in post mortem skin tissue. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2013. [DOI: 10.1016/j.fsigss.2013.10.081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Zhang H, Zhang P, Ma KJ, Lv YH, Li WC, Luo CL, Li LL, Shen YW, He M, Jiang JQ, Chen L. The selection of endogenous genes in human postmortem tissues. Sci Justice 2012; 53:115-20. [PMID: 23601718 DOI: 10.1016/j.scijus.2012.11.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 10/27/2012] [Accepted: 11/19/2012] [Indexed: 11/17/2022]
Abstract
Precisely determining the postmortem interval (PMI), which is crucial to criminal and forensic cases, is a research in which quantitative RT-PCR (also known as qRT-PCR or real-time RT-PCR) has been used to analyse gene expression levels and data normalisation should be required to eliminate the differences among the samples. Therefore, it is quite necessary to find stable molecular biological markers in PMI determination research. In this study, we compared nine commonly used endogenous markers (containing ACTB, GAPDH, B2M, U6, 18S rRNA, hsa-mir-1, hsa-mir-9, hsa-mir-194-1 and hsa-mir-203) in the 109 human tissue samples obtained from autopsy at the aim of finding stable markers in human tissues with consideration of the impact of parameters (PMI and cause of death). After RNA was extracted from four tissues (heart, brain, kidney, skin), the Ct values of nine endogenous markers were obtained by qRT-PCR and assessed by geNorm software. The results showed that U6, GAPDH and 18S rRNA were the suitable markers in our set of samples in various corpse conditions, that B2M and ACTB were reliable internal controls in heart tissue only, and that microRNAs had such high M values that they should not be chosen for endogenous control genes.
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Affiliation(s)
- Heng Zhang
- Forensic Department, Fudan University, Shanghai, China.
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