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Kim BM, Park SU, Lee HY. Comparative analysis of SNaPshot and massively parallel sequencing for body fluid-specific DNA methylation markers. Electrophoresis 2024. [PMID: 39119735 DOI: 10.1002/elps.202400037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 07/05/2024] [Accepted: 07/27/2024] [Indexed: 08/10/2024]
Abstract
The identification of tissue-specific differentially methylated regions has significantly contributed to the field of forensic genetics, particularly in body fluid identification crucial for linking evidence to crimes. Among the various approaches to analyzing DNA methylation, the SNaPshot assay has been popularly studied in numerous researches. However, there is a growing interest in exploring alternative methods such as the use of massively parallel sequencing (MPS), which can process a large number of samples simultaneously. This study compares SNaPshot and MPS multiplex assays using nine cytosine-phosphate-guanine markers for body fluid identification. As a result of analyzing 112 samples, including blood, saliva, vaginal fluid, menstrual blood, and semen, both methods demonstrated high sensitivity and specificity, indicating their reliability in forensic investigations. A total of 92.0% samples were correctly identified by both methods. Although both methods accurately identified all blood, saliva, and semen samples, some vaginal fluid samples showed unexpected methylation signals at nontarget loci in addition to the target loci. In the case of menstrual blood samples, due to their complexity, independent typing criteria were applied, and successful menstrual blood typing was possible, whereas a few samples showed profiles similar to vaginal fluid. The MPS method worked better in vaginal fluid samples, and the SNaPshot method performed better in menstrual blood samples. This study offers valuable insights into body fluid identification based on the characteristics of the SNaPshot and MPS methods, which may help in more efficient forensic applications.
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Affiliation(s)
- Bo Min Kim
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Sang Un Park
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Hwan Young Lee
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, South Korea
- Institute of Forensic and Anthropological Science, Seoul National University College of Medicine, Seoul, South Korea
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2
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Kubo S, Amai K, Tanaka J, Niimi H. Female sample screening using colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) targeting non-coding RNA XIST. Forensic Sci Int 2024; 361:112081. [PMID: 38850616 DOI: 10.1016/j.forsciint.2024.112081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 05/26/2024] [Accepted: 05/29/2024] [Indexed: 06/10/2024]
Abstract
Forensic sample screening is important for establishing an effective DNA typing workflow. The detection of sex-specific markers in forensic samples highlights the necessity for further analysis. Y-chromosome DNA can confirm male contributions, but female contributions are difficult to confirm using DNA-based methods. To address this, we developed a colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay targeting the long non-coding RNA X-inactive specific transcript (XIST) to screen female samples. Operating at 65 °C for 30 min, the assay yielded results discernible from the color change of the pH indicator dye. The assay showed a detection limit of approximately 0.5 µL of blood. The assay also detected XIST RNA in mixed body fluids and mock samples, indicating its potential applicability to casework samples. Taken together, our assay provides a rapid and simple strategy for screening female samples.
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Affiliation(s)
- Seiji Kubo
- Department of Clinical Laboratory and Molecular Pathology, Faculty of Medicine, Academic Assembly, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan; Forensic Science Laboratory, Ishikawa Prefectural Police Headquarters, 1-1 Kuratsuki, Kanazawa 920-8553, Japan.
| | - Keito Amai
- Forensic Science Laboratory, Ishikawa Prefectural Police Headquarters, 1-1 Kuratsuki, Kanazawa 920-8553, Japan
| | - Jin Tanaka
- Forensic Science Laboratory, Ishikawa Prefectural Police Headquarters, 1-1 Kuratsuki, Kanazawa 920-8553, Japan
| | - Hideki Niimi
- Department of Clinical Laboratory and Molecular Pathology, Faculty of Medicine, Academic Assembly, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan.
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3
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Kim BM, Park SU, Schmelzer L, Yang SB, Lee SD, Kim MY, Naue J, Lee HY. DNA methylation-based organ tissue identification: Marker identification, SNaPshot multiplex assay development, and interlaboratory comparison. Forensic Sci Int Genet 2024; 71:103052. [PMID: 38678764 DOI: 10.1016/j.fsigen.2024.103052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/19/2024] [Accepted: 04/20/2024] [Indexed: 05/01/2024]
Abstract
Identifying body fluids and organ tissues is highly significant as they can offer crucial evidence in criminal investigations and aid the court in making informed decisions, primarily through evaluating the biological source and possibly at the activity level up to death or fatal damage. In this study, organ tissue-specific CpG markers were identified from Illumina's methylation EPIC array data of nine organ tissues, including epidermis, dermis, heart, skeletal muscle, blood, kidney, brain, lung, and liver, from autopsies of 10 Koreans. Through the validation test using 43 samples, 18 hypomethylation markers, with two markers for each organ tissue type, were selected to construct a SNaPshot assay. Two multiplex assays involving forward and reverse SBE primers were designed to help investigators accurately determine the organ origin of the analyzed tissue samples through repeated analysis of the same PCR products for markers. The developed multiplex demonstrated high accuracy, achieving 100.0 % correct detection of the presence of nine organ tissue types in 88 samples from autopsies of 10 Asians. However, two lung samples showed additional positive indications of the presence of blood. An interlaboratory comparison using 80 autopsy samples (heart, skeletal muscle, blood, kidney cortex, kidney medulla, brain, lung, and liver) from 10 individuals in Germany revealed overall comparable results with correct detection of the presence of eight organ tissue types in 92.5 % samples (74 of 80 samples). In the case of six samples, it was impossible to determine the correct tissue successfully due to drop-outs of unmethylation signals at target tissue marker loci. One of these lung samples revealed only non-intended off-target signals for blood. The observed differences might be due to differences in sample collection during routine autopsy, technical differences due to the PCR cycler, and the threshold used for signal calling. Indicating the presence of additional tissue type and off-target unmethylation signals seems alleviated by applying more stringent hypomethylation thresholds. Therefore, the developed SNaPshot multiplex assays will be valuable for forensic investigators dealing with organ tissue identification, as well as for prosecutors and defense aiming to establish the circumstances that occurred at the crime scene.
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Affiliation(s)
- Bo Min Kim
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Sang Un Park
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Laura Schmelzer
- Institute of Forensic Medicine, Medical Center -University of Freiburg, Faculty of Medicine, University of Freiburg, Germany
| | - Soo-Bin Yang
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Soong Deok Lee
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea; Institute of Forensic and Anthropological Science, Seoul National University College of Medicine, Seoul, Korea
| | - Moon-Young Kim
- Laboratory of Forensic Medicine, Department of Anatomy and Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Jana Naue
- Institute of Forensic Medicine, Medical Center -University of Freiburg, Faculty of Medicine, University of Freiburg, Germany.
| | - Hwan Young Lee
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea; Institute of Forensic and Anthropological Science, Seoul National University College of Medicine, Seoul, Korea.
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4
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Javan GT, Singh K, Finley SJ, Green RL, Sen CK. Complexity of human death: its physiological, transcriptomic, and microbiological implications. Front Microbiol 2024; 14:1345633. [PMID: 38282739 PMCID: PMC10822681 DOI: 10.3389/fmicb.2023.1345633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 12/28/2023] [Indexed: 01/30/2024] Open
Abstract
Human death is a complex, time-governed phenomenon that leads to the irreversible cessation of all bodily functions. Recent molecular and genetic studies have revealed remarkable experimental evidence of genetically programmed cellular death characterized by several physiological processes; however, the basic physiological function that occurs during the immediate postmortem period remains inadequately described. There is a paucity of knowledge connecting necrotic pathologies occurring in human organ tissues to complete functional loss of the human organism. Cells, tissues, organs, and organ systems show a range of differential resilience and endurance responses that occur during organismal death. Intriguingly, a persistent ambiguity in the study of postmortem physiological systems is the determination of the trajectory of a complex multicellular human body, far from life-sustaining homeostasis, following the gradual or sudden expiry of its regulatory systems. Recent groundbreaking investigations have resulted in a paradigm shift in understanding the cell biology and physiology of death. Two significant findings are that (i) most cells in the human body are microbial, and (ii) microbial cell abundance significantly increases after death. By addressing the physiological as well as the microbiological aspects of death, future investigations are poised to reveal innovative insights into the enigmatic biological activities associated with death and human decomposition. Understanding the elaborate crosstalk of abiotic and biotic factors in the context of death has implications for scientific discoveries important to informing translational knowledge regarding the transition from living to the non-living. There are important and practical needs for a transformative reestablishment of accepted models of biological death (i.e., artificial intelligence, AI) for more precise determinations of when the regulatory mechanisms for homeostasis of a living individual have ceased. In this review, we summarize mechanisms of physiological, genetic, and microbiological processes that define the biological changes and pathways associated with human organismal death and decomposition.
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Affiliation(s)
- Gulnaz T. Javan
- Department of Physical and Forensic Sciences, Alabama State University, Montgomery, AL, United States
| | - Kanhaiya Singh
- Department of Surgery, School of Medicine, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Sheree J. Finley
- Department of Physical and Forensic Sciences, Alabama State University, Montgomery, AL, United States
| | - Robert L. Green
- Department of Physical and Forensic Sciences, Alabama State University, Montgomery, AL, United States
| | - Chandan K. Sen
- Department of Surgery, School of Medicine, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, United States
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Bonin S, D’Errico S, Medeot C, Moreschi C, Ciglieri SS, Peruch M, Concato M, Azzalini E, Previderè C, Fattorini P. Evaluation of a Set of miRNAs in 26 Cases of Fatal Traumatic Brain Injuries. Int J Mol Sci 2023; 24:10836. [PMID: 37446013 PMCID: PMC10341445 DOI: 10.3390/ijms241310836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/20/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
In forensic medicine, identifying novel biomarkers for use as diagnostic tools to ascertain causes of death is challenging because of sample degradation. To that aim, a cohort (n = 26) of fatal traumatic brain injuries (TBIs) were tested for three candidate miRNAs (namely, miR-124-3p, miR-138-5p, and miR144-3p). For each case, three FFPE specimens (coup area (CA), contrecoup area (CCA), and the corpus callosum (CC)) were investigated, whereas the FFPE brain tissues of 45 subjects (deceased due to acute cardiovascular events) were used as controls. Relative quantification via the ∆∆Ct method returned significantly higher expression levels of the three candidate miRNAs (p < 0.01) in the TBI cases. No difference was detected in the expression levels of any miRNA investigated in the study among the CA, CCA, and CC. Furthermore, the analyzed miRNAs were unrelated to the TBI samples' post-mortem intervals (PMIs). On the contrary, has-miR-124-3p ahashsa-miR-144-3p were significantly correlated (p < 0.01) with the agonal time in TBI deaths. Since the RNA was highly degraded in autoptic FFPE tissues, it was impossible to analyze the mRNA targets of the miRNAs investigated in the present study, highlighting the necessity of standardizing pre-analytical processes even for autopsy tissues.
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Affiliation(s)
- Serena Bonin
- DSM—Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (S.B.); (C.M.); (S.S.C.); (M.P.); (M.C.); (E.A.); (P.F.)
| | - Stefano D’Errico
- DSM—Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (S.B.); (C.M.); (S.S.C.); (M.P.); (M.C.); (E.A.); (P.F.)
| | - Caterina Medeot
- DSM—Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (S.B.); (C.M.); (S.S.C.); (M.P.); (M.C.); (E.A.); (P.F.)
| | - Carlo Moreschi
- DAME—Department of Medical Area, University of Udine, 33100 Udine, Italy;
| | - Solange Sorçaburu Ciglieri
- DSM—Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (S.B.); (C.M.); (S.S.C.); (M.P.); (M.C.); (E.A.); (P.F.)
| | - Michela Peruch
- DSM—Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (S.B.); (C.M.); (S.S.C.); (M.P.); (M.C.); (E.A.); (P.F.)
| | - Monica Concato
- DSM—Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (S.B.); (C.M.); (S.S.C.); (M.P.); (M.C.); (E.A.); (P.F.)
| | - Eros Azzalini
- DSM—Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (S.B.); (C.M.); (S.S.C.); (M.P.); (M.C.); (E.A.); (P.F.)
| | - Carlo Previderè
- Department of Public Health, Experimental, and Forensic Medicine, Section of Legal Medicine and Forensic Sciences, University of Pavia, 27100 Pavia, Italy;
| | - Paolo Fattorini
- DSM—Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (S.B.); (C.M.); (S.S.C.); (M.P.); (M.C.); (E.A.); (P.F.)
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6
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Jiang Z, Lu Y, Shi M, Li H, Duan J, Huang J. Effects of storage temperature, storage time, and hemolysis on the RNA quality of blood specimens: A systematic quantitative assessment. Heliyon 2023; 9:e16234. [PMID: 37260878 PMCID: PMC10227325 DOI: 10.1016/j.heliyon.2023.e16234] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 05/05/2023] [Accepted: 05/10/2023] [Indexed: 06/02/2023] Open
Abstract
Introduction Blood samples are the most common biospecimen in biobanks, and RNA from such blood samples is an important material for biomedical research. High-quality RNA is essential for consistent, reliable results. Preanalytical environmental conditions can affect the quality of blood RNA. Here, we carried out a quantitative assessment of the influence of storage temperature, storage time, and hemolysis on the RNA quality of blood specimens in biobanks. Methods Before RNA purification, blood samples from volunteers were exposed to 4 °C for 2, 6, 12, 24, or 48 h, 3 days, or 1 week, or exposed to room temperature (22-30 °C) for 1, 2, 6, 12, or 24 h. Hemolyzed samples were collected from laboratory department and some of them were prepared using the freeze-thaw method. After exposure to different preanalytical environmental conditions, the RNA simple Total RNA Kit was used to purify the RNA, following which a NanoDrop™ One and Qsep 100 Bio-Fragment Analyzer were used to assess RNA concentration, purity, and integrity. In addition, a part of the RNA was immediately reverse transcribed into cDNA when it was purified, then the relative expression levels of 18S, ACTB, HIF1α, HMOX1, and MKI67 were determined by real-time quantitative PCR. Finally, 30 blood samples were collected from the surplus samples in our laboratory department to assess their RNA quality without knowledge of their storage conditions (duration/temperature). Results For blood samples stored at 4 °C, there was a significant difference between the RNA integrity after 1 week compared to after 2 h. For blood samples stored at room temperature (22-30 °C), the RNA integrity was also significantly different at 6 h and 0 h. Hemolysis caused by freeze-thawing severely affected RNA quality, whereas clinical hemolysis generally produced no significant effects. Moreover, expression of 18S, ACTB, HIF1α, HMOX1, and MKI67 in whole blood stored under different conditions showed irregular changes, suggesting that preservation conditions are also important for gene expression. Conclusion RNA integrity was qualified for blood samples stored at 4 °C for up to 72 h or at room temperature (22-30 °C) for up to 2 h. Hemolysis usually does not affect the RNA quality of blood samples unless the hemolysis method damages leukocytes.
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Affiliation(s)
- Zhijun Jiang
- Biobank, Jiangxi Provincial Children's Hospital, Nanchang, China
| | - Yi Lu
- Biobank, Jiangxi Provincial Children's Hospital, Nanchang, China
| | - Manying Shi
- Biobank, Jiangxi Provincial Children's Hospital, Nanchang, China
| | - Hong Li
- Central Laboratory, Jiangxi Provincial Children's Hospital, Nanchang, China
| | - Junkai Duan
- Pediatric Heart Disease Treatment Center, Jiangxi Provincial Children's Hospital, Nanchang, China
| | - Jiyi Huang
- Biobank, Jiangxi Provincial Children's Hospital, Nanchang, China
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7
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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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Hanson E, Dørum G, Zamborlin M, Wang S, Gysi M, Ingold S, Lagace R, Roth C, Haas C, Ballantyne J. Targeted S5 RNA sequencing assay for the identification and direct association of common body fluids with DNA donors in mixtures. Int J Legal Med 2023; 137:13-32. [PMID: 36333511 DOI: 10.1007/s00414-022-02908-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022]
Abstract
The evidentiary value of DNA profiles varies depending upon the context in which the DNA was found. Linking a DNA profile to a particular cellular phenotype in mixtures may aid in assessing its evidentiary relevance and value. We report the development of two dual-function high-resolution messenger RNA (mRNA) sequencing assays that can each identify the presence of 6 body fluids/tissues (blood, semen, saliva, vaginal secretions, menstrual blood, skin) and, via coding region SNPs (cSNPs) present in the body fluid-specific mRNA transcripts, directly associate particular body fluids with their specific DNA donors in mixtures. The original blood, semen, and saliva (BSS) assay contains 23 cSNPs for blood, semen, and saliva, while the expanded 6F (all 6 fluids/tissues) assay encompasses the BSS assay and also contains 23 additional cSNPs for vaginal secretions, menstrual blood, and skin. Software tools were developed to infer the identity of the body fluids present as well as providing the corresponding cSNP genotypes. Concomitant genomic DNA assays (BSS-d and 6F-d), required to genotype the same cSNPs from persons of interest/inferred contributors to the body fluid mixture, were also developed. Body fluid specificity was demonstrated by the ability to identify the body fluid origin of single-source and two-fluid admixtures. The discriminatory power (European Caucasians) for all body fluids is 0.957-0.997, with linkage disequilibrium considered. Reciprocal body fluid admixtures (mixture pairs with the same two donors but reversed body fluid types) were used to demonstrate the ability to identify the body fluid source of origin as well as associate the donor of each of the two fluids.
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Affiliation(s)
- Erin Hanson
- Department of Chemistry, University of Central Florida, P.O. Box 162367, Orlando, FL, 32816-2367, USA.,National Center for Forensic Science, Orlando, FL, USA
| | - Guro Dørum
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Manuel Zamborlin
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Shouyu Wang
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Mario Gysi
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Sabrina Ingold
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Robert Lagace
- Life Sciences/HID, Thermo Fisher Scientific, San Francisco, CA, USA
| | - Chantal Roth
- Life Sciences/HID, Thermo Fisher Scientific, San Francisco, CA, USA
| | - Cordula Haas
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Jack Ballantyne
- Department of Chemistry, University of Central Florida, P.O. Box 162367, Orlando, FL, 32816-2367, USA. .,National Center for Forensic Science, Orlando, FL, USA.
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9
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Castaneda AB, Petty LE, Scholz M, Jansen R, Weiss S, Zhang X, Schramm K, Beutner F, Kirsten H, Schminke U, Hwang SJ, Marzi C, Dhana K, Seldenrijk A, Krohn K, Homuth G, Wolf P, Peters MJ, Dörr M, Peters A, van Meurs JBJ, Uitterlinden AG, Kavousi M, Levy D, Herder C, van Grootheest G, Waldenberger M, Meisinger C, Rathmann W, Thiery J, Polak J, Koenig W, Seissler J, Bis JC, Franceshini N, Giambartolomei C, Hofman A, Franco OH, Penninx BWJH, Prokisch H, Völzke H, Loeffler M, O'Donnell CJ, Below JE, Dehghan A, de Vries PS. Associations of carotid intima media thickness with gene expression in whole blood and genetically predicted gene expression across 48 tissues. Hum Mol Genet 2022; 31:1171-1182. [PMID: 34788810 PMCID: PMC8976428 DOI: 10.1093/hmg/ddab236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 06/11/2021] [Accepted: 08/11/2021] [Indexed: 11/13/2022] Open
Abstract
Carotid intima media thickness (cIMT) is a biomarker of subclinical atherosclerosis and a predictor of future cardiovascular events. Identifying associations between gene expression levels and cIMT may provide insight to atherosclerosis etiology. Here, we use two approaches to identify associations between mRNA levels and cIMT: differential gene expression analysis in whole blood and S-PrediXcan. We used microarrays to measure genome-wide whole blood mRNA levels of 5647 European individuals from four studies. We examined the association of mRNA levels with cIMT adjusted for various potential confounders. Significant associations were tested for replication in three studies totaling 3943 participants. Next, we applied S-PrediXcan to summary statistics from a cIMT genome-wide association study (GWAS) of 71 128 individuals to estimate the association between genetically determined mRNA levels and cIMT and replicated these analyses using S-PrediXcan on an independent GWAS on cIMT that included 22 179 individuals from the UK Biobank. mRNA levels of TNFAIP3, CEBPD and METRNL were inversely associated with cIMT, but these associations were not significant in the replication analysis. S-PrediXcan identified associations between cIMT and genetically determined mRNA levels for 36 genes, of which six were significant in the replication analysis, including TLN2, which had not been previously reported for cIMT. There was weak correlation between our results using differential gene expression analysis and S-PrediXcan. Differential expression analysis and S-PrediXcan represent complementary approaches for the discovery of associations between phenotypes and gene expression. Using these approaches, we prioritize TNFAIP3, CEBPD, METRNL and TLN2 as new candidate genes whose differential expression might modulate cIMT.
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Affiliation(s)
- Andy B Castaneda
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Lauren E Petty
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany.,LIFE Research Center of Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Rick Jansen
- Department of Psychiatry, VU University Medical Center, Amsterdam, the Netherlands
| | - Stefan Weiss
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany.,DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
| | - Xiaoling Zhang
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA.,Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA.,The Framingham Heart Study, Framingham, MA, USA
| | - Katharina Schramm
- Institute of Neurogenomics, Helmholz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Human Genetics, Technical University Munich, Munich, Germany
| | | | - Holger Kirsten
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany.,LIFE Research Center of Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Ulf Schminke
- Department of Neurology, University Medicine Greifswald, Greifswald, Germany
| | - Shih-Jen Hwang
- The Framingham Heart Study, Framingham, MA, USA.,Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD, USA
| | - Carola Marzi
- Institute of Epidemiology, Helmholz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.,German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Klodian Dhana
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands.,Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Adrie Seldenrijk
- Department of Psychiatry, VU University Medical Center, Amsterdam, the Netherlands
| | - Knut Krohn
- Interdisciplinary Center of Clinical Research, University of Leipzig, Leipzig, Germany
| | - Georg Homuth
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Petra Wolf
- Institute of Neurogenomics, Helmholz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Human Genetics, Technical University Munich, Munich, Germany
| | - Marjolein J Peters
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Marcus Dörr
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany.,Department of Internal Medicine B, University Medicine Greifswald, Greifswald, Germany
| | - Annette Peters
- Institute of Epidemiology, Helmholz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Joyce B J van Meurs
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - André G Uitterlinden
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands.,Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Maryam Kavousi
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Daniel Levy
- The Framingham Heart Study, Framingham, MA, USA.,Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD, USA
| | - Christian Herder
- Institute of Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,German Center for Diabetes Research (DZD e.V.), München-Neuherberg, Germany.,Division of Endocrinology and Diabetology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | | | - Melanie Waldenberger
- Institute of Epidemiology, Helmholz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Christa Meisinger
- Institute of Epidemiology, Helmholz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.,Chair of Epidemiology, Ludwig-Maximilians-Universität München, UNIKA-T Augsburg, Augsburg, Germany
| | - Wolfgang Rathmann
- Institute of Biometrics and Epidemiology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Joachim Thiery
- LIFE Research Center of Civilization Diseases, University of Leipzig, Leipzig, Germany.,Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University of Leipzig, Leipzig, Germany
| | - Joseph Polak
- Tufts University School of Medicine, Boston, MA, USA
| | - Wolfgang Koenig
- Deutsches Herzzentrum München, Technische Universität München, Munich, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany.,Department of Internal Medicine II-Cardiology, University of Ulm Medical Center, Ulm, Germany
| | - Jochen Seissler
- Diabetes Center, Diabetes Research Group, Medizinische Klinik und Poliklinik IV, Ludwig-Maximilians-Universität, Munich, Germany
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Nora Franceshini
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | | | | | - Albert Hofman
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Oscar H Franco
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands.,Institute of Social and Preventive Medicine, University of Bern, Switzerland
| | - Brenda W J H Penninx
- Department of Psychiatry, VU University Medical Center, Amsterdam, the Netherlands
| | - Holger Prokisch
- Institute of Neurogenomics, Helmholz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Human Genetics, Technical University Munich, Munich, Germany
| | - Henry Völzke
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany.,Institute of Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Markus Loeffler
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany.,LIFE Research Center of Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Christopher J O'Donnell
- The Framingham Heart Study, Framingham, MA, USA.,Cardiology Section, Department of Medicine, Boston Veteran's Administration Healthcare and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jennifer E Below
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Abbas Dehghan
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands.,Department of Epidemiology and Biostatistics, Imperial College London, London, UK.,MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, Norfolk Place, London, UK.,UK Dementia Research Institute at Imperial College London, Burlington Danes Building, Hammersmith Hospital, Du Cane Road, London W12 0NN UK
| | - Paul S de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA.,Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
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10
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Vibrational spectroscopic approaches for semen analysis in forensic investigation: State of the art and way forward. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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11
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Developments in forensic DNA analysis. Emerg Top Life Sci 2021; 5:381-393. [PMID: 33792660 PMCID: PMC8457771 DOI: 10.1042/etls20200304] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 12/20/2022]
Abstract
The analysis of DNA from biological evidence recovered in the course of criminal investigations can provide very powerful evidence when a recovered profile matches one found on a DNA database or generated from a suspect. However, when no profile match is found, when the amount of DNA in a sample is too low, or the DNA too degraded to be analysed, traditional STR profiling may be of limited value. The rapidly expanding field of forensic genetics has introduced various novel methodologies that enable the analysis of challenging forensic samples, and that can generate intelligence about the donor of a biological sample. This article reviews some of the most important recent advances in the field, including the application of massively parallel sequencing to the analysis of STRs and other marker types, advancements in DNA mixture interpretation, particularly the use of probabilistic genotyping methods, the profiling of different RNA types for the identification of body fluids, the interrogation of SNP markers for predicting forensically relevant phenotypes, epigenetics and the analysis of DNA methylation to determine tissue type and estimate age, and the emerging field of forensic genetic genealogy. A key challenge will be for researchers to consider carefully how these innovations can be implemented into forensic practice to ensure their potential benefits are maximised.
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12
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Forensic blood stain aging using reverse transcription real-time PCR. FORENSIC SCIENCE INTERNATIONAL: REPORTS 2021. [DOI: 10.1016/j.fsir.2021.100205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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13
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Bamberg M, Dierig L, Kulstein G, Kunz SN, Schmidt M, Hadrys T, Wiegand P. Development and validation of an mRNA-based multiplex body fluid identification workflow and a rectal mucosa marker pilot study. Forensic Sci Int Genet 2021; 54:102542. [PMID: 34098418 DOI: 10.1016/j.fsigen.2021.102542] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/24/2021] [Accepted: 05/26/2021] [Indexed: 01/26/2023]
Abstract
Molecular identification of body fluids and tissues is crucial in order to understand the circumstances of crimes. For that reason, molecular investigations used to identify body fluids/tissues have increasingly been examined recently. Various studies have proved that messenger RNA (mRNA) profiling is a sensitive and robust method for body fluid/tissue identification. The forensically relevant body fluids/tissues blood, semen, saliva, vaginal secretion, menstrual blood and skin have all been detected successfully by applying suitable mRNA assay. However, rectal mucosa, which can be found as evidence in sexual assault cases, has been neglected in forensic investigations. So far there is no mRNA marker to detect rectal mucosa, although anal penetration occurs in a large number of sexual assaults (23.2% of female victims and 50% of male victims). In this study, specific and sensitive mRNA markers for forensically relevant body fluids were adapted and validated in an mRNA multiplex assay for routine casework. This included the implementation of a DNA/RNA re-extraction method for automated extraction that can be integrated into casework without loss of DNA. This re-extraction method and the mRNA multiplex assay were tested using casework samples. PCR-primers were designed for the identification of rectal mucosa and the more effective marker MUC12 was integrated into an extended multiplex assay. The result of our study is a highly specific and sensitive mRNA multiplex assay plus an automated DNA/RNA re-extraction method, that can be integrated into casework and identify rectal mucosa for the first time.
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Affiliation(s)
- Malte Bamberg
- Institute of Legal Medicine, University Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany.
| | - Lisa Dierig
- Institute of Legal Medicine, University Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | | | - Sebastian N Kunz
- Institute of Legal Medicine, University Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Max Schmidt
- Institute of Legal Medicine, University Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Thorsten Hadrys
- Bavarian State Criminal Police Office, Institute of Forensic Sciences, DNA Department, Maillingerstr. 15, 80636 Munich, Germany
| | - Peter Wiegand
- Institute of Legal Medicine, University Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
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14
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Lam S, Kommadath A, López-Campos Ó, Prieto N, Aalhus J, Juárez M, Dugan MER, Vahmani P. Evaluation of RNA quality and functional transcriptome of beef longissimus thoracis over time post-mortem. PLoS One 2021; 16:e0251868. [PMID: 34033656 PMCID: PMC8148330 DOI: 10.1371/journal.pone.0251868] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 05/04/2021] [Indexed: 11/19/2022] Open
Abstract
Evaluating RNA quality and transcriptomic profile of beef muscle over time post-mortem may provide insight into RNA degradation and underlying biological and functional mechanisms that accompany biochemical changes occurring post-mortem during transformation of muscle to meat. RNA was extracted from longissimus thoracis (LT) sampled from British Continental crossbred heifer carcasses (n = 7) stored at 4°C in an abattoir drip cooler at 5 time points post-mortem, i.e., 45 min (0 h), 6 h, 24 h, 48 h, and 72 h. Following RNA-Sequencing, processed reads were aligned to the ARS-UCD1.2 bovine genome assembly. Subsequent differential expression (DE) analysis identified from 51 to 1434 upregulated and 27 to 2256 downregulated DE genes at individual time points compared to time 0 h, showing a trend for increasing counts of both upregulated and downregulated genes over time. Gene ontology and biological pathway term enrichment analyses on sets of DE genes revealed several processes and their timelines of activation/deactivation that accompanied or were involved with muscle transformation to meat. Although the quality of RNA in refrigerated LT remained high for several days post-mortem, the expression levels of several known biomarker genes for meat quality began to change from 24 h onwards. Therefore, to ensure accuracy of predictions on meat quality traits based on the expression levels of those biomarker genes in refrigerated beef muscle tissue, it is crucial that those expression measurements be made on RNA sampled within 24 h post-mortem. The present study also highlighted the need for more research on the roles of mitochondrial genes and non-coding genes in orchestrating muscle tissue processes after death, and how pre-mortem immune status might influence post-mortem meat quality.
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Affiliation(s)
- Stephanie Lam
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, Alberta, Canada
| | - Arun Kommadath
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, Alberta, Canada
| | - Óscar López-Campos
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, Alberta, Canada
| | - Nuria Prieto
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, Alberta, Canada
| | - Jennifer Aalhus
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, Alberta, Canada
| | - Manuel Juárez
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, Alberta, Canada
| | - Michael E. R. Dugan
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, Alberta, Canada
| | - Payam Vahmani
- Department of Animal Science, University of California Davis, Davis, California, United States of America
- * E-mail:
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15
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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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16
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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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17
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Zolotarenko AD, Chekalin EV, Bruskin SA. Modern Molecular Genetic Methods for Age Estimation in Forensics. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795419120147] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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18
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Glynn CL. Potential applications of microRNA profiling to forensic investigations. RNA (NEW YORK, N.Y.) 2020; 26:1-9. [PMID: 31658993 PMCID: PMC6913128 DOI: 10.1261/rna.072173.119] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Within the forensic science community, there is a continued push to develop novel tools to aid in criminal investigations. microRNA (miRNA) analysis has been the focus of many researcher's attention in the biomedical field since its discovery in 1993; however, the forensic application of miRNA analysis has only been suggested within the last 10 years and has been gaining considerable traction recently. The primary focus of the forensic application of miRNA analysis has been on body fluid identification to provide confirmatory universal analysis of unknown biological stains obtained from crime scenes or evidence items. There are, however, other forensic applications of miRNA profiling that have shown potential, yet are largely understudied, and warrant further investigation such as organ tissue identification, donor age estimation, and more. This review paper aims to evaluate the current literature and future potential of miRNA analysis within the forensic science field.
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Affiliation(s)
- Claire L Glynn
- Department of Forensic Science, Henry C. Lee College of Criminal Justice and Forensic Sciences, University of New Haven, West Haven, Connecticut 06516, USA
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19
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González-Herrera L, Márquez-Ruiz AB, Serrano MJ, Ramos V, Lorente JA, Valenzuela A. mRNA expression patterns in human myocardial tissue, pericardial fluid and blood, and its contribution to the diagnosis of cause of death. Forensic Sci Int 2019; 302:109876. [PMID: 31419595 DOI: 10.1016/j.forsciint.2019.109876] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 06/11/2019] [Accepted: 07/20/2019] [Indexed: 11/18/2022]
Abstract
Gene expression has become an interesting research area in forensic pathology to investigate the process of death at the molecular level. The aims of this study were to analyze changes in gene expression patterns in relation to the cause of death, and to propose new molecular markers of myocardial ischemia of potential use for the postmortem diagnosis of early ischemic heart damage in cases of sudden cardiac death (SCD). We determined mRNA levels of five proteins related with ischemic myocardial damage and repair - TNNI3, MYL3, TGFB1, MMP9 and VEGFA - in specific sites of the myocardium, blood and pericardial fluid in samples from 30 cadavers with different causes of death (SCD, multiple trauma, mechanical asphyxia, and other natural deaths). TNNI3 expression in blood, and MMP9 expression in pericardial fluid, were significantly higher when the cause of death was mechanical asphyxia, probably because of the more sensitive response of these proteins to acute systemic hypoxia/ischemia. Specifically, among SCD cases, increased MYL3, VEGFA and MMP9 values in the anterior wall of the right ventricle were found when the confirmed cause of death was acute myocardial infarction (AMI). Higher TGFB1 expression was found in the interventricular septum when AMI was not the cause of death, most likely as a reflection of the short duration of ischemia. Molecular biology techniques can provide complementary tools for the forensic diagnosis of early ischemic myocardial damage and AMI, and may make it possible to determine the duration and severity of myocardial ischemia.
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Affiliation(s)
- Lucas González-Herrera
- Department of Forensic Medicine, Faculty of Medicine, University of Granada, Avenida de la Investigación 11, 18016 Granada, Spain.
| | - Ana Belén Márquez-Ruiz
- Department of Forensic Medicine, Faculty of Medicine, University of Granada, Avenida de la Investigación 11, 18016 Granada, Spain
| | - María José Serrano
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, Avenida de la Ilustración 114, 18016 Granada, Spain
| | - Valentín Ramos
- Forensic Pathology Service, Legal Medicine Institute of Malaga, C./Fiscal Luís Portero García 6, 29010 Málaga, Spain
| | - José Antonio Lorente
- Department of Forensic Medicine, Faculty of Medicine, University of Granada, Avenida de la Investigación 11, 18016 Granada, Spain
| | - Aurora Valenzuela
- Department of Forensic Medicine, Faculty of Medicine, University of Granada, Avenida de la Investigación 11, 18016 Granada, Spain
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20
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Analysis of RNA in the estimation of post-mortem interval: a review of current evidence. Int J Legal Med 2019; 133:1629-1640. [DOI: 10.1007/s00414-019-02125-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 07/10/2019] [Indexed: 10/26/2022]
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21
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Estimating time since deposition using quantification of RNA degradation in body fluid-specific markers. Forensic Sci Int 2019; 298:58-63. [DOI: 10.1016/j.forsciint.2019.02.046] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 02/22/2019] [Accepted: 02/23/2019] [Indexed: 02/03/2023]
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22
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Mayes C, Houston R, Seashols-Williams S, LaRue B, Hughes-Stamm S. The stability and persistence of blood and semen mRNA and miRNA targets for body fluid identification in environmentally challenged and laundered samples. Leg Med (Tokyo) 2019; 38:45-50. [PMID: 30959396 DOI: 10.1016/j.legalmed.2019.03.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 03/25/2019] [Accepted: 03/28/2019] [Indexed: 01/27/2023]
Abstract
The identification of body fluids in evidentiary stains may provide investigators with probative information during an investigation. In this study, quantitative reverse transcription polymerase chain reaction (RT-qPCR) assays were performed to detect the presence of mRNA and miRNA in fresh and environmentally challenged samples. Blood, semen, and reference markers were chosen for both mRNA/miRNA testing. Samples of blood and semen were exposed to heat, humidity, and sunlight, and controlled conditions (room temperature, low humidity, and darkness) for 6 months. All mRNA targets were observed through six months under controlled conditions, but were undetected after 30 days in experimental conditions. However, miRNA targets persisted under all test conditions for the duration of the study. Additionally, cotton stained with blood or semen was laundered using a liquid detergent in various washing and drying conditions. An unstained cutting was evaluated for potential transfer. Both miRNA targets were observed in all stained samples regardless of the wash protocol used. Of the mRNA markers, HBB was detected in all bloodstained samples and PRM1 persisted in all but one semen stained sample. The unstained samples showed transfer of at least one body fluid specific miRNA marker in all samples and at least one body fluid specific mRNA in approximately half of the samples. These results support that RNA markers can be used for body fluid identification in challenging samples, and that miRNA markers may be more persistent than mRNA for blood and semen stains. However, some caution is warranted with laundered items due to possible transfer.
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Affiliation(s)
- Carrie Mayes
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, 1003 Bowers Blvd., Huntsville, TX 77340-2525, United States.
| | - Rachel Houston
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, 1003 Bowers Blvd., Huntsville, TX 77340-2525, United States
| | - Sarah Seashols-Williams
- Department of Forensic Science, Virginia Commonwealth University, Box 843079, Richmond, VA 23284, United States
| | - Bobby LaRue
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, 1003 Bowers Blvd., Huntsville, TX 77340-2525, United States
| | - Sheree Hughes-Stamm
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, 1003 Bowers Blvd., Huntsville, TX 77340-2525, United States; School of Biomedical Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
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23
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Fang C, Zhao J, Li J, Qian J, Liu X, Sun Q, Liu W, Tian Y, Ji A, Wu H, Yan J. Massively parallel sequencing of microRNA in bloodstains and evaluation of environmental influences on miRNA candidates using realtime polymerase chain reaction. Forensic Sci Int Genet 2018; 38:32-38. [PMID: 30321749 DOI: 10.1016/j.fsigen.2018.10.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 06/30/2018] [Accepted: 10/01/2018] [Indexed: 12/21/2022]
Abstract
MicroRNAs (miRNA) are small (22-24 nucleotides) non-coding RNAs with potential application in forensic science because of their anti-degradation property and tissue specificity. Recent studies on the use of miRNA in forensic applications have mainly focused on body fluid identification using realtime polymerase chain reaction or microarray analysis. However, the exploration of miRNA in bloodstains, which are the most valuable source of biological evidence during case investigations, is currently lacking, particularly for aged and environmentally compromised forensic samples. Recent developments in massively parallel sequencing (MPS) technology provide the opportunity to establish a whole-genome miRNA profile with high throughput and efficiency. However, MPS analysis of genome-wide miRNA profiles from bloodstains has not been reported to date. In this study, the whole-genome miRNA profiles of bloodstains were examined using MPS, revealing 633 known miRNAs and 266 novel miRNAs. To further explore the stability of miRNAs in bloodstains under various circumstances, the expression levels of six miRNAs (miR-16-5p, miR-20a-5p, miR-486-5p, miR-148a-3p, miR-151a-3p, and miR-451a) that were abundant in blood/bloodstains were examined. The results showed that freezing/thawing and a high concentration of oxidant solution affects the absolute expression of miRNA significantly, while storage for up to 5 months and a temperature of 37 °C did not have any observed effects. This study not only provides a novel method to explore miRNA profiles in bloodstains using MPS, but also points to the circumstantial influences on miRNA expression, which are an important consideration for practical application. Collectively, our work may shed light on MPS-based approaches with miRNA analysis of bloodstains in forensics.
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Affiliation(s)
- Chen Fang
- Beijing Center for Physical and Chemical Analysis, Beijing 100094, PR China; Beijing Engineering Technology Research Centre of Gene Sequencing and Gene Function Analysis, Beijing 100094, PR China
| | - Jing Zhao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100010, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Junbo Li
- Beijing Center for Physical and Chemical Analysis, Beijing 100094, PR China; Beijing Engineering Technology Research Centre of Gene Sequencing and Gene Function Analysis, Beijing 100094, PR China
| | - Jialin Qian
- Beijing Center for Physical and Chemical Analysis, Beijing 100094, PR China; Beijing Engineering Technology Research Centre of Gene Sequencing and Gene Function Analysis, Beijing 100094, PR China
| | - Xu Liu
- Beijing Center for Physical and Chemical Analysis, Beijing 100094, PR China; Beijing Engineering Technology Research Centre of Gene Sequencing and Gene Function Analysis, Beijing 100094, PR China
| | - Qifan Sun
- National Engineering Laboratory for Forensic Science and MPS Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, PR China
| | - Wenli Liu
- Beijing Center for Physical and Chemical Analysis, Beijing 100094, PR China; Beijing Engineering Technology Research Centre of Gene Sequencing and Gene Function Analysis, Beijing 100094, PR China
| | - Yanjie Tian
- Beijing Center for Physical and Chemical Analysis, Beijing 100094, PR China; Beijing Engineering Technology Research Centre of Gene Sequencing and Gene Function Analysis, Beijing 100094, PR China
| | - Anquan Ji
- National Engineering Laboratory for Forensic Science and MPS Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, PR China
| | - Huijuan Wu
- Beijing Center for Physical and Chemical Analysis, Beijing 100094, PR China; Beijing Engineering Technology Research Centre of Gene Sequencing and Gene Function Analysis, Beijing 100094, PR China.
| | - Jiangwei Yan
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100010, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China; School of Forensic Medicine, Shanxi Medical University, Taiyuan 030001, PR China.
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24
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Kowalczyk M, Zawadzka E, Szewczuk D, Gryzińska M, Jakubczak A. Molecular markers used in forensic genetics. MEDICINE, SCIENCE, AND THE LAW 2018; 58:201-209. [PMID: 30269675 DOI: 10.1177/0025802418803852] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Forensic genetics is a field that has become subject to increasing interest in recent years. Both the technology and the markers used for forensic purposes have changed since the 1980s. The minisatellite sequences used in the famous Pitchfork case introduced genetics to the forensic sciences. Minisatellite sequences have now been replaced by more sensitive microsatellite markers, which have become the basis for the creation of genetic profile databases. Modern molecular methods also exploit single nucleotide polymorphisms, which are often the only way to identify degraded DNA samples. The same type of variation is taken into consideration in attempting to establish the ethnicity of a perpetrator and to determine phenotypic traits such as the eye or hair colour of the individual who is the source of the genetic material. This paper contains a review of the techniques and molecular markers used in human and animal forensic genetics, and also presents the potential trends in forensic genetics such as phenotyping.
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Affiliation(s)
- Marek Kowalczyk
- 1 Department of Biological Basis of Animal Production, Faculty of Biology, Animal Sciences and Bioeconomy, University of Life Sciences in Lublin, Poland
| | - Ewelina Zawadzka
- 1 Department of Biological Basis of Animal Production, Faculty of Biology, Animal Sciences and Bioeconomy, University of Life Sciences in Lublin, Poland
| | | | - Magdalena Gryzińska
- 1 Department of Biological Basis of Animal Production, Faculty of Biology, Animal Sciences and Bioeconomy, University of Life Sciences in Lublin, Poland
| | - Andrzej Jakubczak
- 1 Department of Biological Basis of Animal Production, Faculty of Biology, Animal Sciences and Bioeconomy, University of Life Sciences in Lublin, Poland
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25
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Kulstein G, Schacker U, Wiegand P. Old meets new: Comparative examination of conventional and innovative RNA-based methods for body fluid identification of laundered seminal fluid stains after modular extraction of DNA and RNA. Forensic Sci Int Genet 2018; 36:130-140. [DOI: 10.1016/j.fsigen.2018.06.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 06/05/2018] [Accepted: 06/26/2018] [Indexed: 10/28/2022]
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26
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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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27
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Shen Y, Li R, Tian F, Chen Z, Lu N, Bai Y, Ge Q, Lu Z. Impact of RNA integrity and blood sample storage conditions on the gene expression analysis. Onco Targets Ther 2018; 11:3573-3581. [PMID: 29950862 PMCID: PMC6016255 DOI: 10.2147/ott.s158868] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background The reliability of RNA sequencing (RNA-seq) output is affected by the quality of RNAs, which is in turn dependent on the quality of samples. Therefore, the purposes of this study were to reconsider the threshold of the RNA integrity number (RIN) and propose a simple and efficient storage scheme of blood samples for RNA-seq. Patients and methods The RNAs were extracted from blood samples that were stored at different conditions and used for sequencing. The bioinformatic analyses were performed to evaluate the impact of RNA integrity and blood sample storage conditions on the gene expression analysis. Results Our outcomes showed that the samples with RIN values more than 5.3 scarcely affected the quantitative results of RNA-seq, and the influence of inherent cellular physiological processes on RNA-seq output could be negligible. Conclusion The blood samples stored at 4°C within 7 days with RIN values more than 5.3 were available for RNA-seq.
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Affiliation(s)
- Yanting Shen
- School of Biomedical Engineering, Southeast University, Nanjing 210096, Jiangsu Province, People's Republic of China.,State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, Jiangsu Province, People's Republic of China
| | - Rui Li
- School of Biomedical Engineering, Southeast University, Nanjing 210096, Jiangsu Province, People's Republic of China
| | - Fei Tian
- School of Biomedical Engineering, Southeast University, Nanjing 210096, Jiangsu Province, People's Republic of China
| | - Zhenzhu Chen
- School of Biomedical Engineering, Southeast University, Nanjing 210096, Jiangsu Province, People's Republic of China
| | - Na Lu
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, Jiangsu Province, People's Republic of China
| | - Yunfei Bai
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, Jiangsu Province, People's Republic of China
| | - Qinyu Ge
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, Jiangsu Province, People's Republic of China
| | - Zuhong Lu
- School of Biomedical Engineering, Southeast University, Nanjing 210096, Jiangsu Province, People's Republic of China.,State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, Jiangsu Province, People's Republic of China
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28
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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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Mayes C, Seashols-Williams S, Hughes-Stamm S. A capillary electrophoresis method for identifying forensically relevant body fluids using miRNAs. Leg Med (Tokyo) 2017; 30:1-4. [PMID: 29125963 DOI: 10.1016/j.legalmed.2017.10.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 10/25/2017] [Accepted: 10/30/2017] [Indexed: 12/20/2022]
Abstract
Body fluid identification (BFID) can provide crucial information during the course of an investigation. In recent years, microRNAs (miRNAs) have shown considerable body fluid specificity, are able to be co-extracted with DNA, and their small size (18-25 nucleotides) make them ideal for analyzing highly degraded forensic samples. In this study, we designed a preliminary 8-marker system for BFID including an endogenous reference gene (let-7g) to differentiate between venous blood (miR-451a and miR-142-3p), menstrual blood (miR-141-3p and miR-412-3p), semen (miR-891a and miR-10b), and saliva (miR-205) using a capillary electrophoresis approach. This panel uses a linear primer system in order to incorporate additional miRNA markers by forming a multiplex system. The miRNA system was able to distinguish between venous blood, menstrual blood, semen, and saliva using a rudimentary data interpretation strategy. All STR amplifications from co-extracted DNA yielded complete profiles from human identification purposes.
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Affiliation(s)
- Carrie Mayes
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, 1003 Bowers Blvd., Huntsville, TX 77340-2525, United States.
| | - Sarah Seashols-Williams
- Department of Forensic Science, Virginia Commonwealth University, Box 843079, Richmond, VA 23284, United States
| | - Sheree Hughes-Stamm
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, 1003 Bowers Blvd., Huntsville, TX 77340-2525, United States
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30
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Bavykin AS. Circulating microRNAs in the identification of biological fluids: A new approach to standardization of expression-based diagnostics. Mol Biol 2017. [DOI: 10.1134/s0026893317040045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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31
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Born JPL, Matos HDC, de Araujo MA, Castro OW, Duzzioni M, Peixoto-Santos JE, Leite JP, Garcia-Cairasco N, Paçó-Larson ML, Gitaí DLG. Using Postmortem hippocampi tissue can interfere with differential gene expression analysis of the epileptogenic process. PLoS One 2017; 12:e0182765. [PMID: 28783762 PMCID: PMC5544225 DOI: 10.1371/journal.pone.0182765] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 07/24/2017] [Indexed: 12/21/2022] Open
Abstract
Neuropathological studies often use autopsy brain tissue as controls to evaluate changes in protein or RNA levels in several diseases. In mesial temporal lobe epilepsy (MTLE), several genes are up or down regulated throughout the epileptogenic and chronic stages of the disease. Given that postmortem changes in several gene transcripts could impact the detection of changes in case-control studies, we evaluated the effect of using autopsy specimens with different postmortem intervals (PMI) on differential gene expression of the Pilocarpine (PILO)induced Status Epilepticus (SE) of MTLE. For this, we selected six genes (Gfap, Ppia, Gad65, Gad67, Npy, and Tnf-α) whose expression patterns in the hippocampus of PILO-injected rats are well known. Initially, we compared hippocampal expression of naïve rats whose hippocampi were harvested immediately after death (0h-PMI) with those harvested at 6h postmortem interval (6h-PMI): Npy and Ppia transcripts increased and Tnf-α transcripts decreased in the 6h-PMI group (p<0.05). We then investigated if these PMI-related changes in gene expression have the potential to adulterate or mask RT-qPCR results obtained with PILO-injected rats euthanized at acute or chronic phases. In the acute group, Npy transcript was significantly higher when compared with 0h-PMI rats, whereas Ppia transcript was lower than 6h-PMI group. When we used epileptic rats (chronic group), the RT-qPCR results showed higher Tnf-α only when compared to 6h-PMI group. In conclusion, our study demonstrates that PMI influences gene transcription and can mask changes in gene transcription seen during epileptogenesis in the PILO-SE model. Thus, to avoid erroneous conclusions, we strongly recommend that researchers account for changes in postmortem gene expression in their experimental design.
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Affiliation(s)
- João Paulo Lopes Born
- Department of Cellular and Molecular Biology, Institute of Biological Sciences and Health, Federal University of Alagoas, Maceio, Alagoas, Brazil
| | - Heloisa de Carvalho Matos
- Department of Cellular and Molecular Biology, Institute of Biological Sciences and Health, Federal University of Alagoas, Maceio, Alagoas, Brazil
| | - Mykaella Andrade de Araujo
- Department of Cellular and Molecular Biology, Institute of Biological Sciences and Health, Federal University of Alagoas, Maceio, Alagoas, Brazil
| | - Olagide Wagner Castro
- Department of Physiology and Pharmacology, Institute of Biological Sciences and Health, Federal University of Alagoas, Maceio, Alagoas, Brazil
| | - Marcelo Duzzioni
- Department of Physiology and Pharmacology, Institute of Biological Sciences and Health, Federal University of Alagoas, Maceio, Alagoas, Brazil
| | - José Eduardo Peixoto-Santos
- Division of Neurology, Department of Neurosciences and Behavioral Sciences, Ribeirão Preto School of Medicine, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - João Pereira Leite
- Division of Neurology, Department of Neurosciences and Behavioral Sciences, Ribeirão Preto School of Medicine, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Norberto Garcia-Cairasco
- Department of Physiology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Maria Luisa Paçó-Larson
- Department of Cellular and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Daniel Leite Góes Gitaí
- Department of Cellular and Molecular Biology, Institute of Biological Sciences and Health, Federal University of Alagoas, Maceio, Alagoas, Brazil
- * E-mail:
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32
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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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33
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Ferrara SD, Cecchetto G, Cecchi R, Favretto D, Grabherr S, Ishikawa T, Kondo T, Montisci M, Pfeiffer H, Bonati MR, Shokry D, Vennemann M, Bajanowski T. Back to the Future - Part 2. Post-mortem assessment and evolutionary role of the bio-medicolegal sciences. Int J Legal Med 2017; 131:1085-1101. [PMID: 28444439 DOI: 10.1007/s00414-017-1585-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 03/29/2017] [Indexed: 02/06/2023]
Abstract
Part 2 of the review "Back to the Future" is dedicated to the evolutionary role of the bio-medicolegal sciences, reporting the historical profiles, the state of the art, and prospects for future development of the main related techniques and methods of the ancillary disciplines that have risen to the role of "autonomous" sciences, namely, Genetics and Genomics, Toxicology, Radiology, and Imaging, involved in historic synergy in the "post-mortem assessment," together with the mother discipline Legal Medicine, by way of its primary fundament, universally denominated as Forensic Pathology. The evolution of the scientific research and the increased accuracy of the various disciplines will be oriented towards the elaboration of an "algorithm," able to weigh the value of "evidence" placed at the disposal of the "justice system" as real truth and proof.
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Affiliation(s)
- Santo Davide Ferrara
- Department of Legal and Occupational Medicine, Toxicology and Public Health, University-Hospital of Padova, Padua, Italy.
| | - Giovanni Cecchetto
- Department of Legal and Occupational Medicine, Toxicology and Public Health, University-Hospital of Padova, Padua, Italy
| | - Rossana Cecchi
- Department of Biomedical, Biotechnological and Translational Medicine, University of Parma, Parma, Italy
| | - Donata Favretto
- Department of Legal and Occupational Medicine, Toxicology and Public Health, University-Hospital of Padova, Padua, Italy
| | - Silke Grabherr
- University Center of Legal Medicine Lausanne-Geneva, University of Lausanne, Lausanne, Switzerland
| | - Takaki Ishikawa
- Department of Legal Medicine, Osaka City University Medical School, Osaka, Japan
| | - Toshikazu Kondo
- Department of Forensic Medicine, Wakayama Medical University, Wakayama, Japan
| | - Massimo Montisci
- Department of Legal and Occupational Medicine, Toxicology and Public Health, University-Hospital of Padova, Padua, Italy
| | - Heidi Pfeiffer
- Institute of Legal Medicine, University-Hospital Münster, Münster, Germany
| | - Maurizio Rippa Bonati
- Department of Cardiac, Thoracic and Vascular Sciences, Section of Medical Humanities, University of Padova, Padua, Italy
| | - Dina Shokry
- Department of Forensic Medicine and Clinical Toxicology, University of Cairo, Cairo, Egypt
| | - Marielle Vennemann
- Institute of Legal Medicine, University-Hospital Münster, Münster, Germany
| | - Thomas Bajanowski
- Institute of Legal Medicine, University-Hospital Essen, Essen, Germany
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De Vittori E, Barni F, Lewis SW, Antonini G, Rapone C, Berti A. Forensic application of a rapid one-step tetramethylbenzidine-based test for the presumptive trace detection of bloodstains at the crime scene and in the laboratory. Forensic Chem 2016. [DOI: 10.1016/j.forc.2016.10.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Characterization of gene expression profiling of mouse tissues obtained during the postmortem interval. Exp Mol Pathol 2016; 100:482-92. [PMID: 27185020 DOI: 10.1016/j.yexmp.2016.05.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 05/13/2016] [Indexed: 12/27/2022]
Abstract
Attempts to establish a tissue bank from autopsy samples have led to uncovering of the secrets of many diseases. Here, we examined the length of time that the RNA from postmortem tissues is available for microarray analysis and reported the gene expression profile for up- and down-regulated genes during the postmortem interval. We extracted RNA from fresh-frozen (FF) and formalin-fixed paraffin-embedded (FFPE) brains and livers of three different groups of mice: 1) mice immediately after death, 2) mice that were stored at room temperature for 3h after death, and 3) mice that were stored at 4°C for 18h after death, as this storage resembles the human autopsy process in Japan. The RNA quality of the brain and the liver was maintained up to 18h during the postmortem interval. Based on the microarray analysis, we selected genes that were altered by >1.3-fold or <0.77-fold and classified these genes using hierarchical cluster analysis following DAVID gene ontology analysis. These studies revealed that cytoskeleton-related genes were enriched in the set of up-regulated genes, while serine protease inhibitors were enriched in the set of down-regulated genes. Interestingly, although the RNA quality was maintained due to high RNA integrity number (RIN) values, up-regulated genes were not validated by quantitative PCR, suggesting that these genes may become fragmented or modified by an unknown mechanism. Taken together, our findings suggest that under typical autopsy conditions, gene expression profiles that reflect disease pathology can be examined by understanding comprehensive recognition of postmortem fluctuation of gene expression.
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Castelló A, Francès F, Verdú F. The effectiveness of the RSID confirmatory test kit for human alpha amylase: the effects of environmental factors and substrate materials. AUST J FORENSIC SCI 2016. [DOI: 10.1080/00450618.2016.1153147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Ana Castelló
- Legal Medicine, University of Valencia, Valencia, Spain
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37
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Exploration of the R code-based mathematical model for PMI estimation using profiling of RNA degradation in rat brain tissue at different temperatures. Forensic Sci Med Pathol 2015; 11:530-7. [PMID: 26363634 DOI: 10.1007/s12024-015-9703-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/29/2015] [Indexed: 10/23/2022]
Abstract
Precise estimation of postmortem interval (PMI) is crucial in some criminal cases. This study aims to find some optimal markers for PMI estimation and build a mathematical model that could be used in various temperature conditions. Different mRNA and microRNA markers in rat brain samples were detected using real-time fluorescent quantitative PCR at 12 time points within 144 h postmortem and at temperatures of 4, 15, 25, and 35 °C. Samples from 36 other rats were used to verify the animal mathematical model. Brain-specific mir-9 and mir-125b are effective endogenous control markers that are not affected by PMI up to 144 h postmortem under these temperatures, whereas the commonly used U6 is not a suitable endogenous control in this study. Among all the candidate markers, ΔCt (β-actin) has the best correlation coefficient with PMI and was used to build a new model using R software which can simultaneously manage both PMI and temperature parameters. This animal mathematical model is verified using samples from 36 other rats and shows increased accuracy for higher temperatures and longer PMI. In this study, β-actin was found to be an optimal marker to estimate PMI and some other markers were found to be suitable to act as endogenous controls. Additionally, we have used R code software to build a model of PMI estimation that could be used in various temperature conditions.
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39
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Zhao D, Michiue T, Maeda H. Tissue-dependent VEGF and GLUT1 induction in a rat hemorrhage model: With regard to diagnostic application of mRNA quantification in forensic pathology. Forensic Sci Int 2015; 255:118-22. [PMID: 26372538 DOI: 10.1016/j.forsciint.2015.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 06/03/2015] [Accepted: 08/11/2015] [Indexed: 10/23/2022]
Abstract
Systemic hypoxia is inevitably involved in the death process to a varying extent. Hypoxia-response factors proved useful in forensic pathology in previous studies; however, fundamental investigations using animal models are expected to reinforce the findings from autopsy practice. An animal experiment using a rat model of fixed-volume hemorrhage was performed to apply basic insight into quantitative mRNA analyses in forensic pathology. Male Sprague-Dawley rats (n=5) were anesthetized, bled from the femoral artery (24ml/kg; about 30% of total circulating blood volume), and decapitated after 1 or 2h. Tissue samples of the heart, brain (hippocampus), kidney, liver, lung and skeletal muscle were collected for RNA and protein analyses. Quantitative analyses of VEGF, GLUT1 and GAPDH mRNAs were performed with TaqMan real-time RT-PCR assay. In the sham control without bleeding, mRNA quantification revealed the tissue-dependent mRNA levels in physiological condition. Relative quantification of VEGF and GLUT1 showed significant inductions under hemorrhage at the mRNA level, using GAPDH as endogenous reference. In conclusion, tissue-dependent induction patterns of VEGF and GLUT1 were revealed in the volume-fixed hemorrhage rat model. This study could practically guide the selection of mRNA markers and tissue samples in forensic pathology related to tissue ischemia and cellular hypoxia for autopsy cases.
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Affiliation(s)
- Dong Zhao
- Collaborative Innovation Center of Judicial Civilization, Key Laboratory of Evidence Science, China University of Political Science and Law, Ministry of Education, Beijing 100088, China; Department of Legal Medicine, Osaka City University Medical School, Osaka 545-8585, Japan.
| | - Tomomi Michiue
- Department of Legal Medicine, Osaka City University Medical School, Osaka 545-8585, Japan
| | - Hitoshi Maeda
- Department of Legal Medicine, Osaka City University Medical School, Osaka 545-8585, Japan
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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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Valls Trepat E, Castelló A. More about RSID-saliva: the effect of sample age and the environment on the test’s efficacy. AUST J FORENSIC SCI 2015. [DOI: 10.1080/00450618.2014.992473] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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42
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Donfack J, Wiley A. Mass spectrometry-based cDNA profiling as a potential tool for human body fluid identification. Forensic Sci Int Genet 2015; 16:112-120. [PMID: 25594487 DOI: 10.1016/j.fsigen.2014.12.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 12/18/2014] [Accepted: 12/22/2014] [Indexed: 10/24/2022]
Abstract
Several mRNA markers have been exhaustively evaluated for the identification of human venous blood, saliva, and semen in forensic genetics. As new candidate human body fluid specific markers are discovered, evaluated, and reported in the scientific literature, there is an increasing trend toward determining the ideal markers for cDNA profiling of body fluids of forensic interest. However, it has not been determined which molecular genetics-based technique(s) should be utilized to assess the performance of these markers. In recent years, only a few confirmatory, mRNA/cDNA-based methods have been evaluated for applications in body fluid identification. The most frequently described methods tested to date include quantitative polymerase chain reaction (qPCR) and capillary electrophoresis (CE). However these methods, in particular qPCR, often favor narrow multiplex PCR due to the availability of a limited number of fluorescent dyes/tags. In an attempt to address this technological constraint, this study explored matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) for human body fluid identification via cDNA profiling of venous blood, saliva, and semen. Using cDNA samples at 20pg input phosphoglycerate kinase 1 (PGK1) amounts, body fluid specific markers for the candidate genes were amplified in their corresponding body fluid (i.e., venous blood, saliva, or semen) and absent in the remaining two (100% specificity). The results of this study provide an initial indication that MALDI-TOF MS is a potential fluorescent dye-free alternative method for body fluid identification in forensic casework. However, the inherent issues of low amounts of mRNA, and the damage caused to mRNA by environmental exposures, extraction processes, and storage conditions are important factors that significantly hinder the implementation of cDNA profiling into forensic casework.
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Affiliation(s)
- Joseph Donfack
- Counterterrorism and Forensic Science Research Unit, Federal Bureau of Investigation Laboratory Division, 2501 Investigation Parkway, Quantico, VA 22135, USA.
| | - Anissa Wiley
- Counterterrorism and Forensic Science Research Unit, Visiting Scientist Program, Federal Bureau of Investigation Laboratory Division, Quantico, VA 22135, USA
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Forensic miRNA: potential biomarker for body fluids? Forensic Sci Int Genet 2014; 14:1-10. [PMID: 25280377 DOI: 10.1016/j.fsigen.2014.09.002] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 08/06/2014] [Accepted: 09/01/2014] [Indexed: 12/13/2022]
Abstract
In forensic investigation, body fluids represent an important support to professionals when detected, collected and correctly identified. Through many years, various approaches were used, namely serology-based methodologies however, their lack of sensitivity and specificity became difficult to set aside. In order to sidetrack the problem, miRNA profiling surged with a real potential to be used to identify evidences like urine, blood, menstrual blood, saliva, semen and vaginal secretions. MiRNAs are small RNA structures with 20-25 nt whose proprieties makes them less prone to degradation processes when compared to mRNA which is extremely important once, in a crime scene, biological evidences might be exposed to several unfavorable environmental factors. Recently, published studies were able to identify some specific miRNAs, however their results were not always reproducible by others which can possibly be the reflection of different workflow strategies for their profiling studies. Given the current blast of interest in miRNAs, it is important to acknowledge potential limitations of miRNA profiling, yet, the lack of such studies are evident. This review pretends to gather all the information to date and assessed a multitude of factors that have a potential aptitude to discrediting miRNA profiling, such as: methodological approaches, environmental factors, physiological conditions, gender, pathologies and samples storage. It can be asserted that much has yet to be made, but we pretend to highlight a potential answer for the ultimate question: Can miRNA profiling be used as the forensic biomarker for body fluids identification?
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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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Sener MT, Karakus E, Halici Z, Akpinar E, Topcu A, Kok AN. Can early myocardial infarction-related deaths be diagnosed using postmortem urotensin receptor expression levels? Forensic Sci Med Pathol 2014; 10:395-400. [PMID: 24935436 DOI: 10.1007/s12024-014-9575-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2014] [Indexed: 11/30/2022]
Abstract
PURPOSE Myocardial infarction (MI) is one of the most prevalent causes of sudden adult death. It is difficult to diagnose early MI postmortem because there are no typical or characteristic changes in morphology. In this study, changes in the level of the mRNA for the urotensin receptor (UR) were investigated postmortem to determine the suitability of UR as a biomarker for diagnosis of early MI after death. METHODS An MI rat model was developed by injecting rats with isoproterenol (ISO) (lethal dose 850 mg/kg) or normal saline (control group). The hearts of rats in the control and ISO-induced MI groups were harvested at 0, 1, 3, 6, 12, 24, 48, and 72 h (h) postmortem. The hearts were then immediately submerged in 1 mL of RNA stabilization solution and stored at 4 °C for <1 week before RNA extraction. Relative UR expression analysis was performed using the StepOne Plus Real Time PCR System with cDNA synthesized from rat heart. RESULTS Postmortem UR mRNA expression was higher in the ISO-induced MI group than in the control group, at both 4 and 20 °C, at all of the time points examined except 72 h postmortem (p < 0.0001). The largest increases were observed at ambient temperature and 6 h postmortem. CONCLUSIONS Based on our findings, increased postmortem UR expression could serve as a biomarker to aid diagnosis of early MI.
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Affiliation(s)
- Mustafa Talip Sener
- Department of Forensic Medicine, Ataturk University School of Medicine, 25240, Erzurum, Turkey,
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46
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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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47
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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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48
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Exploring the recovery and detection of messenger RNA and DNA from enhanced fingermarks in blood. Sci Justice 2014; 54:192-8. [DOI: 10.1016/j.scijus.2014.01.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 12/23/2013] [Accepted: 01/22/2014] [Indexed: 11/19/2022]
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49
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Son GH, Park SH, Kim Y, Kim JY, Kim JW, Chung S, Kim YH, Kim H, Hwang JJ, Seo JS. Postmortem mRNA expression patterns in left ventricular myocardial tissues and their implications for forensic diagnosis of sudden cardiac death. Mol Cells 2014; 37:241-7. [PMID: 24642708 PMCID: PMC3969045 DOI: 10.14348/molcells.2014.2344] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 01/15/2014] [Accepted: 01/17/2014] [Indexed: 02/03/2023] Open
Abstract
Sudden cardiac death (SCD), which is primarily caused by lethal heart disorders resulting in structural and arrhythmogenic abnormalities, is one of the prevalent modes of death in most developed countries. Myocardial ischemia, mainly due to coronary artery disease, is the most common type of heart disease leading to SCD. However, postmortem diagnosis of SCD is frequently complicated by obscure histological evidence. Here, we show that certain mRNA species, namely those encoding hemoglobin A1/2 and B (Hba1/2 and Hbb, respectively) as well as pyruvate dehydrogenase kinase 4 (Pdk4), exhibit distinct postmortem expression patterns in the left ventricular free wall of SCD subjects when compared with their expression patterns in the corresponding tissues from control subjects with non-cardiac causes of death. Hba1/2 and Hbb mRNA expression levels were higher in ischemic SCD cases with acute myocardial infarction or ischemic heart disease without recent infarction, and even in cardiac death subjects without apparent pathological signs of heart injuries, than control subjects. By contrast, Pdk4 mRNA was expressed at lower levels in SCD subjects. In conclusion, we found that altered myocardial Hba1/2, Hbb, and Pdk4 mRNA expression patterns can be employed as molecular signatures of fatal cardiac dysfunction to forensically implicate SCD as the primary cause of death.
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Affiliation(s)
| | | | | | | | | | | | - Yu-Hoon Kim
- Division of Forensic Medicine, National Forensic Service, Seoul 158-707,
Korea
| | | | | | - Joong-Seok Seo
- Division of Forensic Medicine, National Forensic Service, Seoul 158-707,
Korea
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50
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Vidaki A, Daniel B, Court DS. Forensic DNA methylation profiling—Potential opportunities and challenges. Forensic Sci Int Genet 2013; 7:499-507. [DOI: 10.1016/j.fsigen.2013.05.004] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 05/14/2013] [Indexed: 11/26/2022]
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