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Gao H, Yang S, Gao J, Zhang S, Qin L, Huang M, Wu H, Tang Q. An experimental study to estimate the early postmortem interval based on the degradation of lncRNAs in rat brain tissue. Sci Rep 2024; 14:19586. [PMID: 39179611 PMCID: PMC11343772 DOI: 10.1038/s41598-024-70678-y] [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: 05/31/2024] [Accepted: 08/20/2024] [Indexed: 08/26/2024] Open
Abstract
To study the degradation of lncRNAs in EPMI in rat brain tissue, this study provides a new direction for the estimation of EPMI. LncRNA high-throughput sequencing was performed on the brain tissues of hemorrhagic shock model rats at 0 h and 24 h, and the target lncRNAs were screened. Samples at 0, 1, 3, 6, 12, 18 and 24 h after death were collected, and miRNA-9 and miRNA-125b were used as reference genes. The relative expression levels of lncRNAs at each PMI were detected by RT-qPCR, and a functional model involving lncRNAs and EPMI was established. Samples were collected at 6, 9, 15, and 21 h after death for functional model verification. The expression of several lncRNAs decreased with the prolongation of EPMI, and the mathematical model established by several lncRNA indices exhibited good fit. The verification results of the multi-index joint function model are significantly better than those of the single-index function model, and the established model is more practical. There is a linear relationship between lncRNAs and EPMI, and the multi-index function model is significantly better than the single-index function model, which is important for EPMI inference in forensic pathology practice.
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Affiliation(s)
- Haibo Gao
- Hunan University of Chinese Medicine, Yuelu District, Changsha City, 410208, Hunan Province, China
| | - Siyu Yang
- Hunan University of Chinese Medicine, Yuelu District, Changsha City, 410208, Hunan Province, China
| | - Jie Gao
- Hunan University of Chinese Medicine, Yuelu District, Changsha City, 410208, Hunan Province, China
| | - Siqi Zhang
- Hunan University of Chinese Medicine, Yuelu District, Changsha City, 410208, Hunan Province, China
| | - Li Qin
- Hunan University of Chinese Medicine, Yuelu District, Changsha City, 410208, Hunan Province, China
| | - Meng Huang
- Hunan University of Chinese Medicine, Yuelu District, Changsha City, 410208, Hunan Province, China
| | - Hua Wu
- The Second People's Hospital of Hunan Province, Furong District, Changsha City, 410007, Hunan Province, China.
| | - Qun Tang
- Hunan University of Chinese Medicine, Yuelu District, Changsha City, 410208, Hunan Province, China.
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2
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Wenzlow N, Mills D, Byrd J, Warren M, Long MT. Review of the current and potential use of biological and molecular methods for the estimation of the postmortem interval in animals and humans. J Vet Diagn Invest 2023; 35:97-108. [PMID: 36744749 PMCID: PMC9999395 DOI: 10.1177/10406387231153930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
We provide here an overview of the state of applied techniques in the estimation of the early period of the postmortem interval (PMI). The biological methods included consist of body cooling, CSF potassium, body cooling combined with CSF potassium, and tissue autolysis. For each method, we present its application in human and veterinary medicine and provide current methodology, strengths, and weaknesses, as well as target areas for improvement. We examine current and future molecular methods as they pertain to DNA and primarily to messenger RNA degradation for the estimation of the PMI, as well as the use of RNA in aging wounds, aging blood stains, and the identification of body fluids. Various types of RNA have different lengths, structures, and functions in cells. These differences in RNAs determine various intrinsic properties, such as their half-lives in cells, and, hence, their decay rate as well as their unique use for specific forensic tests. Future applications and refinements of RNA-based techniques provide opportunities for the use of molecular methods in the estimation of PMI and other general forensic applications.
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Affiliation(s)
- Nanny Wenzlow
- Louisiana Animal Disease Diagnostic Laboratory, Louisiana State University, Baton Rouge, LA, USA
| | - DeEtta Mills
- Department of Biological Sciences and International Forensic Research Institute, Florida International University, Miami, FL, USA
| | - Jason Byrd
- Maples Center for Forensic Medicine, University of Florida, Gainesville, FL, USA
| | - Mike Warren
- Maples Center for Forensic Medicine, University of Florida, Gainesville, FL, USA
| | - Maureen T. Long
- Department of Comparative, Diagnostic, and Population Medicine, University of Florida, Gainesville, FL, USA
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3
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Peng M, Curry SM, Liu Y, Lohawala H, Sharma G, Sharma TP. The ex vivo human translaminar autonomous system to study spaceflight associated neuro-ocular syndrome pathogenesis. NPJ Microgravity 2022; 8:44. [PMID: 36307487 DOI: 10.1038/s41526-022-00232-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/12/2022] [Indexed: 11/10/2022] Open
Abstract
Spaceflight-Associated Neuro-ocular Syndrome (SANS) is a significant unexplained adverse reaction to long-duration spaceflight. We employ an ex vivo translaminar autonomous system (TAS) to recreate a human ocular ground-based spaceflight analogue model to study SANS pathogenesis. To recapitulate the human SANS conditions, human ocular posterior segments are cultured in the TAS model for 14 days. Translaminar pressure differentials are generated by simulating various flow rates within intracranial pressure (ICP) and intraocular (IOP) chambers to maintain hydrostatic pressures of ICP: IOP (12:16, 15:16, 12:21, 21:16 mmHg). In addition, optic nerves are mechanically kinked by 6- and 10-degree tilt inserts for the ICP: IOP;15:16 mmHg pressure paradigm. The TAS model successfully maintains various pressure differentials for all experimental groups over 14 days. Post culture, we determine inflammatory and extracellular component expression changes within posterior segments. To further characterize the SANS pathogenesis, axonal transport capacity, optic nerve degeneration and retinal functional are measured. Identifiable pathogenic alterations are observed in posterior segments by morphologic, apoptotic, and inflammatory changes including transport and functional deficits under various simulated SANS conditions. Here we report our TAS model provides a unique preclinical application system to mimic SANS pathology and a viable therapeutic testing device for countermeasures.
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Affiliation(s)
- Michael Peng
- Eugene and Marilyn Glick Eye Institute, Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Stacy M Curry
- North Texas Eye Research Institute, Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, TX, 76107, USA
| | - Yang Liu
- North Texas Eye Research Institute, Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, TX, 76107, USA
| | | | - Gaurav Sharma
- Software Engineer Consultant, Indianapolis, IN, 46074, USA
| | - Tasneem P Sharma
- Eugene and Marilyn Glick Eye Institute, Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA. .,Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA. .,Stark Neurosciences Research Institute, Indianapolis, IN, 46202, USA.
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4
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Common Ground between Biological Rhythms and Forensics. BIOLOGY 2022; 11:biology11071071. [PMID: 36101448 PMCID: PMC9312156 DOI: 10.3390/biology11071071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/12/2022] [Accepted: 07/14/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary Biological clocks regulate the timing of numerous body functions in adaption to daily repeating cycles in the environment, such as the sleep–wake phases that are trained by the cycling changes of night and day light. The identification of a deceased victim is a critical component in a forensic investigation, but it can be significantly hampered by the condition of the dead body and the lack of personal records and documents. This review links current knowledge on the molecular mechanisms of biological rhythms to forensically relevant aspects, including the time period since death, cause of death, the use of insects for forensics, sex and age of a person, ethnic background and development. Putting these findings in context demonstrates how the analysis of molecular clock analysis could be used as tool for future personal identification in forensic investigations. Abstract Biological clocks set the timing for a large number of essential processes in the living human organism. After death, scientific evidence is required in forensic investigations in order to collect as much information as possible on the death circumstances and personal identifiers of the deceased victim. We summarize the associations between the molecular mechanisms of biological rhythms and forensically relevant aspects, including post-mortem interval and cause of death, entomological findings, sex, age, ethnicity and development. Given their importance during lifetime, biological rhythms could be potential tools to draw conclusions on the death circumstances and the identity of a deceased person by mechanistic investigations of the different biological clocks in a forensic context. This review puts the known effects of biological rhythms on the functions of the human organism in context with potential applications in forensic fields of interest, such as personal identification, entomology as well as the determination of the post-mortem interval and cause of death.
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5
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Haas C, Neubauer J, Salzmann AP, Hanson E, Ballantyne J. Forensic transcriptome analysis using massively parallel sequencing. Forensic Sci Int Genet 2021; 52:102486. [PMID: 33657509 DOI: 10.1016/j.fsigen.2021.102486] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 02/11/2021] [Accepted: 02/12/2021] [Indexed: 12/15/2022]
Abstract
The application of transcriptome analyses in forensic genetics has experienced tremendous growth and development in the past decade. The earliest studies and main applications were body fluid and tissue identification, using targeted RNA transcripts and a reverse transcription endpoint PCR method. A number of markers have been identified for the forensically most relevant body fluids and tissues and the method has been successfully used in casework. The introduction of Massively Parallel Sequencing (MPS) opened up new perspectives and opportunities to advance the field. Contrary to genomic DNA where two copies of an autosomal DNA segment are present in a cell, abundant RNA species are expressed in high copy numbers. Even whole transcriptome sequencing (RNA-Seq) of forensically relevant body fluids and of postmortem material was shown to be possible. This review gives an overview on forensic transcriptome analyses and applications. The methods cover whole transcriptome as well as targeted MPS approaches. High resolution forensic transcriptome analyses using MPS are being applied to body fluid/ tissue identification, determination of the age of stains and the age of the donor, the estimation of the post-mortem interval and to post mortem death investigations.
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Affiliation(s)
- Cordula Haas
- University of Zurich, Zurich Institute of Forensic Medicine, Forensic Genetics, Winterthurerstrasse 190/52, CH-8057 Zurich, Switzerland.
| | - Jacqueline Neubauer
- University of Zurich, Zurich Institute of Forensic Medicine, Forensic Genetics, Winterthurerstrasse 190/52, CH-8057 Zurich, Switzerland
| | - Andrea Patrizia Salzmann
- University of Zurich, Zurich Institute of Forensic Medicine, Forensic Genetics, Winterthurerstrasse 190/52, CH-8057 Zurich, Switzerland
| | - Erin Hanson
- National Center for Forensic Science, University of Central Florida, 12354 Research Parkway, Suite 225, Orlando, FL 32826, USA
| | - Jack Ballantyne
- National Center for Forensic Science, University of Central Florida, 12354 Research Parkway, Suite 225, Orlando, FL 32826, USA; Department of Chemistry, National Center for Forensic Science, University of Central Florida, 12354 Research Parkway, Suite 225, Orlando, FL 32826, USA
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6
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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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7
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Heng Y, Dubbelaar ML, Marie SKN, Boddeke EWGM, Eggen BJL. The effects of postmortem delay on mouse and human microglia gene expression. Glia 2020; 69:1053-1060. [PMID: 33296111 PMCID: PMC7898322 DOI: 10.1002/glia.23948] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 11/26/2020] [Accepted: 11/30/2020] [Indexed: 12/12/2022]
Abstract
Microglia are specialized macrophages of the central nervous system (CNS) and first to react to pathogens or injury. Over the last decade, transcriptional profiling of microglia significantly contributed to our understanding of their functions. In the case of human CNS samples, either potential CNS pathology in the case of surgery samples, or a postmortem delay (PMD) due to the time needed for tissue access and collection, are potential factors that affect gene expression profiles. To determine the effect of PMD on the microglia transcriptome, we first analyzed mouse microglia, where genotype, antemortem conditions and PMD can be controlled. Microglia were isolated from mice after different PMDs (0, 4, 6, 12, and 24 hr) using fluorescence‐activated cell sorting (FACS). The number of viable microglia significantly decreased with increasing PMD, but even after a 12 hr PMD, high‐quality RNA could be obtained. PMD had very limited effect on mouse microglia gene expression, only 50 genes were differentially expressed between different PMDs. These genes were related to mitochondrial, ribosomal, and protein binding functions. In human microglia transcriptomes we previously generated, 31 of the 50 PMD‐associated mouse genes had human homologs, and their relative expression was also affected by PMD. This study provides a set of genes that shows relative expression changes in relation to PMD, both in mouse and human microglia. Although the gene expression changes detected are subtle, these genes need to be accounted for when analyzing microglia transcriptomes generated from samples with variable PMDs.
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Affiliation(s)
- Yang Heng
- Department of Biomedical Sciences of Cells & Systems, Section Molecular Neurobiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Marissa L Dubbelaar
- Department of Biomedical Sciences of Cells & Systems, Section Molecular Neurobiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Suely K N Marie
- Laboratory of Molecular and Cellular Biology (LIM 15), Department of Neurology, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Erik W G M Boddeke
- Department of Biomedical Sciences of Cells & Systems, Section Molecular Neurobiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Center for Healthy Ageing, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Bart J L Eggen
- Department of Biomedical Sciences of Cells & Systems, Section Molecular Neurobiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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8
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Jensen PSH, Johansen M, Bak LK, Jensen LJ, Kjær C. Yield and Integrity of RNA from Brain Samples are Largely Unaffected by Pre-analytical Procedures. Neurochem Res 2020; 46:447-454. [PMID: 33249516 DOI: 10.1007/s11064-020-03183-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/13/2020] [Accepted: 11/17/2020] [Indexed: 11/28/2022]
Abstract
Gene expression studies are reported to be influenced by pre-analytical factors that can compromise RNA yield and integrity, which in turn may confound the experimental findings. Here we investigate the impact of four pre-analytical factors on brain-derived RNA: time-before-collection, tissue specimen size, tissue collection method, and RNA isolation method. We report no significant differences in RNA yield or integrity between 20 mg and 60 mg tissue samples collected in either liquid nitrogen or the RNAlater stabilizing solution. Isolation of RNA employing the TRIzol reagent resulted in a higher yield compared to isolation via the QIAcube kit while the latter resulted in RNA of slightly better integrity. Keeping brain tissue samples at room temperature for up to 160 min prior to collection and isolation of RNA resulted in no significant difference in yield or integrity. Our findings have significant practical and financial consequences for clinical genomic departments and other laboratory settings performing large-scale routine RNA expression analysis of brain samples.
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Affiliation(s)
- Pernille Søs Hovgaard Jensen
- Department of Technology, Faculty of Health and Technology, University College Copenhagen, 2200, Copenhagen, Denmark
| | - Maja Johansen
- Department of Technology, Faculty of Health and Technology, University College Copenhagen, 2200, Copenhagen, Denmark
| | - Lasse K Bak
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Lars Juhl Jensen
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Christina Kjær
- Department of Technology, Faculty of Health and Technology, University College Copenhagen, 2200, Copenhagen, Denmark. .,Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark.
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9
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Fattorini P, Bonin S, Marrubini G, Bertoglio B, Grignani P, Recchia E, Pitacco P, Zupanič Pajnič I, Sorçaburu-Ciglieri S, Previderè C. Highly degraded RNA can still provide molecular information: An in vitro approach. Electrophoresis 2020; 41:386-393. [PMID: 31967656 DOI: 10.1002/elps.201900200] [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: 06/01/2019] [Revised: 01/13/2020] [Accepted: 01/15/2020] [Indexed: 01/01/2023]
Abstract
The long-term survival of RNA in postmortem tissues is a tricky topic. Many aged/forensic specimens show, in fact, high rates of null/inconclusive PCR-based results, while reliable outcomes were sometimes achieved from archaeological samples. On the other hand, several data show that the RNA is a molecule that survives even to several physical-chemical stresses. In the present study, a simple protocol, which was already developed for the prolonged hydrolysis of DNA, was applied to a RNA sample extracted from blood. This protocol is based on the heat-mediated (70°C) hydrolysis for up to 36 h using ultrapure water and di-ethyl-pyro-carbonate-water as hydrolysis medium. Measurable levels of depurination were not found even if microfluidic devices showed a progressive pattern of degradation. The reverse transcription/quantitative PCR analysis of two (60 bp long) housekeeping targets (glyceraldehyde-3-phosphate dehydrogenase and porphobilinogen deaminase) showed that the percentage of amplifiable target (%AT) decreased in relation to the duration of the damaging treatment (r2 > 0.973). The comparison of the %AT in the degraded RNA and in the DNA samples that underwent the same damaging treatment showed that the %AT is always higher in RNA, reaching up to three orders of magnitude. Lastly, even the end-point PCR of blood-specific markers gave reliable results, which is in agreement with the body fluid origin of the sample. In conclusion, all the PCR-based results show that RNA maintains the ability to be retro-transcribed in short cDNA fragments even after 36 h of incubation at 70°C in mildly acidic buffers. It is therefore likely that the long-term survival of RNA samples depends mainly on the protection against RNAase attacks rather than on environmental factors (such as humidity and acidity) that are instead of great importance for the stability of DNA. As a final remark, our results suggest that the RNA analysis can be successfully performed even when DNA profiling failed.
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Affiliation(s)
- Paolo Fattorini
- Department of Medicine, Surgery and Health, University of Trieste, Trieste, Italy
| | - Serena Bonin
- Department of Medicine, Surgery and Health, University of Trieste, Trieste, Italy
| | | | - Barbara Bertoglio
- Department of Public Health, Experimental and Forensic Medicine, Section of Legal Medicine and Forensic Sciences, University of Pavia, Pavia, Italy
| | - Pierangela Grignani
- Department of Public Health, Experimental and Forensic Medicine, Section of Legal Medicine and Forensic Sciences, University of Pavia, Pavia, Italy
| | - Elisa Recchia
- Department of Medicine, Surgery and Health, University of Trieste, Trieste, Italy
| | - Paola Pitacco
- Department of Medicine, Surgery and Health, University of Trieste, Trieste, Italy
| | - Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | | | - Carlo Previderè
- Department of Public Health, Experimental and Forensic Medicine, Section of Legal Medicine and Forensic Sciences, University of Pavia, Pavia, Italy
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10
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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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11
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Peng D, Lv M, Li Z, Tian H, Qu S, Jin B, Long B, Liang W, Zhang L. Postmortem interval determination using mRNA markers and DNA normalization. Int J Legal Med 2020; 134:149-157. [PMID: 31773316 DOI: 10.1007/s00414-019-02199-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 10/25/2019] [Indexed: 02/07/2023]
Abstract
Postmortem interval (PMI) determination is an important part of criminal investigations, but it is still subject to uncertainty. Degradation of mRNA in PMI determination has been studied in decays; however, some studies have reported no correlation between PMI and RNA degradation. Thus, we aimed to determine whether RNA quantity was correlated with PMI. Heart and brain tissues were separated from a mouse model of a 0-48 h PMI with 29 time points. We then coextracted the DNA and RNA in one tube with Bioteke coextraction kits and selected some mRNA markers associated with cell oxygen deprivation and apoptosis as target genes, such as hypoxia-associated factor (HAF), apoptosis-inducing factor (AIF), hypoxia-inducible factor 2 alpha (HIF2a), and factor inhibiting HIF (FIH). We measured the quantity of these markers using real-time quantitative PCR (qPCR), and Caspase-3 DNA and 18S were each used for normalization. The results showed that in the heart tissue, the degradation of HIF2a, AIF, and FIH was correlated with PMI, as was the degradation of HIF2a, FIH, and AIF in brain tissue when normalized with Caspase-3 DNA. However, when normalized with 18S, only the degradation of HIF2a in brain tissue was correlated with PMI. Interestingly, the quantity of HAF in brain tissue was found to increase after death with either 18S or Caspase-3 DNA normalization, and it was significantly correlated with 0-48 h PMI. These results indicated that mRNA quantity can be used to determine PMI and that Caspase-3 DNA is feasible for PMI estimation. In summary, we established mathematical models for PMI determination using multiple mRNA markers and multiple tissues and further studies are needed to validate and investigate these markers and mathematical models in human tissues.Duo Peng and Meili Lv contributed equally to this work.
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Affiliation(s)
- Duo Peng
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Meili Lv
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Zhilong Li
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Huan Tian
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan, China
| | - ShengQiu Qu
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Bo Jin
- Department of Forensic Medicine, North Sichuan Medical College, Nanchong, 637000, Sichuan, China
| | - Bing Long
- Sichuan Police College, Luzhou, 646000, Sichuan, China
| | - Weibo Liang
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - Lin Zhang
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan, China.
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12
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Halawa AA, El-Adl MA, Marghani BH. Postmortem Heat Stress upregulates Thanatotranscriptome of Genes encode Inflammation, Apoptosis and Neuronal Stress in Brain of Rats at Short Postmortem Intervals. AUST J FORENSIC SCI 2019. [DOI: 10.1080/00450618.2019.1682669] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Amal A. Halawa
- Department of Forensic Medicine and Toxicology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
| | - Mohamed A. El-Adl
- Department of Biochemistry, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
| | - Basma H. Marghani
- Department of Physiology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
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13
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Kallestad L, Blackshaw S, Khalil AM, Palczewski K. Tissue- and Species-Specific Patterns of RNA metabolism in Post-Mortem Mammalian Retina and Retinal Pigment Epithelium. Sci Rep 2019; 9:14821. [PMID: 31616038 PMCID: PMC6794289 DOI: 10.1038/s41598-019-51379-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 09/29/2019] [Indexed: 12/13/2022] Open
Abstract
Accurate analysis of gene expression in human tissues using RNA sequencing is dependent on the quality of source material. One major source of variation in mRNA quality is post-mortem time. While it is known that individual transcripts show differential post-mortem stability, few studies have directly and comprehensively analyzed mRNA stability following death, and in particular the extent to which tissue- and species-specific factors influence post-mortem mRNA stability are poorly understood. This knowledge is particularly important for ocular tissues studies, where tissues obtained post-mortem are frequently used for research or therapeutic applications. To directly investigate this question, we profiled mRNA levels in both neuroretina and retinal pigment epithelium (RPE) from mouse and baboon over a series of post-mortem intervals. We found substantial changes in gene expression as early as 15 minutes in the mouse and as early as three hours in the baboon eye tissues. Importantly, our findings demonstrate both tissue- and species- specific patterns of RNA metabolism, by identifying a set of genes that are either rapidly degraded or very stable in both species and/or tissues. Taken together, the data from this study lay the foundation for understanding RNA regulation post-mortem and provide novel insights into RNA metabolism in the tissues of the mammalian eye.
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Affiliation(s)
- Les Kallestad
- Gavin Herbert Eye Institute and the Department of Ophthalmology, University of California-Irvine, Irvine, CA, 92657, USA.
| | - Seth Blackshaw
- Department of Neuroscience, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Ahmad M Khalil
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Krzysztof Palczewski
- Gavin Herbert Eye Institute and the Department of Ophthalmology, University of California-Irvine, Irvine, CA, 92657, USA.
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14
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Amadoz A, Hidalgo MR, Çubuk C, Carbonell-Caballero J, Dopazo J. A comparison of mechanistic signaling pathway activity analysis methods. Brief Bioinform 2019; 20:1655-1668. [PMID: 29868818 PMCID: PMC6917216 DOI: 10.1093/bib/bby040] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 03/31/2018] [Indexed: 12/11/2022] Open
Abstract
Understanding the aspects of cell functionality that account for disease mechanisms or drug modes of action is a main challenge for precision medicine. Classical gene-based approaches ignore the modular nature of most human traits, whereas conventional pathway enrichment approaches produce only illustrative results of limited practical utility. Recently, a family of new methods has emerged that change the focus from the whole pathways to the definition of elementary subpathways within them that have any mechanistic significance and to the study of their activities. Thus, mechanistic pathway activity (MPA) methods constitute a new paradigm that allows recoding poorly informative genomic measurements into cell activity quantitative values and relate them to phenotypes. Here we provide a review on the MPA methods available and explain their contribution to systems medicine approaches for addressing challenges in the diagnostic and treatment of complex diseases.
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Affiliation(s)
- Alicia Amadoz
- Department of Bioinformatics, Igenomix S.L., 46980 Valencia, Spain
| | - Marta R Hidalgo
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), CDCA, Hospital Virgen del Rocio, Sevilla 41013, Spain
| | - Cankut Çubuk
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), CDCA, Hospital Virgen del Rocio, Sevilla 41013, Spain
| | - José Carbonell-Caballero
- Chromatin and Gene expression Lab, Gene Regulation, Stem Cells and Cancer Program, Centre de Regulació Genòmica (CRG), The Barcelona Institute of Science and Technology, PRBB, Barcelona 08003, Spain
| | - Joaquín Dopazo
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), CDCA, Hospital Virgen del Rocio, Sevilla 41013, Spain
- Chromatin and Gene expression Lab, Gene Regulation, Stem Cells and Cancer Program, Centre de Regulació Genòmica (CRG), The Barcelona Institute of Science and Technology, PRBB, Barcelona 08003, Spain
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), CDCA, Hospital Virgen del Rocio, Sevilla 41013, Spain, Functional Genomics Node (INB), FPS, Hospital Virgen del Rocío, Sevilla 41013, Spain and Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocío, Sevilla 41013, Spain
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15
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Lee SY, Ha EJ, Cho HW, Kim HR, Lee D, Eom YB. Potential forensic application of receptor for advanced glycation end products (RAGE) and aquaporin 5 (AQP5) as novel biomarkers for diagnosis of drowning. J Forensic Leg Med 2019; 62:56-62. [PMID: 30677703 DOI: 10.1016/j.jflm.2019.01.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 10/15/2018] [Accepted: 01/11/2019] [Indexed: 02/08/2023]
Abstract
Drowning is the most common cause of unnatural death worldwide. There is no single biomarker to diagnose drowning, so the diagnosis of drowning is one of the most difficult tasks in forensic medicine. Especially, distinguishing a victim of drowning from a body disposed of in water following death remains a problem. The objective of this study was to identify specific biomarkers of drowning compared with other causes of death such as hypoxia and postmortem submersion. The present study investigated the intrapulmonary expression of receptor for advanced glycation end products (RAGE), aquaporin-5 (AQP5), surfactant protein-A (SP-A), interleukin 6 (IL-6) and interleukin 1β (IL-1β) as markers of drowning. In animal experiments, all rats (n = 45) were classified into four groups (drowning, postmortem-submersion, hypoxia and control group). The lungs of experimental animals were analyzed as mRNA expression, immunoblot expression and immunohistochemical staining. qRT-PCR demonstrated increased mRNA expression of RAGE and AQP5 in drowning group compared with that in control, hypoxia and postmortem-submersion group, but not other molecules. Western blotting also showed high expression of RAGE and AQP5 in drowning group, immunostaining of RAGE and AQP5 was highly detected in a linear pattern in type I alveolar epithelial cells, compared with control and postmortem-submersion group. These observations indicate a difference of expression in pulmonary molecular pathology compared with other causes, suggesting RAGE and AQP5 may be useful for differentiation between drowning and postmortem-submersion.
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Affiliation(s)
- So-Yeon Lee
- Department of Medical Science, College of Medical Sciences, Soonchunhyang University, Asan, Chungnam, 31538, Republic of Korea.
| | - Eun-Ju Ha
- Department of Biomedical Laboratory Science, College of Medical Sciences, Soonchunhyang University, Asan, Chungnam, 31538, Republic of Korea.
| | - Hye-Won Cho
- Department of Biomedical Laboratory Science, College of Medical Sciences, Soonchunhyang University, Asan, Chungnam, 31538, Republic of Korea.
| | - Hye-Rim Kim
- Department of Biomedical Laboratory Science, College of Medical Sciences, Soonchunhyang University, Asan, Chungnam, 31538, Republic of Korea.
| | - Dongsup Lee
- Department of Clinical Laboratory Science, Hyejeon College, Hongseoung, Chungnam, 32244, Republic of Korea.
| | - Yong-Bin Eom
- Department of Medical Science, College of Medical Sciences, Soonchunhyang University, Asan, Chungnam, 31538, Republic of Korea; Department of Biomedical Laboratory Science, College of Medical Sciences, Soonchunhyang University, Asan, Chungnam, 31538, Republic of Korea.
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16
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Rovito R, Warnatz HJ, Kiełbasa SM, Mei H, Amstislavskiy V, Arens R, Yaspo ML, Lehrach H, Kroes ACM, Goeman JJ, Vossen ACTM. Impact of congenital cytomegalovirus infection on transcriptomes from archived dried blood spots in relation to long-term clinical outcome. PLoS One 2018; 13:e0200652. [PMID: 30024899 PMCID: PMC6053152 DOI: 10.1371/journal.pone.0200652] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 06/30/2018] [Indexed: 01/16/2023] Open
Abstract
Congenital Cytomegalovirus infection (cCMV) is the leading infection in determining permanent long-term impairments (LTI), and its pathogenesis is largely unknown due to the complex interplay between viral, maternal, placental, and child factors. The cellular activity, considered to be the result of the response to exogenous and endogenous factors, is captured by the determination of gene expression profiles. In this study, we determined whole blood transcriptomes in relation to cCMV, CMV viral load and LTI development at 6 years of age by using RNA isolated from neonatal dried blood spots (DBS) stored at room temperature for 8 years. As DBS were assumed to mainly reflect the neonatal immune system, particular attention was given to the immune pathways using the global test. Additionally, differential expression of individual genes was performed using the voom/limma function packages. We demonstrated feasibility of RNA sequencing from archived neonatal DBS of children with cCMV, and non-infected controls, in relation to LTI and CMV viral load. Despite the lack of statistical power to detect individual genes differences, pathway analysis suggested the involvement of innate immune response with higher CMV viral loads, and of anti-inflammatory markers in infected children that did not develop LTI. Finally, the T cell exhaustion observed in infected neonates, in particular with higher viral load, did not correlate with LTI, therefore other mechanisms are likely to be involved in the long-term immune dysfunction. Despite these data demonstrate limitation in determining prognostic markers for LTI by means of transcriptome analysis, this exploratory study represents a first step in unraveling the pathogenesis of cCMV, and the aforementioned pathways certainly merit further evaluation.
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Affiliation(s)
- Roberta Rovito
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
- * E-mail:
| | - Hans-Jörg Warnatz
- Otto Warburg Laboratory Gene Regulation and Systems Biology of Cancer, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Szymon M. Kiełbasa
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Hailiang Mei
- Sequencing Analysis Support Core, Leiden University Medical Center, Leiden, The Netherlands
| | - Vyacheslav Amstislavskiy
- Otto Warburg Laboratory Gene Regulation and Systems Biology of Cancer, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Ramon Arens
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Marie-Laure Yaspo
- Otto Warburg Laboratory Gene Regulation and Systems Biology of Cancer, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | - Aloys C. M. Kroes
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jelle J. Goeman
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Ann C. T. M. Vossen
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
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17
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The thanatotranscriptome: Gene expression of male reproductive organs after death. Gene 2018; 675:191-196. [PMID: 30180965 DOI: 10.1016/j.gene.2018.06.090] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 06/25/2018] [Accepted: 06/26/2018] [Indexed: 11/23/2022]
Abstract
The prostate gland is one of the last internal organs to deteriorate during human decomposition; however, this phenomenon is still mysterious. Gene expression in antemortem cases has been widely studied and a majority of the analyses concentrate on discovering basic physiological processes. The question of "What happens to gene expression after a human dies?" is a novel and emerging topic. Thanatotranscriptome (thanatos-, Greek for death) involves research on mRNA transcript abundances and gene expression in human tissues after death. Our previous studies have shown that RNA is a suitable and stable molecule in postmortem liver samples up to two days. Consequently, we hypothesized that there are also measurable and significant differences in mRNA transcript abundances in prostate tissues from human remains. In the current study, the goal was to identify apoptotic molecular markers (i.e., pro- and/or anti-apoptosis genes) that provide accurate gene expression profiles regarding the time of death. Tissue samples were removed by a medical examiner from the prostate of five cadavers during autopsy. After RNA extraction, cDNA was synthesized and the concentration was determined. The cDNA was reacted in apoptosis-related gene expression profiling by human PCR Array. The PCR Array results showed that at 38 h after death, a majority of the genes for apoptosis induction and positive regulation (i.e., caspases) were over-expressed more than at five days. The expression of anti-apoptotic genes such as BAG1, BCL2, and negative regulator of apoptosis, XIAP, was significantly elevated in a time-dependent manner. However, pro-apoptotic gene expression such as TP53 and TNFSF10 was not significantly upregulated. Therefore, postmortem prostate cells counteract programmed cell death with its anti-apoptotic machinery; yet as time progresses, pro-apoptotic mechanisms dominate. In conclusion, our study implies that over-expression of genes in male reproductive organs still occurs during decomposition, which may play substantial roles in forensic research and clinical application. These findings demonstrate that there is still active postmortem gene expression; however, our future research question will be, "When does gene expression terminate after death?"
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18
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White K, Yang P, Li L, Farshori A, Medina AE, Zielke HR. Effect of Postmortem Interval and Years in Storage on RNA Quality of Tissue at a Repository of the NIH NeuroBioBank. Biopreserv Biobank 2018; 16:148-157. [PMID: 29498539 PMCID: PMC5906728 DOI: 10.1089/bio.2017.0099] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Brain tissue from 1068 donors was analyzed for RNA quality as a function of postmortem interval (PMI) and years in storage. Approximately 83% of the cortical and cerebellar samples had an RNA integrity number (RIN) of 6 or greater, indicating their likely suitability for real-time quantitative polymerase chain reaction research. The average RIN value was independent of the PMI, up to at least 36 hours. The RNA quality for specific donated brains could not be predicted based on the PMI. Individual samples with a low PMI could have a poor RIN value, while a sample with a PMI over 36 hours may have a high RIN value. The RIN values for control brain donors, all of whom died suddenly and unexpectedly, were marginally higher than for individuals with clinical brain disorders. Polymerase chain reaction (PCR) analysis of samples confirmed that RIN values were more critical than PMI for determining suitability of tissue for molecular biological studies and samples should be matched by their RIN values rather than PMI. Importantly, PCR analysis established that tissue stored up to 23 years at −80°C yielded high-quality RNA. These results confirm that postmortem human brain tissue collected by brain and tissue banks over decades can serve as high quality material for the study of human disorders.
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Affiliation(s)
- Kimberly White
- 1 Department of Pediatrics, University of Maryland School of Medicine , Baltimore, Maryland
| | - Peixin Yang
- 2 Department of Obstetrics and Gynecology, University of Maryland School of Medicine , Baltimore, Maryland
| | - Ling Li
- 1 Department of Pediatrics, University of Maryland School of Medicine , Baltimore, Maryland.,3 Office of the Chief Medical Examiner, Baltimore, Maryland
| | - Amna Farshori
- 4 Degree Program in Osteopathic Medicine, Edward Via College of Osteopathic Medicine , Blacksburg, Virginia
| | - Alexandre E Medina
- 1 Department of Pediatrics, University of Maryland School of Medicine , Baltimore, Maryland
| | - Horst Ronald Zielke
- 1 Department of Pediatrics, University of Maryland School of Medicine , Baltimore, Maryland
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19
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Ferreira PG, Muñoz-Aguirre M, Reverter F, Sá Godinho CP, Sousa A, Amadoz A, Sodaei R, Hidalgo MR, Pervouchine D, Carbonell-Caballero J, Nurtdinov R, Breschi A, Amador R, Oliveira P, Çubuk C, Curado J, Aguet F, Oliveira C, Dopazo J, Sammeth M, Ardlie KG, Guigó R. The effects of death and post-mortem cold ischemia on human tissue transcriptomes. Nat Commun 2018; 9:490. [PMID: 29440659 PMCID: PMC5811508 DOI: 10.1038/s41467-017-02772-x] [Citation(s) in RCA: 156] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Accepted: 12/22/2017] [Indexed: 12/05/2022] Open
Abstract
Post-mortem tissues samples are a key resource for investigating patterns of gene expression. However, the processes triggered by death and the post-mortem interval (PMI) can significantly alter physiologically normal RNA levels. We investigate the impact of PMI on gene expression using data from multiple tissues of post-mortem donors obtained from the GTEx project. We find that many genes change expression over relatively short PMIs in a tissue-specific manner, but this potentially confounding effect in a biological analysis can be minimized by taking into account appropriate covariates. By comparing ante- and post-mortem blood samples, we identify the cascade of transcriptional events triggered by death of the organism. These events do not appear to simply reflect stochastic variation resulting from mRNA degradation, but active and ongoing regulation of transcription. Finally, we develop a model to predict the time since death from the analysis of the transcriptome of a few readily accessible tissues. RNA levels in post-mortem tissue can differ greatly from those before death. Studying the effect of post-mortem interval on the transcriptome in 36 human tissues, Ferreira et al. find that the response to death is largely tissue-specific and develop a model to predict time since death based on RNA data.
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Affiliation(s)
- Pedro G Ferreira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, Porto, 4200-135, Portugal. .,Institute of Molecular Pathology and Immunology, University of Porto, Rua Dr. Roberto Frias s/n, Porto, 4200-625, Portugal.
| | - Manuel Muñoz-Aguirre
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, E-08003, Catalonia, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, E-08003, Catalonia, Spain.,Institut Hospital del Mar d'Investigacions Mediques (IMIM), Barcelona, E-08003, Catalonia, Spain.,Departament d'Estadística i Investigació Operativa, Universitat Politècnica de Catalunya, Barcelona, E-08034, Catalonia, Spain
| | - Ferran Reverter
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, E-08003, Catalonia, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, E-08003, Catalonia, Spain.,Institut Hospital del Mar d'Investigacions Mediques (IMIM), Barcelona, E-08003, Catalonia, Spain.,Universitat de Barcelona, Barcelona, E-08028, Catalonia, Spain
| | - Caio P Sá Godinho
- Institute of Biophysics Carlos Chagas Filho (IBCCF), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, 21941-902, Brazil
| | - Abel Sousa
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, Porto, 4200-135, Portugal.,Institute of Molecular Pathology and Immunology, University of Porto, Rua Dr. Roberto Frias s/n, Porto, 4200-625, Portugal.,European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, CB10 1 SD, UK
| | - Alicia Amadoz
- Department of Bioinformatics, Igenomix S.A, Valencia, 46980, Spain
| | - Reza Sodaei
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, E-08003, Catalonia, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, E-08003, Catalonia, Spain.,Institut Hospital del Mar d'Investigacions Mediques (IMIM), Barcelona, E-08003, Catalonia, Spain
| | - Marta R Hidalgo
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocio, Sevilla, 41013, Spain
| | - Dmitri Pervouchine
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, E-08003, Catalonia, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, E-08003, Catalonia, Spain.,Institut Hospital del Mar d'Investigacions Mediques (IMIM), Barcelona, E-08003, Catalonia, Spain.,Skolkovo Institute of Science and Technology, 100 Novaya Street, Skolkovo, Moscow Region, 143025, Russia
| | - Jose Carbonell-Caballero
- Chromatin and Gene expression Lab, Gene Regulation, Stem Cells and Cancer Program, Centre de Regulació Genòmica (CRG), The Barcelona Institute of Science and Technology, PRBB, Barcelona, 08003, Spain
| | - Ramil Nurtdinov
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, E-08003, Catalonia, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, E-08003, Catalonia, Spain.,Institut Hospital del Mar d'Investigacions Mediques (IMIM), Barcelona, E-08003, Catalonia, Spain
| | - Alessandra Breschi
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, E-08003, Catalonia, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, E-08003, Catalonia, Spain.,Institut Hospital del Mar d'Investigacions Mediques (IMIM), Barcelona, E-08003, Catalonia, Spain
| | - Raziel Amador
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, E-08003, Catalonia, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, E-08003, Catalonia, Spain.,Institut Hospital del Mar d'Investigacions Mediques (IMIM), Barcelona, E-08003, Catalonia, Spain
| | - Patrícia Oliveira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, Porto, 4200-135, Portugal.,Institute of Molecular Pathology and Immunology, University of Porto, Rua Dr. Roberto Frias s/n, Porto, 4200-625, Portugal
| | - Cankut Çubuk
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocio, Sevilla, 41013, Spain
| | - João Curado
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, E-08003, Catalonia, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, E-08003, Catalonia, Spain.,Institut Hospital del Mar d'Investigacions Mediques (IMIM), Barcelona, E-08003, Catalonia, Spain
| | - François Aguet
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Carla Oliveira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, Porto, 4200-135, Portugal.,Institute of Molecular Pathology and Immunology, University of Porto, Rua Dr. Roberto Frias s/n, Porto, 4200-625, Portugal
| | - Joaquin Dopazo
- Department of Bioinformatics, Igenomix S.A, Valencia, 46980, Spain.,Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocio, Sevilla, 41013, Spain.,Functional Genomics Node (INB), FPS, Hospital Virgen del Rocio, Sevilla, 41013, Spain.,Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocio, Sevilla, 41013, Spain
| | - Michael Sammeth
- Institute of Biophysics Carlos Chagas Filho (IBCCF), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, 21941-902, Brazil
| | - Kristin G Ardlie
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, E-08003, Catalonia, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, E-08003, Catalonia, Spain. .,Institut Hospital del Mar d'Investigacions Mediques (IMIM), Barcelona, E-08003, Catalonia, Spain.
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20
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Elghamry HA, Mohamed MI, Hassan FM, Abdelfattah DS, Abdelaal AG. Potential use of GAPDH m-RNA in estimating PMI in brain tissue of albino rats at different environmental conditions. EGYPTIAN JOURNAL OF FORENSIC SCIENCES 2017. [DOI: 10.1186/s41935-017-0024-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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21
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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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22
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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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23
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Raddatz BB, Spitzbarth I, Matheis KA, Kalkuhl A, Deschl U, Baumgärtner W, Ulrich R. Microarray-Based Gene Expression Analysis for Veterinary Pathologists: A Review. Vet Pathol 2017. [PMID: 28641485 DOI: 10.1177/0300985817709887] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
High-throughput, genome-wide transcriptome analysis is now commonly used in all fields of life science research and is on the cusp of medical and veterinary diagnostic application. Transcriptomic methods such as microarrays and next-generation sequencing generate enormous amounts of data. The pathogenetic expertise acquired from understanding of general pathology provides veterinary pathologists with a profound background, which is essential in translating transcriptomic data into meaningful biological knowledge, thereby leading to a better understanding of underlying disease mechanisms. The scientific literature concerning high-throughput data-mining techniques usually addresses mathematicians or computer scientists as the target audience. In contrast, the present review provides the reader with a clear and systematic basis from a veterinary pathologist's perspective. Therefore, the aims are (1) to introduce the reader to the necessary methodological background; (2) to introduce the sequential steps commonly performed in a microarray analysis including quality control, annotation, normalization, selection of differentially expressed genes, clustering, gene ontology and pathway analysis, analysis of manually selected genes, and biomarker discovery; and (3) to provide references to publically available and user-friendly software suites. In summary, the data analysis methods presented within this review will enable veterinary pathologists to analyze high-throughput transcriptome data obtained from their own experiments, supplemental data that accompany scientific publications, or public repositories in order to obtain a more in-depth insight into underlying disease mechanisms.
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Affiliation(s)
- Barbara B Raddatz
- 1 Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany.,2 Center of Systems Neuroscience, Hannover, Germany
| | - Ingo Spitzbarth
- 1 Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany.,2 Center of Systems Neuroscience, Hannover, Germany
| | - Katja A Matheis
- 3 Department of Nonclinical Drug Safety, Boehringer Ingelheim Pharma GmbH & Co KG, Biberach (Riß), Germany
| | - Arno Kalkuhl
- 3 Department of Nonclinical Drug Safety, Boehringer Ingelheim Pharma GmbH & Co KG, Biberach (Riß), Germany
| | - Ulrich Deschl
- 3 Department of Nonclinical Drug Safety, Boehringer Ingelheim Pharma GmbH & Co KG, Biberach (Riß), Germany
| | - Wolfgang Baumgärtner
- 1 Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany.,2 Center of Systems Neuroscience, Hannover, Germany
| | - Reiner Ulrich
- 1 Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany.,2 Center of Systems Neuroscience, Hannover, Germany.,4 Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institute, Greifswald, Germany
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24
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Pozhitkov AE, Neme R, Domazet-Lošo T, Leroux BG, Soni S, Tautz D, Noble PA. Tracing the dynamics of gene transcripts after organismal death. Open Biol 2017; 7:160267. [PMID: 28123054 PMCID: PMC5303275 DOI: 10.1098/rsob.160267] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Accepted: 12/12/2016] [Indexed: 12/13/2022] Open
Abstract
In life, genetic and epigenetic networks precisely coordinate the expression of genes-but in death, it is not known if gene expression diminishes gradually or abruptly stops or if specific genes and pathways are involved. We studied this by identifying mRNA transcripts that apparently increase in relative abundance after death, assessing their functions, and comparing their abundance profiles through postmortem time in two species, mouse and zebrafish. We found mRNA transcript profiles of 1063 genes became significantly more abundant after death of healthy adult animals in a time series spanning up to 96 h postmortem. Ordination plots revealed non-random patterns in the profiles by time. While most of these transcript levels increased within 0.5 h postmortem, some increased only at 24 and 48 h postmortem. Functional characterization of the most abundant transcripts revealed the following categories: stress, immunity, inflammation, apoptosis, transport, development, epigenetic regulation and cancer. The data suggest a step-wise shutdown occurs in organismal death that is manifested by the apparent increase of certain transcripts with various abundance maxima and durations.
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Affiliation(s)
- Alex E Pozhitkov
- Department of Oral Health Sciences, University of Washington, PO Box 357444, Seattle, WA 98195, USA
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Strasse 2, 24306 Ploen, Germany
| | - Rafik Neme
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Strasse 2, 24306 Ploen, Germany
| | - Tomislav Domazet-Lošo
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, 10002 Zagreb, Croatia
- Catholic University of Croatia, Ilica 242, Zagreb, Croatia
| | - Brian G Leroux
- Department of Oral Health Sciences, University of Washington, PO Box 357444, Seattle, WA 98195, USA
| | - Shivani Soni
- Department of Biological Sciences, Alabama State University, Montgomery, AL 36101-0271, USA
| | - Diethard Tautz
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Strasse 2, 24306 Ploen, Germany
| | - Peter A Noble
- Department of Periodontics, University of Washington, PO Box 357444, Seattle, WA 98195, USA
- Department of Biological Sciences, Alabama State University, Montgomery, AL 36101-0271, USA
- PhD Program in Microbiology, Alabama State University, Montgomery, AL 36101-0271, USA
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25
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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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26
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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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27
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Differential expression and localization of Ankrd2 isoforms in human skeletal and cardiac muscles. Histochem Cell Biol 2016; 146:569-584. [PMID: 27393496 DOI: 10.1007/s00418-016-1465-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2016] [Indexed: 01/03/2023]
Abstract
Four human Ankrd2 transcripts, reported in the Ensembl database, code for distinct protein isoforms (360, 333, 327 and 300 aa), and so far, their existence, specific expression and localization patterns have not been studied in detail. Ankrd2 is preferentially expressed in the slow fibers of skeletal muscle. It is found in both the nuclei and the cytoplasm of skeletal muscle cells, and its localization is prone to change during differentiation and upon stress. Ankrd2 has also been detected in the heart, in ventricular cardiomyocytes and in the intercalated disks (ICDs). The main objective of this study was to distinguish between the Ankrd2 isoforms and to determine the contribution of each one to the general profile of Ankrd2 expression in striated muscles. We demonstrated that the known expression and localization pattern of Ankrd2 in striated muscle can be attributed to the isoform of 333 aa which is dominant in both tissues, while the designated cardiac and canonical isoform of 360 aa was less expressed in both tissues. The 360 aa isoform has a distinct nuclear localization in human skeletal muscle, as well as in primary myoblasts and myotubes. In contrast to the isoform of 333 aa, it was not preferentially expressed in slow fibers and not localized to the ICDs of human cardiomyocytes. Regulation of the expression of both isoforms is achieved at the transcriptional level. Our results set the stage for investigation of the specific functions and interactions of the Ankrd2 isoforms in healthy and diseased human striated muscles.
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28
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Walker DG, Whetzel AM, Serrano G, Sue LI, Lue LF, Beach TG. Characterization of RNA isolated from eighteen different human tissues: results from a rapid human autopsy program. Cell Tissue Bank 2016; 17:361-75. [PMID: 27083469 DOI: 10.1007/s10561-016-9555-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 04/07/2016] [Indexed: 11/25/2022]
Abstract
Many factors affect the integrity of messenger RNA from human autopsy tissues including postmortem interval (PMI) between death and tissue preservation and the pre-mortem agonal and disease states. In this communication, we describe RNA isolation and characterization of 389 samples from 18 different tissues from elderly donors who were participants in a rapid whole-body autopsy program located in Sun City, Arizona ( www.brainandbodydonationprogram.org ). Most tissues were collected within a PMI of 2-6 h (median 3.15 h; N = 455), but for this study, tissue from cases with longer PMIs (1.25-29.25 h) were included. RNA quality was assessed by RNA integrity number (RIN) and total yield (ng RNA/mg tissue). RIN correlated with PMI for heart (r = -0.531, p = 0.009) and liver (r = -558, p = 0.0017), while RNA yield correlated with PMI for colon (r = -485, p = 0.016) and skin (r = -0.460, p = 0.031). RNAs with the lowest integrity were from skin and cervix where 22.7 and 31.4 % of samples respectively failed to produce intact RNA; by contrast all samples from esophagus, lymph node, jejunum, lung, stomach, submandibular gland and kidney produced RNA with measurable RINs. Expression levels in heart RNA of 4 common housekeeping normalization genes showed significant correlations of Ct values with RIN, but only one gene, glyceraldehyde-3 phosphate dehydrogenase, showed a correlation of Ct with PMI. There were no correlations between RIN values obtained for liver, adrenal, cervix, esophagus and lymph node and those obtained from corresponding brain samples. We show that high quality RNA can be produced from most human autopsy tissues, though with significant differences between tissues and donors. The RNA stability and yield did not depend solely on PMI; other undetermined factors are involved, but these do not include the age of the donor.
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Affiliation(s)
- Douglas G Walker
- Banner Sun Health Research Institute, Sun City, AZ, USA.
- Laboratory of Neuroinflammation, Biodesign Neurodegenerative Disease Research Center, Arizona State University, Room 538, School of Life Sciences - E Wing, 427 E. Tyler Mall, Tempe, AZ, 85287, USA.
| | | | - Geidy Serrano
- Banner Sun Health Research Institute, Sun City, AZ, USA
| | - Lucia I Sue
- Banner Sun Health Research Institute, Sun City, AZ, USA
| | - Lih-Fen Lue
- Laboratory of Neuroinflammation, Biodesign Neurodegenerative Disease Research Center, Arizona State University, Room 538, School of Life Sciences - E Wing, 427 E. Tyler Mall, Tempe, AZ, 85287, USA
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29
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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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30
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van der Linden A, Blokker BM, Kap M, Weustink AC, Riegman PHJ, Oosterhuis JW. Post-mortem tissue biopsies obtained at minimally invasive autopsy: an RNA-quality analysis. PLoS One 2014; 9:e115675. [PMID: 25531551 PMCID: PMC4274113 DOI: 10.1371/journal.pone.0115675] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 11/26/2014] [Indexed: 12/21/2022] Open
Abstract
INTRODUCTION Bereaved relatives often refuse to give consent for post-mortem investigation of deceased cancer patients, mainly because of the mutilation due to conventional autopsy (CA). Minimally invasive autopsy (MIA) may be a more acceptable alternative and, if implemented in clinical practice, creates an opportunity to more often obtain post-mortem tissue samples of (recurred) primary tumors and metastases for molecular research. As a measure for tissue quality for molecular studies, we hereby present a feasibility study, comparing the RNA quality of MIA and CA samples, and fresh frozen samples as reference. MATERIALS AND METHODS Tissue samples of heart, liver and kidney were prospectively collected from 24 MIAs followed by CA, and compared to corresponding archival fresh frozen tissue. After RNA isolation and RT-qPCR, RNA integrity numbers (RIN) and GAPDH expression (six amplicon sizes ranging from 71 to 530 base pairs) were measured. RIN values and GAPDH Cq values were analyzed and compared between all sample groups and post-mortem intervals (PMI). RESULTS RIN values in MIA samples were significantly higher than those in CA samples. GAPDH was expressed significantly higher in MIA samples than in CA samples and 530 bp PCR products could be measured in all cases. GAPDH expression was significantly lower in samples with PMI >15 hours. As expected, the samples of the fresh frozen reference standard performed best in all analyses. CONCLUSION MIA samples showed better RNA quality than CA samples, probably due to shorter PMI. Both had lower RNA quality and expression levels than fresh frozen tissue, however, remaining GAPDH RNA was still sufficiently intact. Therefore, other highly expressed genes are most likely also detectable. Gene array analysis should be performed to gain insight into the quality of entire post-mortem genomes. Reducing PMI will further improve the feasibility of demanding molecular research on post-mortem tissues, this is most likely more feasible with MIA than CA.
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Affiliation(s)
| | | | - Marcel Kap
- Department of Pathology, Erasmus MC, Rotterdam, The Netherlands
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31
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Schweighardt AJ, Tate CM, Scott KA, Harper KA, Robertson JM. Evaluation of Commercial Kits for Dual Extraction of DNA and RNA from Human Body Fluids,,. J Forensic Sci 2014; 60:157-65. [DOI: 10.1111/1556-4029.12586] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 11/30/2013] [Accepted: 12/21/2013] [Indexed: 11/27/2022]
Affiliation(s)
- Andrew J. Schweighardt
- Counterterrorism and Forensic Science Research Unit; Visiting Scientist Program; Federal Bureau of Investigation Laboratory Division; 2501 Investigation Parkway Quantico VA 22135
| | - Courtney M. Tate
- Counterterrorism and Forensic Science Research Unit; Visiting Scientist Program; Federal Bureau of Investigation Laboratory Division; 2501 Investigation Parkway Quantico VA 22135
| | - Kristina A. Scott
- Counterterrorism and Forensic Science Research Unit; Visiting Scientist Program; Federal Bureau of Investigation Laboratory Division; 2501 Investigation Parkway Quantico VA 22135
| | - Kathryn A. Harper
- Counterterrorism and Forensic Science Research Unit; Visiting Scientist Program; Federal Bureau of Investigation Laboratory Division; 2501 Investigation Parkway Quantico VA 22135
| | - James M. Robertson
- Counterterrorism and Forensic Science Research Unit; Federal Bureau of Investigation Laboratory Division; 2501 Investigation Parkway Quantico VA 22135
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32
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Molecular analysis of different classes of RNA molecules from formalin-fixed paraffin-embedded autoptic tissues: a pilot study. Int J Legal Med 2014; 129:11-21. [PMID: 25135750 DOI: 10.1007/s00414-014-1066-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 08/08/2014] [Indexed: 10/24/2022]
Abstract
For a long time, it has been thought that fresh and frozen tissues are the only possible source of biological material useful to extract nucleic acids suitable for downstream molecular analysis. Recently, for forensic purpose such as personal identification, also fixed tissues have been used to recover DNA molecules, whereas RNA extracted from such material is still considered too degraded for gene expression studies. In the present pilot study, we evaluated the possibility to use forensic formalin-fixed paraffin-embedded (FFPE) samples, collected at autopsy at different postmortem intervals (PMI) from four individuals, to perform advanced molecular analyses. In particular, we performed qualitative and quantitative analyses of total RNAs extracted from different FFPE tissues and put expression profiles in relation with the organ type and the duration of PMI. Different classes of RNA molecular targets were studied by real-time quantitative RT-PCR. We report molecular evidence that small RNAs are the only RNA molecules still detectable in all the FFPE autoptic tissues. In particular, microRNAs (miRNAs) represent a consistent, stable, and well-preserved molecular target detectable even from tissue sources displaying signs of ongoing putrefaction at autopsy. In this pilot study, we show that miRNAs could represent a highly sensitive and potentially useful forensic marker. Amplification of specific miRNAs using paraffin-embedded blocks could facilitate retrospective molecular analysis using specific forensic-archived tissues chosen as most suitable according to PMI, and this approach would address molecular evidence in forensic cases in which fresh or frozen material is no longer available.
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FADD adaptor and PEA-15/ERK1/2 partners in major depression and schizophrenia postmortem brains: basal contents and effects of psychotropic treatments. Neuroscience 2014; 277:541-51. [PMID: 25075716 DOI: 10.1016/j.neuroscience.2014.07.027] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 06/26/2014] [Accepted: 07/18/2014] [Indexed: 01/05/2023]
Abstract
Enhanced brain apoptosis (neurons and glia) may be involved in major depression (MD) and schizophrenia (SZ), mainly through the activation of the intrinsic (mitochondrial) apoptotic pathway. In the extrinsic death pathway, pro-apoptotic Fas-associated death domain (FADD) adaptor and its non-apoptotic p-Ser194 FADD form have critical roles interacting with other death regulators such as phosphoprotein enriched in astrocytes of 15 kDa (PEA-15) and extracellular signal-regulated kinase (ERK). The basal status of FADD (protein and messenger RNA (mRNA)) and the effects of psychotropic drugs (detected in blood/urine samples) were first assessed in postmortem prefrontal cortex of MD and SZ subjects (including a non-MD/SZ suicide group). In MD, p-FADD, but not total FADD (and mRNA), was increased (26%, n=24; all MD subjects) as well as p-FADD/FADD ratio (a pro-survival marker) in antidepressant-free MD subjects (50%, n=10). In contrast, cortical FADD (and mRNA), p-FADD, and p-FADD/FADD were not altered in SZ brains (n=21) regardless of antipsychotic medications (except enhanced mRNA in treated subjects). Similar negative results were quantified in the non-MD/SZ suicide group. In MD, the regulation of multifunctional PEA-15 (i.e., p-Ser116 PEA-15 blocks pro-apoptotic FADD and PEA-15 prevents pro-survival ERK action) and the modulation of p-ERK1/2 were also investigated. Cortical p-PEA-15 was not changed whereas PEA-15 was increased mainly in antidepressant-treated subjects (16-20%). Interestingly, cortical p-ERK1/2/ERK1/2 ratio was reduced (33%) in antidepressant-free when compared to antidepressant-treated MD subjects. The neurochemical adaptations of brain FADD (increased p-FADD and pro-survival p-FADD/FADD ratio), as well as its interaction with PEA-15, could play a major role to counteract the known activation of the mitochondrial apoptotic pathway in MD.
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34
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Hayashi T, Ikematsu K, Abe Y, Ihama Y, Ago K, Ago M, Miyazaki T, Ogata M. Temporal changes of the adrenal endocrine system in a restraint stressed mouse and possibility of postmortem indicators of prolonged psychological stress. Leg Med (Tokyo) 2014; 16:193-6. [DOI: 10.1016/j.legalmed.2014.03.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Revised: 03/12/2014] [Accepted: 03/21/2014] [Indexed: 12/12/2022]
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35
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DNA and RNA analysis of blood and muscle from bodies with variable postmortem intervals. Forensic Sci Med Pathol 2014; 10:322-8. [DOI: 10.1007/s12024-014-9567-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/08/2014] [Indexed: 10/25/2022]
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36
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Perán M, López-Ruiz E, González-Herrera L, Bustamante M, Valenzuela A, Marchal JA. Cellular extracts from post-mortem human cardiac tissue direct cardiomyogenic differentiation of human adipose tissue-derived stem cells. Cytotherapy 2014; 15:1541-8. [PMID: 24199593 DOI: 10.1016/j.jcyt.2013.06.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 05/14/2013] [Accepted: 06/22/2013] [Indexed: 01/31/2023]
Abstract
BACKGROUND AIMS Human adipose tissue-derived stem cells (hASCs) can be easily (and inexpensively) expanded in culture, and their high plasticity allows their conversion to different cell types. We study the potential capacity of postmortem cardiac tissue to direct cardiac differentiation of hASCs in vitro. METHODS Cardiac tissue collected from autopsies was used to obtain cell extracts and conditioned medium, and both approaches were tested for cardiac induction. RESULTS Gene expression analyses proved that post-mortem human cardiac tissue maintains genetic integrity. hASCs exposed to the cell extracts or conditioned medium for 2 weeks achieved the appearance of myotube-like structures and were positive for cardiac markers such as sarcomeric α-actinin, cardiac troponin I and T and desmin as proved by immunofluorescence. In addition, differentiated cells showed increased expression of cardiomyocyte-related genes analyzed by reverse transcriptase polymerase chain reaction (GATA-4, myocyte-enhancer factor-2c, α-cardiac actin and cardiac troponin I). CONCLUSIONS For the first time, post-mortem human cardiac tissue was used to induce hASC differentiation into myocardial-like cells. The methodology described here would serve as a useful model to obtain cardiomyocyte-like cells in vitro.
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Affiliation(s)
- Macarena Perán
- Department of Health Sciences, University of Jaén, Spain.
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37
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Gallego Romero I, Pai AA, Tung J, Gilad Y. RNA-seq: impact of RNA degradation on transcript quantification. BMC Biol 2014; 12:42. [PMID: 24885439 PMCID: PMC4071332 DOI: 10.1186/1741-7007-12-42] [Citation(s) in RCA: 290] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 05/27/2014] [Indexed: 12/03/2022] Open
Abstract
Background The use of low quality RNA samples in whole-genome gene expression profiling remains controversial. It is unclear if transcript degradation in low quality RNA samples occurs uniformly, in which case the effects of degradation can be corrected via data normalization, or whether different transcripts are degraded at different rates, potentially biasing measurements of expression levels. This concern has rendered the use of low quality RNA samples in whole-genome expression profiling problematic. Yet, low quality samples (for example, samples collected in the course of fieldwork) are at times the sole means of addressing specific questions. Results We sought to quantify the impact of variation in RNA quality on estimates of gene expression levels based on RNA-seq data. To do so, we collected expression data from tissue samples that were allowed to decay for varying amounts of time prior to RNA extraction. The RNA samples we collected spanned the entire range of RNA Integrity Number (RIN) values (a metric commonly used to assess RNA quality). We observed widespread effects of RNA quality on measurements of gene expression levels, as well as a slight but significant loss of library complexity in more degraded samples. Conclusions While standard normalizations failed to account for the effects of degradation, we found that by explicitly controlling for the effects of RIN using a linear model framework we can correct for the majority of these effects. We conclude that in instances in which RIN and the effect of interest are not associated, this approach can help recover biologically meaningful signals in data from degraded RNA samples.
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Affiliation(s)
| | | | | | - Yoav Gilad
- Department of Human Genetics, University of Chicago, 920 E 58th St, CLSC 317, Chicago, IL 60637, USA.
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Yamagishi A, Matsumoto S, Watanabe A, Mizuguchi Y, Hara K, Kan H, Yamada T, Koizumi M, Shinji S, Matsuda A, Sasaki J, Shimada T, Uchida E. Gene profiling and bioinformatics analyses reveal time course differential gene expression in surgically resected colorectal tissues. Oncol Rep 2014; 31:1531-8. [PMID: 24573535 PMCID: PMC3975991 DOI: 10.3892/or.2014.3053] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 12/03/2013] [Indexed: 12/20/2022] Open
Abstract
It has previously been reported that gene profiles in surgically-resected colorectal cancer tissues are altered over time possibly due to the different tissue-acquisition methods and sample extraction timing that were used. However, the changes that occur are still not clearly understood. In the present study, time-dependent changes in gene expression profiling in colorectal surgical specimens were analyzed. Normal and tumor tissues at several time-points (0, 30, 60 and 120 min) were extracted, and RNA quality, microarray experiments, quantitative PCR and bioinformatics clustering were performed. Although RNA integrity was preserved 2 h after resection, inherent increased/decreased gene expression was observed from 30–120 min in approximately 10% of genes. Bioinformatics clustering could not distinguish case-by-case, probably due to gene profiling changes. Irregular changes in gene expression after surgical resection were found, which could be a crucial confounding factor for quantitative analyses.
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Affiliation(s)
- Aya Yamagishi
- Surgery for Organ Function and Biological Regulation, Graduate School of Medicine, Nippon Medical School, Tokyo 113-8603, Japan
| | - Satoshi Matsumoto
- Surgery for Organ Function and Biological Regulation, Graduate School of Medicine, Nippon Medical School, Tokyo 113-8603, Japan
| | - Atsushi Watanabe
- Department of Biochemistry and Molecular Biology, Nippon Medical School, Tokyo 113-8603, Japan
| | - Yoshiaki Mizuguchi
- Surgery for Organ Function and Biological Regulation, Graduate School of Medicine, Nippon Medical School, Tokyo 113-8603, Japan
| | - Keisuke Hara
- Surgery for Organ Function and Biological Regulation, Graduate School of Medicine, Nippon Medical School, Tokyo 113-8603, Japan
| | - Hayato Kan
- Surgery for Organ Function and Biological Regulation, Graduate School of Medicine, Nippon Medical School, Tokyo 113-8603, Japan
| | - Takeshi Yamada
- Surgery for Organ Function and Biological Regulation, Graduate School of Medicine, Nippon Medical School, Tokyo 113-8603, Japan
| | - Michihiro Koizumi
- Surgery for Organ Function and Biological Regulation, Graduate School of Medicine, Nippon Medical School, Tokyo 113-8603, Japan
| | - Seiichi Shinji
- Surgery for Organ Function and Biological Regulation, Graduate School of Medicine, Nippon Medical School, Tokyo 113-8603, Japan
| | - Akihisa Matsuda
- Surgery for Organ Function and Biological Regulation, Graduate School of Medicine, Nippon Medical School, Tokyo 113-8603, Japan
| | - Junpei Sasaki
- Surgery for Organ Function and Biological Regulation, Graduate School of Medicine, Nippon Medical School, Tokyo 113-8603, Japan
| | - Takashi Shimada
- Department of Biochemistry and Molecular Biology, Nippon Medical School, Tokyo 113-8603, Japan
| | - Eiji Uchida
- Surgery for Organ Function and Biological Regulation, Graduate School of Medicine, Nippon Medical School, Tokyo 113-8603, Japan
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Maeda H, Ishikawa T, Michiue T. Forensic molecular pathology: its impacts on routine work, education and training. Leg Med (Tokyo) 2014; 16:61-9. [PMID: 24480586 DOI: 10.1016/j.legalmed.2014.01.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2013] [Accepted: 01/07/2014] [Indexed: 01/14/2023]
Abstract
The major role of forensic pathology is the investigation of human death in relevance to social risk management to determine the cause and process of death, especially in violent and unexpected sudden deaths, which involve social and medicolegal issues of ultimate, personal and public concerns. In addition to the identification of victims and biological materials, forensic molecular pathology contributes to general explanation of the human death process and assessment of individual death on the basis of biological molecular evidence, visualizing dynamic functional changes involved in the dying process that cannot be detected by morphology (pathophysiological or molecular biological vital reactions); the genetic background (genomics), dynamics of gene expression (up-/down-regulation: transcriptomics) and vital phenomena, involving activated biological mediators and degenerative products (proteomics) as well as metabolic deterioration (metabolomics), are detected by DNA analysis, relative quantification of mRNA transcripts using real-time reverse transcription-PCR (RT-PCR), and immunohisto-/immunocytochemistry combined with biochemistry, respectively. Thus, forensic molecular pathology involves the application of omic medical sciences to investigate the genetic basis, and cause and process of death at the biological molecular level in the context of forensic pathology, that is, 'advanced molecular autopsy'. These procedures can be incorporated into routine death investigations as well as guidance, education and training programs in forensic pathology for 'dynamic assessment of the cause and process of death' on the basis of autopsy and laboratory data. Postmortem human data can also contribute to understanding patients' critical conditions in clinical management.
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Affiliation(s)
- Hitoshi Maeda
- Department of Legal Medicine, Osaka City University Medical School, Asahi-machi 1-4-3, Abeno, 545-8585 Osaka, Japan; Forensic Autopsy Section, Medico-legal Consultation and Postmortem Investigation Support Center (MLCPI-SC), c/o Osaka City University Medical School, Asahi-machi 1-4-3, Abeno, 545-8585 Osaka, Japan.
| | - Takaki Ishikawa
- Department of Legal Medicine, Osaka City University Medical School, Asahi-machi 1-4-3, Abeno, 545-8585 Osaka, Japan; Forensic Autopsy Section, Medico-legal Consultation and Postmortem Investigation Support Center (MLCPI-SC), c/o Osaka City University Medical School, Asahi-machi 1-4-3, Abeno, 545-8585 Osaka, Japan; Division of Legal Medicine, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago, 683-8503 Tottori, Japan
| | - Tomomi Michiue
- Department of Legal Medicine, Osaka City University Medical School, Asahi-machi 1-4-3, Abeno, 545-8585 Osaka, Japan; Forensic Autopsy Section, Medico-legal Consultation and Postmortem Investigation Support Center (MLCPI-SC), c/o Osaka City University Medical School, Asahi-machi 1-4-3, Abeno, 545-8585 Osaka, Japan
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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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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: 81] [Impact Index Per Article: 7.4] [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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Deng W, Lv M, Wang L, Bai P, Liang W, Zhang L. mRNA degradation pattern analysis in post-mortem normalized using the DNA. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2013. [DOI: 10.1016/j.fsigss.2013.10.136] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Naumova OY, Lee M, Rychkov SY, Vlasova NV, Grigorenko EL. Gene expression in the human brain: the current state of the study of specificity and spatiotemporal dynamics. Child Dev 2012; 84:76-88. [PMID: 23145569 DOI: 10.1111/cdev.12014] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Gene expression is one of the main molecular processes regulating the differentiation, development, and functioning of cells and tissues. In this review a handful of relevant terms and concepts are introduced and the most common techniques used in studies of gene expression/expression profiling (also referred to as studies of the transcriptome or transcriptomics) are described. The main foci of this review are the advancements in studies of the transcriptome in the human brain, the transcriptome's variability across different brain structures, and the systematic changes that occur through different developmental stages across the life span in general and childhood in particular. Finally, the question of how the accumulating data on the spatial and temporal dynamics of the transcriptome may shed light on the molecular mechanisms of the typical and atypical development of the central nervous system is addressed.
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44
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Chung U, Seo JS, Kim YH, Son GH, Hwang JJ. Quantitative analyses of postmortem heat shock protein mRNA profiles in the occipital lobes of human cerebral cortices: implications in cause of death. Mol Cells 2012; 34:473-80. [PMID: 23135635 PMCID: PMC3887795 DOI: 10.1007/s10059-012-0214-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Revised: 09/24/2012] [Accepted: 10/03/2012] [Indexed: 01/11/2023] Open
Abstract
Quantitative RNA analyses of autopsy materials to diagnose the cause and mechanism of death are challenging tasks in the field of forensic molecular pathology. Alterations in mRNA profiles can be induced by cellular stress responses during supravital reactions as well as by lethal insults at the time of death. Here, we demonstrate that several gene transcripts encoding heat shock proteins (HSPs), a gene family primarily responsible for cellular stress responses, can be differentially expressed in the occipital region of postmortem human cerebral cortices with regard to the cause of death. HSPA2 mRNA levels were higher in subjects who died due to mechanical asphyxiation (ASP), compared with those who died by traumatic injury (TI). By contrast, HSPA7 and A13 gene transcripts were much higher in the TI group than in the ASP and sudden cardiac death (SCD) groups. More importantly, relative abundances between such HSP mRNA species exhibit a stronger correlation to, and thus provide more discriminative information on, the death process than does routine normalization to a housekeeping gene. Therefore, the present study proposes alterations in HSP mRNA composition in the occipital lobe as potential forensic biological markers, which may implicate the cause and process of death.
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Affiliation(s)
- Ukhee Chung
- Department of Legal Medicine, College of Medicine, Korea University, Seoul 136-705,
Korea
| | | | | | - Gi Hoon Son
- Department of Legal Medicine, College of Medicine, Korea University, Seoul 136-705,
Korea
| | - Juck-Joon Hwang
- Department of Legal Medicine, College of Medicine, Korea University, Seoul 136-705,
Korea
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45
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Apparent versus true gene expression changes of three hypoxia-related genes in autopsy derived tissue and the importance of normalisation. Int J Legal Med 2012; 127:335-44. [DOI: 10.1007/s00414-012-0787-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Accepted: 10/16/2012] [Indexed: 01/21/2023]
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46
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Ma Y, Dai H, Kong X. Impact of warm ischemia on gene expression analysis in surgically removed biosamples. Anal Biochem 2012; 423:229-35. [DOI: 10.1016/j.ab.2012.02.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Revised: 01/15/2012] [Accepted: 02/03/2012] [Indexed: 02/01/2023]
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47
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Song HJ, Choi YL, Kang SY, Chae JM. The Effect of Elapsed Time on the Quantity of mRNA in Skin: A Study to Evaluate the Potential Forensic Use of mRNA to Determine the Postmortem Interval. ACTA ACUST UNITED AC 2012. [DOI: 10.7580/koreanjlegmed.2012.36.2.151] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Hye Jong Song
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Yoon La Choi
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - So Young Kang
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jong Min Chae
- Department of Forensic Medicine, Kyungpook National University School of Medicine, Daegu, Korea
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Simard AM, DesGroseillers L, Sarafian V. Assessment of RNA Stability for Age Determination of Body Fluid Stains. CANADIAN SOCIETY OF FORENSIC SCIENCE JOURNAL 2012. [DOI: 10.1080/00085030.2012.10757192] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Current genetic methodologies in the identification of disaster victims and in forensic analysis. J Appl Genet 2011; 53:41-60. [PMID: 22002120 PMCID: PMC3265735 DOI: 10.1007/s13353-011-0068-7] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2011] [Revised: 09/22/2011] [Accepted: 09/23/2011] [Indexed: 12/16/2022]
Abstract
This review presents the basic problems and currently available molecular techniques used for genetic profiling in disaster victim identification (DVI). The environmental conditions of a mass disaster often result in severe fragmentation, decomposition and intermixing of the remains of victims. In such cases, traditional identification based on the anthropological and physical characteristics of the victims is frequently inconclusive. This is the reason why DNA profiling became the gold standard for victim identification in mass-casualty incidents (MCIs) or any forensic cases where human remains are highly fragmented and/or degraded beyond recognition. The review provides general information about the sources of genetic material for DNA profiling, the genetic markers routinely used during genetic profiling (STR markers, mtDNA and single-nucleotide polymorphisms [SNP]) and the basic statistical approaches used in DNA-based disaster victim identification. Automated technological platforms that allow the simultaneous analysis of a multitude of genetic markers used in genetic identification (oligonucleotide microarray techniques and next-generation sequencing) are also presented. Forensic and population databases containing information on human variability, routinely used for statistical analyses, are discussed. The final part of this review is focused on recent developments, which offer particularly promising tools for forensic applications (mRNA analysis, transcriptome variation in individuals/populations and genetic profiling of specific cells separated from mixtures).
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Sherwood KR, Head MW, Walker R, Smith C, Ironside JW, Fazakerley JK. RNA integrity in post mortem human variant Creutzfeldt-Jakob disease (vCJD) and control brain tissue. Neuropathol Appl Neurobiol 2011; 37:633-42. [DOI: 10.1111/j.1365-2990.2011.01162.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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