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Gao N, Huo Y, Yu D, Cheng F, Wang T, Zhang X, Zhang L, Hu W, Li J, Yuan P, Liu J, Wang Y, Yan J. Evaluation of reverse transcription yield of RNA standards and forensic samples based on droplet digital PCR. Biochem Biophys Res Commun 2024; 711:149909. [PMID: 38615573 DOI: 10.1016/j.bbrc.2024.149909] [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: 03/24/2024] [Accepted: 04/05/2024] [Indexed: 04/16/2024]
Abstract
RNA analysis has shown great value in forensic science, such as body fluids and tissue identification, postmortem interval estimation, biological age prediction, etc. Currently, most RNA follow-up experiments involve reverse transcription (RT) procedures. It has been shown that the RT step is variable and has a greater impact on subsequent data analysis, especially for forensic trace samples. However, the pattern of variation between different RNA template inputs and complementary DNA (cDNA) yield is unclear. In this study, a series of 2-fold gradient dilutions of RNA standards (1 μg/μL - 0.24 ng/μL) and forensic samples (including blood samples, saliva samples, bloodstains, and saliva stains) were reverse-transcribed using EasyQuick RT MasterMix. The obtained cDNA was quantified by droplet digital PCR (ddPCR) to assess the RT yield of the ACTB gene. The results showed that the 125 ng RNA template had the highest RT yield in a 10 μL RT reaction system with the selected kit. For all stain samples, the RT yield improved as the amount of RNA template input increased since RNA quantities were below 125 ng. As many commercialized reverse transcription kits using different kinds of enzymes are available for forensic RNA research, we recommend that systematic experiments should be performed in advance to determine the amount of RNA input at the optimum RT yield when using any kit for reverse transcription experiments.
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Affiliation(s)
- Niu Gao
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Yumei Huo
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Daijing Yu
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Feng Cheng
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Tian Wang
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Xiaomeng Zhang
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Liwei Zhang
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Wenjing Hu
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Junli Li
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Piao Yuan
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Jinding Liu
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China.
| | - Yan Wang
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China; Clinical Biobank Center, Medical Innovation Research Division of Chinese, PLA General Hospital, Beijing, China.
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China.
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2
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de los Santos MR, Kopell BH, Grice AB, Ganesh G, Yang A, Amini P, Liharska LE, Vornholt E, Fullard JF, Dong P, Park E, Zipkowitz S, Kaji DA, Thompson RC, Liu D, Park YJ, Cheng E, Ziafat K, Moya E, Fennessy B, Wilkins L, Silk H, Linares LM, Sullivan B, Cohen V, Kota P, Feng C, Johnson JS, Rieder MK, Scarpa J, Nadkarni GN, Wang M, Zhang B, Sklar P, Beckmann ND, Schadt EE, Roussos P, Charney AW, Breen MS. Divergent landscapes of A-to-I editing in postmortem and living human brain. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.06.24306763. [PMID: 38765961 PMCID: PMC11100843 DOI: 10.1101/2024.05.06.24306763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Adenosine-to-inosine (A-to-I) editing is a prevalent post-transcriptional RNA modification within the brain. Yet, most research has relied on postmortem samples, assuming it is an accurate representation of RNA biology in the living brain. We challenge this assumption by comparing A-to-I editing between postmortem and living prefrontal cortical tissues. Major differences were found, with over 70,000 A-to-I sites showing higher editing levels in postmortem tissues. Increased A-to-I editing in postmortem tissues is linked to higher ADAR1 and ADARB1 expression, is more pronounced in non-neuronal cells, and indicative of postmortem activation of inflammation and hypoxia. Higher A-to-I editing in living tissues marks sites that are evolutionarily preserved, synaptic, developmentally timed, and disrupted in neurological conditions. Common genetic variants were also found to differentially affect A-to-I editing levels in living versus postmortem tissues. Collectively, these discoveries illuminate the nuanced functions and intricate regulatory mechanisms of RNA editing within the human brain.
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Affiliation(s)
| | - Brian H. Kopell
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Gauri Ganesh
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Andy Yang
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Pardis Amini
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Lora E. Liharska
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Eric Vornholt
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - John F. Fullard
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Pengfei Dong
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Eric Park
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Sarah Zipkowitz
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Deepak A. Kaji
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ryan C. Thompson
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Donjing Liu
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - You Jeong Park
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Esther Cheng
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kimia Ziafat
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Emily Moya
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Brian Fennessy
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Lillian Wilkins
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Hannah Silk
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Lisa M. Linares
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Brendan Sullivan
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Vanessa Cohen
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Prashant Kota
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Claudia Feng
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | | | - Joseph Scarpa
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Minghui Wang
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bin Zhang
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Pamela Sklar
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Noam D. Beckmann
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Eric E. Schadt
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Panos Roussos
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Michael S. Breen
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
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Jo TS. Larger particle size distribution of environmental RNA compared to environmental DNA: a case study targeting the mitochondrial cytochrome b gene in zebrafish (Danio rerio) using experimental aquariums. THE SCIENCE OF NATURE - NATURWISSENSCHAFTEN 2024; 111:18. [PMID: 38502308 DOI: 10.1007/s00114-024-01904-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/07/2024] [Accepted: 03/08/2024] [Indexed: 03/21/2024]
Abstract
Environmental RNA (eRNA) analysis is conventionally expected to infer physiological information about organisms within their ecosystems, whereas environmental DNA (eDNA) analysis only infers their presence and abundance. Despite the promise of eRNA application, basic research on eRNA characteristics and dynamics is limited. The present study conducted aquarium experiments using zebrafish (Danio rerio) to estimate the particle size distribution (PSD) of eRNA in order to better understand the persistence state of eRNA particles. Rearing water samples were sequentially filtered using different pore-size filters, and the resulting size-fractioned mitochondrial cytochrome b (CytB) eDNA and eRNA data were modeled with the Weibull complementary cumulative distribution function (CCDF) to estimate the parameters characterizing the PSDs. It was revealed that the scale parameter (α) was significantly higher (i.e., the mean particle size was larger) for eRNA than eDNA, while the shape parameter (β) was not significantly different between them. This result supports the hypothesis that most eRNA particles are likely in a protected, intra-cellular state, which mitigates eRNA degradation in water. Moreover, these findings also imply the heterogeneous dispersion of eRNA relative to eDNA and suggest an efficient method of eRNA collection using a larger pore-size filter. Further studies on the characteristics and dynamics of eRNA particles should be pursued in the future.
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Affiliation(s)
- Toshiaki S Jo
- Research Fellow of Japan Society for the Promotion of Science, 5-3-1 Kojimachi, Chiyoda-Ku, Tokyo, 102-0083, Japan.
- Ryukoku Center for Biodiversity Science, 1-5, Yokotani, Oe-Cho, Seta, Otsu City, Shiga, 520-2194, Japan.
- Faculty of Advanced Science and Technology, Ryukoku University, 1-5, Yokotani, Oe-Cho, Seta, Otsu City, Shiga, 520-2194, Japan.
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4
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Song B, Qian J, Fu J. Research progress and potential application of microRNA and other non-coding RNAs in forensic medicine. Int J Legal Med 2024; 138:329-350. [PMID: 37770641 DOI: 10.1007/s00414-023-03091-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 09/18/2023] [Indexed: 09/30/2023]
Abstract
At present, epigenetic markers have been extensively studied in various fields and have a high value in forensic medicine due to their unique mode of inheritance, which does not involve DNA sequence alterations. As an epigenetic phenomenon that plays an important role in gene expression, non-coding RNAs (ncRNAs) act as key factors mediating gene silencing, participating in cell division, and regulating immune response and other important biological processes. With the development of molecular biology, genetics, bioinformatics, and next-generation sequencing (NGS) technology, ncRNAs such as microRNA (miRNA), circular RNA (circRNA), long non-coding RNA (lncRNA), and P-element induced wimpy testis (PIWI)-interacting RNA (piRNA) are increasingly been shown to have potential in the practice of forensic medicine. NcRNAs, mainly miRNA, may provide new strategies and methods for the identification of tissues and body fluids, cause-of-death analysis, time-related estimation, age estimation, and the identification of monozygotic twins. In this review, we describe the research progress and application status of ncRNAs, mainly miRNA, and other ncRNAs such as circRNA, lncRNA, and piRNA, in forensic practice, including the identification of tissues and body fluids, cause-of-death analysis, time-related estimation, age estimation, and the identification of monozygotic twins. The close links between ncRNAs and forensic medicine are presented, and their research values and application prospects in forensic medicine are also discussed.
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Affiliation(s)
- Binghui Song
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
- Laboratory of Precision Medicine and DNA Forensic Medicine, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Jie Qian
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
- Laboratory of Precision Medicine and DNA Forensic Medicine, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Junjiang Fu
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China.
- Laboratory of Precision Medicine and DNA Forensic Medicine, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China.
- Laboratory of Forensic DNA, the Judicial Authentication Center, Southwest Medical University, Luzhou, 646000, Sichuan, China.
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5
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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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Tomassini L, Lancia M, Scendoni R, Manta AM, Fruttini D, Terribile E, Gambelunghe C. Dating Skin Lesions of Forensic Interest by Immunohistochemistry and Immunofluorescence Techniques: A Scoping Literature Review. Diagnostics (Basel) 2024; 14:168. [PMID: 38248045 PMCID: PMC10814027 DOI: 10.3390/diagnostics14020168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 01/23/2024] Open
Abstract
Wound age estimation is a significant issue in forensic pathology. Although various methods have been evaluated, no gold standard system or model has been proposed, and accurate injury time estimation is still challenging. The distinction between vital skin wounds-i.e., ante-mortem lesions-and skin alterations that occur after death is a crucial goal in forensic pathology. Once the vitality of the wound has been confirmed, the assessment of the post-trauma interval (PTI) is also fundamental in establishing the causal relationship between the traumatic event and death. The most frequently used techniques in research studies are biochemistry, molecular biology, and immunohistochemistry (IHC). Biochemical methods take advantage of the chemical and physical techniques. A systematic literature search of studies started on 18 February 2023. The search was conducted in the main databases for biomedical literature, i.e., PubMed and Scopus, for papers published between 1973 and 2022, focusing on different techniques of immunohistochemistry and immunofluorescence (IF) for estimating the PTI of skin wounds. The present study involves a comprehensive and structured analysis of the existing literature to provide a detailed and comprehensive overview of the different IHC techniques used to date skin lesions, synthesize the available evidence, critically evaluate the methodologies, and eventually draw meaningful conclusions about the reliability and effectiveness of the different markers that have been discovered and used in wound age estimation.
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Affiliation(s)
- Luca Tomassini
- International School of Advanced Studies, University of Camerino, 62032 Camerino, Italy
| | - Massimo Lancia
- Forensic Medicine, Forensic Science and Sports Medicine Section, Department of Medicine and Surgery, University of Perugia, Piazza Lucio Severi, 06132 Perugia, Italy; (M.L.); (E.T.); (C.G.)
| | - Roberto Scendoni
- Department of Law, Institute of Legal Medicine, University of Macerata, 62100 Macerata, Italy;
| | - Anna Maria Manta
- Department of Anatomical, Histological, Forensic Medicine and Orthopedic Sciences, Sapienza University, 00185 Rome, Italy;
| | - Daniela Fruttini
- Section of Internal Medicine and Endocrine and Metabolic Sciences, Department of Medicine and Surgery, University of Perugia, 06123 Perugia, Italy;
| | - Erika Terribile
- Forensic Medicine, Forensic Science and Sports Medicine Section, Department of Medicine and Surgery, University of Perugia, Piazza Lucio Severi, 06132 Perugia, Italy; (M.L.); (E.T.); (C.G.)
| | - Cristiana Gambelunghe
- Forensic Medicine, Forensic Science and Sports Medicine Section, Department of Medicine and Surgery, University of Perugia, Piazza Lucio Severi, 06132 Perugia, Italy; (M.L.); (E.T.); (C.G.)
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7
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Liu Y, Fan J, Zhang M, Liu Z, Wang J, Liu J, Li Z, Yang F, Zhang G. A human identification system for hair shaft using RNA polymorphism. Forensic Sci Int Genet 2023; 67:102929. [PMID: 37611365 DOI: 10.1016/j.fsigen.2023.102929] [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: 06/04/2023] [Revised: 08/06/2023] [Accepted: 08/08/2023] [Indexed: 08/25/2023]
Abstract
Hair is one of the common pieces of evidence at crime scenes, with abundant mitochondrial DNA but limited nuclear DNA in its shaft. It also helps to narrow the investigation scope to maternal lineage but fails to provide unique individual information. We assumed that RNA in hair shafts would be an alternative resource used to perform human identification based on the facts that (1) RNA retains the polymorphic information; (2) the multi-copy of RNA in a cell resists degradation as compared to the one-copy of nuclear DNA. In this study, we explored the potential of RNA polymorphism in hair shafts for forensic individual identification. A SNaPshot typing system was constructed using 18 SNPs located on 11 genes (ABCA13, AHNAK, EXPH5, KMT2D, KRT35, PPP1R15A, RBM33, S100A5, TBC1D4, TMC5, TRPV2). The RNA typing system was evaluated for sensitivity, species specificity, and feasibility for aged hair samples. Hair samples from a Shanxi population in China were used for the population study of the system. The detection limit of the assay was 2 ng RNA. The CDP of these 11 genes was 0.999969 in the Shanxi population. We also identified the concordance of the RNA and DNA typing results. In summary, we developed an RNA typing method to perform human identification from hair shafts, which performed as accurately as nuclear DNA typing. Our method provides a potential basis for solving the human identification problem from hair shafts, as well as other biological materials that lack nuclear DNA.
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Affiliation(s)
- Yao Liu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Jiajia Fan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Mingming Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Zidong Liu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Jiaqi Wang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Jinding Liu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Zeqin Li
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Fan Yang
- Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China.
| | - Gengqian Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China.
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8
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DeJaco RF, Roberts MJ, Romsos EL, Vallone PM, Kearsley AJ. Reducing Bias and Quantifying Uncertainty in Fluorescence Produced by PCR. Bull Math Biol 2023; 85:83. [PMID: 37574503 PMCID: PMC10423706 DOI: 10.1007/s11538-023-01182-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 06/20/2023] [Indexed: 08/15/2023]
Abstract
We present a new approach for relating nucleic-acid content to fluorescence in a real-time Polymerase Chain Reaction (PCR) assay. By coupling a two-type branching process for PCR with a fluorescence analog of Beer's Law, the approach reduces bias and quantifies uncertainty in fluorescence. As the two-type branching process distinguishes between complementary strands of DNA, it allows for a stoichiometric description of reactions between fluorescent probes and DNA and can capture the initial conditions encountered in assays targeting RNA. Analysis of the expected copy-number identifies additional dynamics that occur at short times (or, equivalently, low cycle numbers), while investigation of the variance reveals the contributions from liquid volume transfer, imperfect amplification, and strand-specific amplification (i.e., if one strand is synthesized more efficiently than its complement). Linking the branching process to fluorescence by the Beer's Law analog allows for an a priori description of background fluorescence. It also enables uncertainty quantification (UQ) in fluorescence which, in turn, leads to analytical relationships between amplification efficiency (probability) and limit of detection. This work sets the stage for UQ-PCR, where both the input copy-number and its uncertainty are quantified from fluorescence kinetics.
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Affiliation(s)
- Robert F. DeJaco
- Applied and Computational Mathematics Division, National Institute of Standards and Technology, 100 Bureau Dr., MS 8910, Gaithersburg, MD 20899-8910 USA
- Department of Chemistry and Biochemistry, University of Maryland, 8051 Regents Dr., College Park, MD 20742-4454 USA
| | - Matthew J. Roberts
- Applied and Computational Mathematics Division, National Institute of Standards and Technology, 100 Bureau Dr., MS 8910, Gaithersburg, MD 20899-8910 USA
- Cost Analysis and Research Division, Institute for Defense Analyses, 730 E. Glebe Rd., Alexandria, VA 22305-3086 USA
| | - Erica L. Romsos
- Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Dr., MS 8314, Gaithersburg, MD 20899-8314 USA
| | - Peter M. Vallone
- Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Dr., MS 8314, Gaithersburg, MD 20899-8314 USA
| | - Anthony J. Kearsley
- Applied and Computational Mathematics Division, National Institute of Standards and Technology, 100 Bureau Dr., MS 8910, Gaithersburg, MD 20899-8910 USA
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9
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Cappelletti C, Henriksen SP, Geut H, Rozemuller AJM, van de Berg WDJ, Pihlstrøm L, Toft M. Transcriptomic profiling of Parkinson's disease brains reveals disease stage specific gene expression changes. Acta Neuropathol 2023; 146:227-244. [PMID: 37347276 PMCID: PMC10329075 DOI: 10.1007/s00401-023-02597-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 05/02/2023] [Accepted: 06/06/2023] [Indexed: 06/23/2023]
Abstract
Parkinson´s disease (PD) is a progressive neurodegenerative disorder characterized by both motor and non-motor symptoms. Aggravation of symptoms is mirrored by accumulation of protein aggregates mainly composed by alpha-synuclein in different brain regions, called Lewy bodies (LB). Previous studies have identified several molecular mechanisms as autophagy and inflammation playing a role in PD pathogenesis. Increased insights into mechanisms involved in early disease stages and driving the progression of the LB pathology are required for the development of disease-modifying strategies. Here, we aimed to elucidate disease stage-specific transcriptomic changes in brain tissue of well-characterized PD and control donors. We collected frontal cortex samples from 84 donors and sequenced both the coding and non-coding RNAs. We categorized our samples into groups based on their degree of LB pathology aiming to recapitulate a central aspect of disease progression. Using an analytical pipeline that corrected for sex, age at death, RNA quality, cell composition and unknown sources of variation, we found major disease stage-specific transcriptomic changes. Gene expression changes were most pronounced in donors at the disease stage when microscopic LB changes first occur in the sampled brain region. Additionally, we identified disease stage-specific enrichment of brain specific pathways and immune mechanisms. On the contrary, we showed that mitochondrial mechanisms are enriched throughout the disease course. Our data-driven approach also suggests a role for several poorly characterized lncRNAs in disease development and progression of PD. Finally, by combining genetic and epigenetic information, we highlighted two genes (MAP4K4 and PHYHIP) as candidate genes for future functional studies. Together our results indicate that transcriptomic dysregulation and associated functional changes are highly disease stage-specific, which has major implications for the study of neurodegenerative disorders.
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Affiliation(s)
- Chiara Cappelletti
- Department of Mechanical, Electronics and Chemical Engineering, Faculty of Technology, Art and Design, OsloMet-Oslo Metropolitan University, Oslo, Norway
- Department of Research, Innovation and Education, Oslo University Hospital, Oslo, Norway
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | | | - Hanneke Geut
- Amsterdam UMC, Section Clinical Neuroanatomy and Biobanking, Department of Anatomy and Neurosciences, Amsterdam Neuroscience, Vrije Universiteit, Amsterdam, Netherlands
- Netherlands Brain Bank, Netherlands Institute of Neurosciences, Amsterdam, Netherlands
| | - Annemieke J M Rozemuller
- Department of Pathology, Amsterdam UMC, Amsterdam Neuroscience, Vrije Universiteit, Amsterdam, Netherlands
| | - Wilma D J van de Berg
- Amsterdam UMC, Section Clinical Neuroanatomy and Biobanking, Department of Anatomy and Neurosciences, Amsterdam Neuroscience, Vrije Universiteit, Amsterdam, Netherlands
| | - Lasse Pihlstrøm
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Mathias Toft
- Department of Neurology, Oslo University Hospital, Oslo, Norway.
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
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10
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Bazyar H. On the Application of Microfluidic-Based Technologies in Forensics: A Review. SENSORS (BASEL, SWITZERLAND) 2023; 23:5856. [PMID: 37447704 PMCID: PMC10346202 DOI: 10.3390/s23135856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/21/2023] [Accepted: 06/22/2023] [Indexed: 07/15/2023]
Abstract
Microfluidic technology is a powerful tool to enable the rapid, accurate, and on-site analysis of forensically relevant evidence on a crime scene. This review paper provides a summary on the application of this technology in various forensic investigation fields spanning from forensic serology and human identification to discriminating and analyzing diverse classes of drugs and explosives. Each aspect is further explained by providing a short summary on general forensic workflow and investigations for body fluid identification as well as through the analysis of drugs and explosives. Microfluidic technology, including fabrication methodologies, materials, and working modules, are touched upon. Finally, the current shortcomings on the implementation of the microfluidic technology in the forensic field are discussed along with the future perspectives.
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Affiliation(s)
- Hanieh Bazyar
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Leeghwaterstraat 39, 2628CB Delft, The Netherlands
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11
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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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12
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Brusletto BS, Hellerud BC, Olstad OK, Øvstebø R, Brandtzaeg P. Transcriptomic changes in the large organs in lethal meningococcal shock are reflected in a porcine shock model. Front Cell Infect Microbiol 2022; 12:908204. [PMID: 36034711 PMCID: PMC9413276 DOI: 10.3389/fcimb.2022.908204] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 07/06/2022] [Indexed: 11/26/2022] Open
Abstract
Background Fulminant meningococcal sepsis with shock and multiple organ failure is associated with a massive systemic inflammatory response involving solid organs. We have previously established a porcine model of the disease to study pathophysiologic and possible therapeutic strategies. Objective This study examined whether the organ specific gene expression profile in such a large animal model reflects the profile seen in patients with fulminant meningococcal sepsis. Patients and methods Data from gene expression profiles induced in organs from patients (n=5) and the porcine model (n=8) were imported into the Ingenuity pathway analysis (IPA) software for comparison analysis. The number of meningococci in the organs were quantified by real time-PCR. Results The all-over transcriptional activation between different organs revealed a striking concordance between the patients and the pigs regarding the pattern of transcriptional activation and activated pathways. Comparison analysis demonstrated similar pattern of upregulation of genes being associated with a large range of inflammatory biofunctions in the patients and the porcine model. Genes associated with biofunctions such as organismal death, morbidity and mortality were similarly downregulated in the patients and the porcine model. Comparison analysis of main predicted canonical pathways also demonstrated a high degree of similarity regarding up- and downregulation in both groups. Core analysis revealed different top-upstream regulators in the different organs in the patients. In the patients pro-inflammatory regulators were most activated in the lungs. In the other organs up-stream factors that regulate signaling pathways involved in development, growth, repair and homeostasis and triglyceride synthesis were most activated. In the porcine model, the top-upstream regulators were pro-inflammatory in all organs. The difference may reflect the shorter duration of the porcine experiment than the duration of the patient’s infection before death. Conclusion The inflammatory responses measured on the transcriptomic level in organs in patients with fulminant meningococcal sepsis is reproduced in the porcine model of the disease, although some differences may exist regarding the top-upregulated factors in individual organs. Thus, this large animal model reproduces important immunological features of meningococcal sepsis and can be a valuable tool in further investigations of inflammatory aspects and possible treatment options
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Affiliation(s)
- Berit Sletbakk Brusletto
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
- *Correspondence: Berit Sletbakk Brusletto,
| | | | | | - Reidun Øvstebø
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
| | - Petter Brandtzaeg
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
- Department of Pediatrics, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
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13
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Neidel V, Sint D, Wallinger C, Traugott M. RNA allows identifying the consumption of carrion prey. Mol Ecol Resour 2022; 22:2662-2671. [PMID: 35668675 PMCID: PMC9541938 DOI: 10.1111/1755-0998.13659] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 05/05/2022] [Accepted: 05/17/2022] [Indexed: 11/30/2022]
Abstract
Facultative scavenging by predatory carnivores is a prevalent but frequently underestimated feeding strategy. DNA‐based methods for diet analysis, however, do not allow to distinguish between scavenging and predation, thus, the significance of scavenging on population dynamics and resource partitioning is widely unknown. Here, we present a methodological innovation to differentiate between scavenging and fresh prey consumption using prey RNA as a target molecule. We hypothesized that the rapid post‐mortem breakdown of RNA in prey tissue should lead to a significantly lower detection probability of prey RNA than DNA when carrion rather than fresh prey is consumed. To test this hypothesis, ground beetles (Pseudoophonus rufipes [De Geer]) were offered either fresh or 1‐day‐old dead Drosophila melanogaster fruit flies (carrion). The detectability of prey RNA and DNA in the beetles' regurgitates was assessed with diagnostic Drosophila‐specific RT‐PCR and PCR assays at 0, 6, 12, 24 and 48 h post‐feeding. After fresh fly consumption, prey RNA and DNA were detectable equally well at all times. When carrion prey was consumed, the detection strength of prey RNA immediately after feeding was significantly lower than that of prey DNA and reached zero in most samples within 6 h of digestion. Our findings provide evidence that prey RNA allows distinguishing between the consumption of fresh and scavenged prey, thereby overcoming a long‐known weakness of molecular diet analysis. The assessment of prey RNA offers a generally applicable approach for examining the importance of scavenging in food webs to unravel its functional consequences for populations, communities, and ecosystems.
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Affiliation(s)
- Veronika Neidel
- Applied Animal Ecology, Department of Zoology, University of Innsbruck, Innsbruck, Austria
| | - Daniela Sint
- Applied Animal Ecology, Department of Zoology, University of Innsbruck, Innsbruck, Austria
| | - Corinna Wallinger
- Applied Animal Ecology, Department of Zoology, University of Innsbruck, Innsbruck, Austria
| | - Michael Traugott
- Applied Animal Ecology, Department of Zoology, University of Innsbruck, Innsbruck, Austria
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14
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Elliott CI, Stotesbury TE, Shafer ABA. Using total RNA quality metrics for time since deposition estimates in degrading bloodstains. J Forensic Sci 2022; 67:1776-1785. [PMID: 35665927 DOI: 10.1111/1556-4029.15072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/15/2022] [Accepted: 05/24/2022] [Indexed: 12/23/2022]
Abstract
The physicochemical changes occurring in biomolecules in degrading bloodstains can be used to approximate the time since deposition (TSD) of bloodstains. This would provide forensic scientists with critical information regarding the timeline of the events involving bloodshed. Our study aims to quantify the timewise degradation trends and temperature dependence found in total RNA from bloodstains without the use of amplification, expanding the scope of the RNA TSD research which has traditionally targeted mRNA and miRNA. Bovine blood with ACD-A anticoagulant was deposited and stored in plastic microcentrifuge tubes at 21 or 4°C and tested over different timepoints spanning 1 week. Total RNA was extracted from each sample and analyzed using automated high sensitivity gel electrophoresis. Nine RNA metrics were visually assessed and quantified using linear and mixed models. The RNA Integrity Number equivalent (RINe) and DV200 were not influenced by the addition of anticoagulant and demonstrated strong negative trends over time. The RINe model fit was high (R2 = 0.60), and while including the biological replicate as a random effect increased the fit for all RNA metrics, no significant differences were found between biological replicates stored at the same temperature for the RINe and DV200. This suggests that these standardized metrics can be directly compared between scenarios and individuals, with DV200 having an inflection point at approximately 28 h. This study provides a novel approach for blood TSD research, revealing metrics that are not affected by inter-individual variation, and improving our understanding of the rapid RNA degradation occurring in bloodstains.
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Affiliation(s)
- Colin I Elliott
- Department of Forensic Science, Trent University, Peterborough, Ontario, Canada.,Applied Bioscience Graduate Program, Faculty of Science, Ontario Tech University, Oshawa, Ontario, Canada
| | - Theresa E Stotesbury
- Faculty of Science, Forensic Science, Ontario Tech University, Oshawa, Ontario, Canada
| | - Aaron B A Shafer
- Department of Forensic Science, Trent University, Peterborough, Ontario, Canada.,Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
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15
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Soudier P, Rodriguez Pinzon D, Reif-Trauttmansdorff T, Hijazi H, Cherrière M, Goncalves Pereira C, Blaise D, Pispisa M, Saint-Julien A, Hamlet W, Nguevo M, Gomes E, Belkhelfa S, Niarakis A, Kushwaha M, Grigoras I. Toehold switch based biosensors for sensing the highly trafficked rosewood Dalbergia maritima. Synth Syst Biotechnol 2022; 7:791-801. [PMID: 35415278 PMCID: PMC8976095 DOI: 10.1016/j.synbio.2022.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 02/28/2022] [Accepted: 03/14/2022] [Indexed: 01/05/2023] Open
Abstract
Nucleic acid sensing is a 3 decades old but still challenging area of application for different biological sub-domains, from pathogen detection to single cell transcriptomics analysis. The many applications of nucleic acid detection and identification are mostly carried out by PCR techniques, sequencing, and their derivatives used at large scale. However, these methods’ limitations on speed, cost, complexity and specificity have motivated the development of innovative detection methods among which nucleic acid biosensing technologies seem promising. Toehold switches are a particular class of RNA sensing devices relying on a conformational switch of secondary structure induced by the pairing of the detected trigger RNA with a de novo designed synthetic sensing mRNA molecule. Here we describe a streamlined methodology enabling the development of such a sensor for the RNA-mediated detection of an endangered plant species in a cell-free reaction system. We applied this methodology to help identify the rosewood Dalbergia maritima, a highly trafficked wood, whose protection is limited by the capacity of the authorities to distinguish protected logs from other unprotected but related species. The streamlined pipeline presented in this work is a versatile framework enabling cheap and rapid development of new sensors for custom RNA detection.
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16
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Unlocking the potential of forensic traces: Analytical approaches to generate investigative leads. Sci Justice 2022; 62:310-326. [PMID: 35598924 DOI: 10.1016/j.scijus.2022.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 03/17/2022] [Accepted: 03/19/2022] [Indexed: 11/21/2022]
Abstract
Forensic investigation involves gathering the information necessary to understand the criminal events as well as linking objects or individuals to an item, location or other individual(s) for investigative purposes. For years techniques such as presumptive chemical tests, DNA profiling or fingermark analysis have been of great value to this process. However, these techniques have their limitations, whether it is a lack of confidence in the results obtained due to cross-reactivity, subjectivity and low sensitivity; or because they are dependent on holding reference samples in a pre-existing database. There is currently a need to devise new ways to gather as much information as possible from a single trace, particularly from biological traces commonly encountered in forensic casework. This review outlines the most recent advancements in the forensic analysis of biological fluids, fingermarks and hair. Special emphasis is placed on analytical methods that can expand the information obtained from the trace beyond what is achieved in the usual practices. Special attention is paid to those methods that accurately determine the nature of the sample, as well as how long it has been at the crime scene, along with individualising information regarding the donor source of the trace.
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17
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Deffner F, Gleiser C, Mattheus U, Wagner A, Neckel PH, Fallier-Becker P, Hirt B, Mack AF. Aquaporin-4 expression in the human choroid plexus. Cell Mol Life Sci 2022; 79:90. [PMID: 35072772 PMCID: PMC8785037 DOI: 10.1007/s00018-022-04136-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 01/02/2022] [Accepted: 01/05/2022] [Indexed: 01/15/2023]
Abstract
The choroid plexus (CP) consists of specialized ependymal cells and underlying blood vessels and stroma producing the bulk of the cerebrospinal fluid (CSF). CP epithelial cells are considered the site of the internal blood-cerebrospinal fluid barrier, show epithelial characteristics (basal lamina, tight junctions), and express aquaporin-1 (AQP1) apically. In this study, we analyzed the expression of aquaporins in the human CP using immunofluorescence and qPCR. As previously reported, AQP1 was expressed apically in CP epithelial cells. Surprisingly, and previously unknown, many cells in the CP epithelium were also positive for aquaporin-4 (AQP4), normally restricted to ventricle-lining ependymal cells and astrocytes in the brain. Expression of AQP1 and AQP4 was found in the CP of all eight body donors investigated (3 males, 5 females; age 74–91). These results were confirmed by qPCR, and by electron microscopy detecting orthogonal arrays of particles. To find out whether AQP4 expression correlated with the expression pattern of relevant transport-related proteins we also investigated expression of NKCC1, and Na/K-ATPase. Immunostaining with NKCC1 was similar to AQP1 and revealed no particular pattern related to AQP4. Co-staining of AQP4 and Na/K-ATPase indicated a trend for an inverse correlation of their expression. We hypothesized that AQP4 expression in the CP was caused by age-related changes. To address this, we investigated mouse brains from young (2 months), adult (12 months) and old (30 months) mice. We found a significant increase of AQP4 on the mRNA level in old mice compared to young and adult animals. Taken together, we provide evidence for AQP4 expression in the CP of the aging brain which likely contributes to the water flow through the CP epithelium and CSF production. In two alternative hypotheses, we discuss this as a beneficial compensatory, or a detrimental mechanism influencing the previously observed CSF changes during aging.
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Affiliation(s)
- Felix Deffner
- Institute of Clinical Anatomy and Cell Analysis, University of Tübingen, Österbergstr. 3, 72074, Tübingen, Germany
| | - Corinna Gleiser
- Institute of Clinical Anatomy and Cell Analysis, University of Tübingen, Österbergstr. 3, 72074, Tübingen, Germany
| | - Ulrich Mattheus
- Institute of Clinical Anatomy and Cell Analysis, University of Tübingen, Österbergstr. 3, 72074, Tübingen, Germany
| | - Andreas Wagner
- Institute of Clinical Anatomy and Cell Analysis, University of Tübingen, Österbergstr. 3, 72074, Tübingen, Germany
| | - Peter H Neckel
- Institute of Clinical Anatomy and Cell Analysis, University of Tübingen, Österbergstr. 3, 72074, Tübingen, Germany
| | - Petra Fallier-Becker
- Institute of Pathology and Neuropathology, University of Tübingen, Tübingen, Germany
| | - Bernhard Hirt
- Institute of Clinical Anatomy and Cell Analysis, University of Tübingen, Österbergstr. 3, 72074, Tübingen, Germany
| | - Andreas F Mack
- Institute of Clinical Anatomy and Cell Analysis, University of Tübingen, Österbergstr. 3, 72074, Tübingen, Germany.
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18
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De Simone S, Giacani E, Bosco MA, Vittorio S, Ferrara M, Bertozzi G, Cipolloni L, La Russa R. The Role of miRNAs as New Molecular Biomarkers for Dating the Age of Wound Production: A Systematic Review. Front Med (Lausanne) 2022; 8:803067. [PMID: 35096893 PMCID: PMC8795691 DOI: 10.3389/fmed.2021.803067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/22/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The timing of wounds production is a significant issue in forensic pathology. Although various methods have been evaluated, obtaining an accurate dating of lesions is still a challenge. The pathologist uses many parameters to value wound age, such as histological and immunohistochemical. In recent years, there have been many studies regarding the use of miRNAs in wound-age estimation; indeed, miRNAs have multiple potential uses in forensic pathology. SCOPE This review aims to verify the efficacy and feasibility of miRNAs as a tool for determining the timing of lesions. MATERIALS AND METHODS The authors conducted the systematic review according to the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines. PubMed was used as a search engine to find articles published between January, 1st 2016 and October, 1st 2021, to evaluate the current state of the art regarding wound-age estimation. RESULTS A total of 256 articles were collected; after screening according to PRISMA guidelines, the systematic review included 8 articles. The studies included in this review were all Original articles evaluating the use of biomarkers for wound-age determination. DISCUSSION AND CONCLUSION The literature review showed that analysis of miRNA is an innovative field of study with significant potentiality in forensic pathology. There are few studies, and almost all of them are at an early stage. The challenge is to understand how to standardize the samples' selection to obtain reliable experimental data. This observation represents a necessary prerequisite to planning further clinical trials.
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Affiliation(s)
- Stefania De Simone
- Department of Clinical and Experimental Medicine, Section of Legal Medicine, University of Foggia, Foggia, Italy
| | - Elena Giacani
- Department of Clinical and Experimental Medicine, Section of Legal Medicine, University of Foggia, Foggia, Italy
| | - Maria Antonella Bosco
- Department of Clinical and Experimental Medicine, Section of Legal Medicine, University of Foggia, Foggia, Italy
| | - Simona Vittorio
- Department of Anatomical, Histological, Forensic and Orthopedic Sciences, Sapienza University of Rome, Rome, Italy
| | - Michela Ferrara
- Department of Clinical and Experimental Medicine, Section of Legal Medicine, University of Foggia, Foggia, Italy
| | - Giuseppe Bertozzi
- Department of Clinical and Experimental Medicine, Section of Legal Medicine, University of Foggia, Foggia, Italy
| | - Luigi Cipolloni
- Department of Clinical and Experimental Medicine, Section of Legal Medicine, University of Foggia, Foggia, Italy
| | - Raffaele La Russa
- Department of Clinical and Experimental Medicine, Section of Legal Medicine, University of Foggia, Foggia, Italy
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19
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Doménech-Carbó MT, Doménech-Carbó A. Spot tests: past and present. CHEMTEXTS 2022; 8:4. [PMID: 34976574 PMCID: PMC8710564 DOI: 10.1007/s40828-021-00152-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 10/11/2021] [Indexed: 11/21/2022]
Abstract
Microchemistry, i.e., the chemistry performed at the scale of a microgram or less, has its roots in the late eighteenth and early nineteenth centuries. In the first half of the twentieth century a wide range of spot tests have been developed. For didactic reasons, they are still part of the curriculum of chemistry students. However, they are even highly important for applied analyses in conservation of cultural heritage, food science, forensic science, clinical and pharmacological sciences, geochemistry, and environmental sciences. Modern pregnancy tests, virus tests, etc. are the most recent examples of sophisticated spot tests. The present ChemTexts contribution aims to provide an overview of the past and present of this analytical methodology.
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Affiliation(s)
- María Teresa Doménech-Carbó
- Institut de Restauració del Patrimoni, Universitat Politècnica de València, Camí de Vera 14, 46022 Valencia, Spain
| | - Antonio Doménech-Carbó
- Departament de Química Analítica, Universitat de València. Dr. Moliner, 50, Burjassot, 46100 Valencia, Spain
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20
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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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21
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Wang S, Shanthan G, Bouzga MM, Thi Dinh HM, Haas C, Fonneløp AE. Evaluating the performance of five up-to-date DNA/RNA co-extraction methods for forensic application. Forensic Sci Int 2021; 328:110996. [PMID: 34592582 DOI: 10.1016/j.forsciint.2021.110996] [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: 07/01/2021] [Revised: 08/31/2021] [Accepted: 09/06/2021] [Indexed: 12/21/2022]
Abstract
The importance of RNA evidence is growing with new developments in RNA profiling methods and purposes. As forensic samples often can be of small quantity, extraction methods with high yields of both DNA and RNA are desirable. In order to identify the optimal DNA/RNA co-extraction workflow for forensic samples, we evaluated the performance of three frequently-used methods, two new approaches for DNA/RNA co-extraction and a manual phenol/chloroform RNA-only extraction method on blood and saliva samples. Based on a comprehensive analysis of the RNA and DNA quantities, as well as the STR genotyping and mRNA profiling results, we conclude that the two frequently-used co-extraction methods, combining commercially available DNA and RNA extraction kits, achieved the best performance. However, not any combination of commercially available DNA and RNA extraction kits works well and extensive optimization is necessary, as seen in the poor results of the two new approaches.
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Affiliation(s)
- Shouyu Wang
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland; Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | | | | | | | - Cordula Haas
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
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22
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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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Tian H, Huang S, Bai P, Xiao X, Peng D, Zhao H, Liu Y, Feng Q, Liao M, Li F, Liang W. The effect of infertile semen on the mRNA-based body fluid identification. Electrophoresis 2021; 42:1614-1622. [PMID: 34233021 DOI: 10.1002/elps.202000238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 05/31/2021] [Accepted: 06/06/2021] [Indexed: 11/08/2022]
Abstract
In the past decade, mRNA markers have been well demonstrated as promising molecular markers in forensic body fluid identification (BFI), and successfully used in wide applications. Several studies have assessed the performance of semen-specific mRNA markers in distinguishing semen from other common body fluids at the crime scene. Infertility has been reported as a global health problem that is affecting approximately 15% of couples worldwide. Therefore, it is important for forensic researchers to consider the impact of infertility on semen identification. This study aimed to explore the effect of semen from infertile men (hereinafter "infertile semen") on BFI and to identify semen-specific mRNAs that can efficiently and accurately distinguish normal and infertile semen samples from other body fluids. Results showed that the selected five mRNAs (KLK3, TGM4, SEMG1, PRM1, and PRM2) performed a significantly high semen specificity in normal semen. Moreover, KLK3 was slightly influenced by infertile semen samples with over 98% positive results in all semen samples. The accuracy to predict normal semen reached up to 96.6% using the discrimination function Y1 with KLK3 and PRM1. However, when the infertile semen samples were included in discrimination function (function Y2 with KLK3), the accuracy rate of semen identification (including the normal and infertile semen) was down to 89.5%. Besides, the sensitivity of multiplex assay could reach down to 50pg. Our results suggest that it is important to consider the presence of infertile semen when using mRNAs to identify semen samples, which would have a far-reaching impact in forensic identification.
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Affiliation(s)
- Huan Tian
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Sicheng Huang
- Institute of Forensic Science, Chengdu Public Security Bureau, Chengdu, Sichuan, P. R. China
| | - Peng Bai
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Xiao Xiao
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Duo Peng
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Huan Zhao
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Yuqing Liu
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Qian Feng
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Miao Liao
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Fuping Li
- Human Sperm Bank, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second University Hospital of Sichuan University, Chengdu, Sichuan, P. R. China
| | - Weibo Liang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
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Díez López C, Kayser M, Vidaki A. Estimating the Time Since Deposition of Saliva Stains With a Targeted Bacterial DNA Approach: A Proof-of-Principle Study. Front Microbiol 2021; 12:647933. [PMID: 34149638 PMCID: PMC8206545 DOI: 10.3389/fmicb.2021.647933] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 04/14/2021] [Indexed: 01/04/2023] Open
Abstract
Information on the time when a stain was deposited at a crime scene can be valuable in forensic investigations. It can link a DNA-identified stain donor with a crime or provide a post-mortem interval estimation in cases with cadavers. The available methods for estimating stain deposition time have limitations of different types and magnitudes. In this proof-of-principle study we investigated for the first time the use of microbial DNA for this purpose in human saliva stains. First, we identified the most abundant and frequent bacterial species in saliva using publicly available 16S rRNA gene next generation sequencing (NGS) data from 1,848 samples. Next, we assessed time-dependent changes in 15 identified species using de-novo 16S rRNA gene NGS in the saliva stains of two individuals exposed to indoor conditions for up to 1 year. We selected four bacterial species, i.e., Fusobacterium periodonticum, Haemophilus parainfluenzae, Veillonella dispar, and Veillonella parvula showing significant time-dependent changes and developed a 4-plex qPCR assay for their targeted analysis. Then, we analyzed the saliva stains of 15 individuals exposed to indoor conditions for up to 1 month. Bacterial counts generally increased with time and explained 54.9% of the variation (p = <2.2E–16). Time since deposition explained ≥86.5% and ≥88.9% of the variation in each individual and species, respectively (p = <2.2E–16). Finally, based on sample duplicates we built and tested multiple linear regression models for predicting the stain deposition time at an individual level, resulting in an average mean absolute error (MAE) of 5 days (ranging 3.3–7.8 days). Overall, the deposition time of 181 (81.5%) stains was correctly predicted within 1 week. Prediction models were also assessed in stains exposed to similar conditions up to 1 month 7 months later, resulting in an average MAE of 8.8 days (ranging 3.9–16.9 days). Our proof-of-principle study suggests the potential of the DNA profiling of human commensal bacteria as a method of estimating saliva stains time since deposition in the forensic scenario, which may be expanded to other forensically relevant tissues. The study considers practical applications of this novel approach, but various forensic developmental validation and implementation criteria will need to be met in more dedicated studies in the future.
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Affiliation(s)
- Celia Díez López
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Athina Vidaki
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
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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: 1] [Impact Index Per Article: 0.3] [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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26
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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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Heneghan N, Fu J, Pritchard J, Payton M, Allen RW. The effect of environmental conditions on the rate of RNA degradation in dried blood stains. Forensic Sci Int Genet 2020; 51:102456. [PMID: 33444974 DOI: 10.1016/j.fsigen.2020.102456] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 12/11/2020] [Accepted: 12/13/2020] [Indexed: 11/18/2022]
Abstract
The relationship between RNA degradation and the age of a bloodstain has been suggested by the work of several investigators. A prior study from this laboratory described a qPCR assay that was effective at estimating the age of bloodstains stored in an environmentally controlled laboratory for periods of up to one year. In this study, the effect of the environmental conditions on the rate of RNA degradation during storage was analyzed. Bloodstains were prepared on stain cards and stored in one of 9 different environments for periods of up to 24 weeks. At selected times during the storage term, RNA was extracted, reverse transcribed, and the integrity of select transcripts analyzed. Three temperatures (37 °C, 20 °C, and 4 °C) and three relative humidities (rH) (75 %, 35 %, and 10 %) were combined pairwise. The rate of RNA degradation was found to increase 5-10 fold in stains stored at 37 °C versus those stored at 20 °C. The rate of RNA degradation was faster for stains stored at 20 °C compared to 4 °C but differed only 2-4 fold. Multivariate regression analysis suggests elevations in temperature or rH will accelerate RNA degradation and will do so to a similar extent. It is clear from the data that the integrity of the transcriptome in dried bloodstains is better preserved in a cold and dry environment. Investigations are ongoing to develop an approach for the estimation of sample age that incorporates the environmental conditions of a crime scene into the age estimate.
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Affiliation(s)
- Nicole Heneghan
- Harris County Institute of Forensic Sciences, Houston, TX, United States
| | - Jun Fu
- School of Forensic Sciences, Oklahoma State University Center for Health Sciences Tulsa, OK, United States
| | - Jane Pritchard
- School of Forensic Sciences, Oklahoma State University Center for Health Sciences Tulsa, OK, United States
| | - Mark Payton
- Chair and Professor, Department of Biomedical Sciences, Rocky Vista University, Denver, CO, United States
| | - Robert W Allen
- School of Forensic Sciences, Oklahoma State University Center for Health Sciences Tulsa, OK, United States.
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28
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MicroRNAs: An Update of Applications in Forensic Science. Diagnostics (Basel) 2020; 11:diagnostics11010032. [PMID: 33375374 PMCID: PMC7823886 DOI: 10.3390/diagnostics11010032] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/17/2020] [Accepted: 12/23/2020] [Indexed: 12/25/2022] Open
Abstract
MicroRNAs (miRNAs) are a class of non-coding RNAs containing 18–24 nucleotides that are involved in the regulation of many biochemical mechanisms in the human body. The level of miRNAs in body fluids and tissues increases because of altered pathophysiological mechanisms, thus they are employed as biomarkers for various diseases and conditions. In recent years, miRNAs obtained a great interest in many fields of forensic medicine given their stability and specificity. Several specific miRNAs have been studied in body fluid identification, in wound vitality in time of death determination, in drowning, in the anti-doping field, and other forensic fields. However, the major problems are (1) lack of universal protocols for diagnostic expression testing and (2) low reproducibility of independent studies. This review is an update on the application of these molecular markers in forensic biology.
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29
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Kennedy K, Heaton C, Langenburg G, Cole L, Clark T, Clench MR, Sears V, Sealey M, McColm R, Francese S. Pre-validation of a MALDI MS proteomics-based method for the reliable detection of blood and blood provenance. Sci Rep 2020; 10:17087. [PMID: 33051553 PMCID: PMC7555906 DOI: 10.1038/s41598-020-74253-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 09/28/2020] [Indexed: 12/18/2022] Open
Abstract
The reliable identification of blood, as well as the determination of its origin (human or animal) is of great importance in a forensic investigation. Whilst presumptive tests are rapid and deployed in situ, their very nature requires confirmatory tests to be performed remotely. However, only serological tests can determine blood provenance. The present study improves on a previously devised Matrix Assisted Laser Desorption Ionisation Mass Spectrometry (MALDI MS)—proteomics based method for the reliable detection of blood by enabling the determination of blood provenance. The overall protocol was developed to be more specific than presumptive tests and faster/easier than the gold standard liquid chromatography (LC) MS/MS analysis. This is considered a pre-validation study that has investigated stains and fingermarks made in blood, other biofluids and substances that can elicit a false-positive response to colorimetric or presumptive tests, in a blind fashion. Stains and marks were either untreated or enhanced with a range of presumptive tests. Human and animal blood were correctly discriminated from other biofluids and non-biofluid related matrices; animal species determination was also possible within the system investigated. The procedure is compatible with the prior application of presumptive tests. The refined strategy resulting from iterative improvements through a trial and error study of 56 samples was applied to a final set of 13 blind samples. This final study yielded 12/13 correct identifications with the 13th sample being correctly identified as animal blood but with no species attribution. This body of work will contribute towards the validation of MALDI MS based methods and deployment in violent crimes involving bloodshed.
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Affiliation(s)
- Katie Kennedy
- Centre for Mass Spectrometry Imaging, Biomolecular Sciences Research Centre, Sheffield Hallam University, Sheffield, UK
| | - Cameron Heaton
- Centre for Mass Spectrometry Imaging, Biomolecular Sciences Research Centre, Sheffield Hallam University, Sheffield, UK
| | | | - Laura Cole
- Centre for Mass Spectrometry Imaging, Biomolecular Sciences Research Centre, Sheffield Hallam University, Sheffield, UK
| | - Tom Clark
- Sheffield Hallam University, Sheffield, UK
| | - Malcolm R Clench
- Centre for Mass Spectrometry Imaging, Biomolecular Sciences Research Centre, Sheffield Hallam University, Sheffield, UK
| | - Vaughn Sears
- Former Centre for Applied Science and Technology (CAST), Home Office, St Albans, UK
| | - Mark Sealey
- Defence Science and Technology Laboratories (DSTL), Porton Down, Salisbury, UK
| | - Richard McColm
- Defence Science and Technology Laboratories (DSTL), Porton Down, Salisbury, UK
| | - Simona Francese
- Centre for Mass Spectrometry Imaging, Biomolecular Sciences Research Centre, Sheffield Hallam University, Sheffield, UK.
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30
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Sandstrom TS, Burke Schinkel SC, Angel JB. Medical Assistance in Death as a Unique Opportunity to Advance Human Immunodeficiency Virus Cure Research. Clin Infect Dis 2020; 69:1063-1067. [PMID: 30715211 DOI: 10.1093/cid/ciz068] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 11/12/2018] [Accepted: 01/18/2019] [Indexed: 12/31/2022] Open
Abstract
The inability to sample deep-tissue reservoirs in individuals living with human immunodeficiency virus (HIV) has greatly hindered accurate estimates of viral reservoir size and distribution. Animal models and collection of tissues during autopsies of HIV-positive individuals are 2 proposed solutions to this problem. Each, however, has its limitations. In this Viewpoint, we argue that tissue donation following medical assistance in death (MAiD) will form an invaluable resource for the characterization of the viral reservoir in the context of current HIV cure research. In support, we discuss a recent instance in which an individual living with HIV chose to donate their body/tissues to HIV research prior to undergoing MAiD at our institution. Going forward, we hope this will help provide support to individuals in their decisions around tissue donation following MAiD, while highlighting how healthcare providers, by complying with such wishes, can affect patient satisfaction in the last days of life.
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Affiliation(s)
- Teslin S Sandstrom
- Ottawa Hospital Research Institute.,Department of Biochemistry, Microbiology & Immunology, University of Ottawa
| | | | - Jonathan B Angel
- Ottawa Hospital Research Institute.,Department of Biochemistry, Microbiology & Immunology, University of Ottawa.,Division of Infectious Diseases, Ottawa Hospital-General Campus, Canada
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31
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Nido GS, Dick F, Toker L, Petersen K, Alves G, Tysnes OB, Jonassen I, Haugarvoll K, Tzoulis C. Common gene expression signatures in Parkinson's disease are driven by changes in cell composition. Acta Neuropathol Commun 2020; 8:55. [PMID: 32317022 PMCID: PMC7175586 DOI: 10.1186/s40478-020-00932-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 04/14/2020] [Indexed: 12/21/2022] Open
Abstract
The etiology of Parkinson’s disease is largely unknown. Genome-wide transcriptomic studies in bulk brain tissue have identified several molecular signatures associated with the disease. While these studies have the potential to shed light into the pathogenesis of Parkinson’s disease, they are also limited by two major confounders: RNA post-mortem degradation and heterogeneous cell type composition of bulk tissue samples. We performed RNA sequencing following ribosomal RNA depletion in the prefrontal cortex of 49 individuals from two independent case-control cohorts. Using cell type specific markers, we estimated the cell type composition for each sample and included this in our analysis models to compensate for the variation in cell type proportions. Ribosomal RNA depletion followed by capture by random primers resulted in substantially more even transcript coverage, compared to poly(A) capture, in post-mortem tissue. Moreover, we show that cell type composition is a major confounder of differential gene expression analysis in the Parkinson’s disease brain. Accounting for cell type proportions attenuated numerous transcriptomic signatures that have been previously associated with Parkinson’s disease, including vesicle trafficking, synaptic transmission, immune and mitochondrial function. Conversely, pathways related to endoplasmic reticulum, lipid oxidation and unfolded protein response were strengthened and surface as the top differential gene expression signatures in the Parkinson’s disease prefrontal cortex. Our results indicate that differential gene expression signatures in Parkinson’s disease bulk brain tissue are significantly confounded by underlying differences in cell type composition. Modeling cell type heterogeneity is crucial in order to unveil transcriptomic signatures that represent regulatory changes in the Parkinson’s disease brain and are, therefore, more likely to be associated with underlying disease mechanisms.
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32
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Javan GT, Hanson E, Finley SJ, Visonà SD, Osculati A, Ballantyne J. Identification of cadaveric liver tissues using thanatotranscriptome biomarkers. Sci Rep 2020; 10:6639. [PMID: 32313164 PMCID: PMC7170907 DOI: 10.1038/s41598-020-63727-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 03/31/2020] [Indexed: 01/10/2023] Open
Abstract
Thanatotranscriptome studies involve the examination of mRNA transcript abundance and gene expression patterns in the internal organs of deceased humans. Postmortem gene expression is indicative of the cellular status of a corpse at the time of death, a portion of which may represent a cascade of molecular events occasioned by death. Specific gene biomarkers identify perceptible transcriptional changes induced by stochastic responses to the cessation of biological functions. Transcriptome analyses of postmortem mRNA from a tissue fragment may determine unique molecular identifiers for specific organs and demonstrate unique patterns of gene expression that can provide essential contextual anatomical information. We evaluated the impact of targeted transcriptome analysis using RNA sequencing to reveal global changes in postmortem gene expression in liver tissues from 27 Italian and United States corpses: 3.5-hour-old to 37-day-old. We found that our single blind study using eight liver tissue-specific gene biomarkers (e.g. AMBP and AHSG) is highly specific, with autopsy-derived organ samples correctly identified as tissues originating from postmortem livers. The results demonstrate that 98–100% of sequencing reads were mapped to these liver biomarkers. Our findings indicate that gene expression signatures of mRNA exposed up to 37 days of autolysis, can be used to validate the putative identity of tissue fragments.
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Affiliation(s)
- Gulnaz T Javan
- Forensic Science Program, Physical Sciences Department, Alabama State University, Montgomery, AL, USA.
| | - Erin Hanson
- National Center for Forensic Science, University of Central Florida, Orlando, FL, USA
| | - Sheree J Finley
- Forensic Science Program, Physical Sciences Department, Alabama State University, Montgomery, AL, USA
| | - Silvia D Visonà
- Department of Public Health, Experimental and Forensic Medicine, University of Pavia, Pavia, Italy
| | - Antonio Osculati
- Department of Public Health, Experimental and Forensic Medicine, University of Pavia, Pavia, Italy
| | - Jack Ballantyne
- National Center for Forensic Science, University of Central Florida, Orlando, FL, USA
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Body fluid identification and assignment to donors using a targeted mRNA massively parallel sequencing approach – results of a second EUROFORGEN / EDNAP collaborative exercise. Forensic Sci Int Genet 2020; 45:102208. [DOI: 10.1016/j.fsigen.2019.102208] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/19/2019] [Accepted: 11/21/2019] [Indexed: 12/30/2022]
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34
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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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35
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Kim HJ, Lee YJ, Lee S, Lee YR, Son H, Shin M, Choi H, Yu J, Lee J, Kang HG. Metabolomic profiling of bloodstains on various absorbent and non-absorbent surfaces. Anal Bioanal Chem 2020; 412:1407-1417. [PMID: 31955234 DOI: 10.1007/s00216-019-02371-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 12/11/2019] [Accepted: 12/20/2019] [Indexed: 11/30/2022]
Abstract
Bloodstains found at crime scenes contain immense information about the crime; thus, studies involving analysis of small molecules in bloodstains have been conducted. However, most of these studies have not accounted for the difference in the results of small molecule analysis due to the surface of bloodstains. To evaluate the "surface effect," we prepared bloodstains on seven surfaces, including both absorbent and non-absorbent surfaces, and performed global small molecule analysis by high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). We used three indicators: (1) count recovery rate (%) of molecular features (MFs), (2) the number of MFs extracted from the surface without bloodstains, and (3) difference in abundance recovery rate (%) of MFs, to determine the ranking of the seven surfaces in the order of their similarity with blood. We also confirmed the correlation between each surface and blood through multivariate analysis. We found that the non-absorbent surfaces ranked better than the absorbent surfaces; wooden flooring was ranked as the most efficient surface, followed by stainless, vinyl flooring, glass, tile, filter paper, and mixed cotton. This study will help in the selection of the most efficient surface for collection of bloodstains for small molecule analysis from a crime scene. This is the first study to identify the effects of surface on extraction of global small molecules from bloodstains; it will help forensic scientists in obtaining more accurate information from small molecules present in the bloodstains collected at the field. Graphical abstract.
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Affiliation(s)
- Hyo-Jin Kim
- Department of Senior Healthcare, BK21 Plus Program, Graduate School, Eulji University, Seongnam, 13135, South Korea
| | - Yoo-Jin Lee
- Department of Senior Healthcare, BK21 Plus Program, Graduate School, Eulji University, Seongnam, 13135, South Korea
| | - Seungyeon Lee
- Department of Biomedical Laboratory Science, College of Health Sciences, Eulji University, Seongnam, 13135, South Korea
| | - You-Rim Lee
- Department of Senior Healthcare, BK21 Plus Program, Graduate School, Eulji University, Seongnam, 13135, South Korea
| | - Hyunsong Son
- Department of Senior Healthcare, BK21 Plus Program, Graduate School, Eulji University, Seongnam, 13135, South Korea
| | - Miji Shin
- Department of Senior Healthcare, BK21 Plus Program, Graduate School, Eulji University, Seongnam, 13135, South Korea
| | - Hyebin Choi
- Department of Senior Healthcare, BK21 Plus Program, Graduate School, Eulji University, Seongnam, 13135, South Korea
| | - Jaehee Yu
- Department of Biomedical Laboratory Science, College of Health Sciences, Eulji University, Seongnam, 13135, South Korea
| | - Jiyeong Lee
- Department of Biomedical Laboratory Science, College of Health Sciences, Eulji University, Seongnam, 13135, South Korea.
| | - Hee-Gyoo Kang
- Department of Senior Healthcare, BK21 Plus Program, Graduate School, Eulji University, Seongnam, 13135, South Korea. .,Department of Biomedical Laboratory Science, College of Health Sciences, Eulji University, Seongnam, 13135, South Korea. .,Seongnam Senior Industry Innovation Center, Eulji University, Seongnam, 13503, South Korea.
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36
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Life and death: A systematic comparison of antemortem and postmortem gene expression. Gene 2020; 731:144349. [PMID: 31935499 DOI: 10.1016/j.gene.2020.144349] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 01/06/2020] [Accepted: 01/07/2020] [Indexed: 12/30/2022]
Abstract
Gene expression is the process by which DNA is decoded to produce a functional transcript. The collection of all transcripts is referred to as the transcriptome and has extensively been used to evaluate differentially expressed genes in a certain cell or tissue type. In response to internal or external stimuli, the transcriptome is greatly regulated by epigenetic changes. Many studies have elucidated that antemortem gene expression (transcriptome) may be linked to an array of disease etiologies as well as potential targets for drug discovery; on the other hand, a number of studies have utilized postmortem gene expression (thanatotranscriptome) patterns to determine cause and time of death. The "transcriptome after death" involves the study of mRNA transcripts occurring in human tissues after death (thanatos, Greek for death). While antemortem gene expression can provide a wide range of important information about the host, the determination of the communication of genes after a human dies has recently been explored. After death a plethora of genes are regulated via activation versus repression as well as diverse regulatory factors such as the absence or presence of stimulated feedback. Even postmortem transcriptional regulation contains many more cellular constituents and is massively more complicated. The rates of degradation of mRNA transcripts vary depending on the types of postmortem tissues and their combinatorial gene expression signatures. mRNA molecules have been shown to persist for extended time frames; nevertheless, they are highly susceptible to degradation, with half-lives of selected mRNAs varying between minutes to weeks for specifically induced genes. Furthermore, postmortem genetic studies may be used to improve organ transplantation techniques. This review is the first of its kind to fully explore both gene expression and mRNA stability after death and the trove of information that can be provided about phenotypical characteristics of specific genes postmortem.
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Iacobuzio-Donahue CA, Michael C, Baez P, Kappagantula R, Hooper JE, Hollman TJ. Cancer biology as revealed by the research autopsy. Nat Rev Cancer 2019; 19:686-697. [PMID: 31519982 PMCID: PMC7453489 DOI: 10.1038/s41568-019-0199-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/13/2019] [Indexed: 12/19/2022]
Abstract
A research autopsy is a post-mortem medical procedure performed on a deceased individual with the primary goal of collecting tissue to support basic and translational research. This approach has increasingly been used to investigate the pathophysiological mechanisms of cancer evolution, metastasis and treatment resistance. In this Review, we discuss the rationale for the use of research autopsies in cancer research and provide an evidence-based discussion of the quality of post-mortem tissues compared with other types of biospecimens. We also discuss the advantages of using post-mortem tissues over other types of biospecimens, including the large amounts of tissue that can be obtained and the extent of multiregion sampling that is achievable, which is not otherwise possible in living patients. We highlight how the research autopsy has supported the identification of the clonal origins and modes of spread among metastases, the extent that selective pressures imposed by treatments cause bottlenecks leading to parallel and convergent tumour evolution, and the creation of rare tissue banks and patient-derived model systems. Finally, we comment on the future of the research autopsy as an integral component of precision medicine strategies.
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Affiliation(s)
- Christine A Iacobuzio-Donahue
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Chelsea Michael
- Department of Health Informatics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Priscilla Baez
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rajya Kappagantula
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jody E Hooper
- Department of Pathology, The Johns Hopkins University, Baltimore, MD, USA
| | - Travis J Hollman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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38
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Nonhuman forensic genetics. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.09.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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39
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Fujimoto S, Manabe S, Hirai E, Morimoto C, Tamaki K. Novel index of body fluid-RNA integrity based on small RNA electropherogram. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.10.131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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40
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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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41
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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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42
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Martínez PN, Menéndez ST, Villaronga MDLÁ, Ubelaker DH, García-Pedrero JM, C Zapico S. "The big sleep: Elucidating the sequence of events in the first hours of death to determine the postmortem interval". Sci Justice 2019; 59:418-424. [PMID: 31256813 DOI: 10.1016/j.scijus.2019.03.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 02/24/2019] [Accepted: 03/03/2019] [Indexed: 12/20/2022]
Abstract
Recent developments on postmortem interval estimation (PMI) take an advantage of the autolysis process, pointing out to the analysis of the expression of apoptosis and autophagy genes towards this purpose. Oxidative stress plays a role in this signaling as a regulatory mechanism and/or as a consequence of cell death. Additionally, melatonin has been implicated on apoptosis and autophagy signaling, making melatonin a suitable target for PMI determination. The aim of this study was to investigate the early PMI through the analysis of the expression of autophagy genes as well as oxidative stress and melatonin receptor. Our results demonstrated a rapidly increased on the expression of autophagy genes according to the expected sequence of events, then a marked decrease in this expression, matched with the switch to the apoptosis signaling. These results revealed potential candidates to analyze the PMI in the first hours of death, helping to estimate the time-since-death.
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Affiliation(s)
- Paula Núñez Martínez
- Departamento de Biología Funcional (Área de Fisiología), Facultad de Medicina y Ciencias de la Salud, Universidad de Oviedo, Spain
| | - Sofía T Menéndez
- Hospital Universitario Central de Asturias, Instituto de Investigación Sanitaria del Principado de Asturias, Instituto Universitario de Oncología del Principado de Asturias, Oviedo, Spain; CIBER de Cáncer (CIBERONC), Madrid, Spain
| | - María de Los Ángeles Villaronga
- Hospital Universitario Central de Asturias, Instituto de Investigación Sanitaria del Principado de Asturias, Instituto Universitario de Oncología del Principado de Asturias, Oviedo, Spain; CIBER de Cáncer (CIBERONC), Madrid, Spain
| | - Douglas H Ubelaker
- Anthropology Department, NMNH, Smithsonian Institution, MRC 112, Washington, DC, USA
| | - Juana M García-Pedrero
- Hospital Universitario Central de Asturias, Instituto de Investigación Sanitaria del Principado de Asturias, Instituto Universitario de Oncología del Principado de Asturias, Oviedo, Spain; CIBER de Cáncer (CIBERONC), Madrid, Spain
| | - Sara C Zapico
- Anthropology Department, NMNH, Smithsonian Institution, MRC 112, Washington, DC, USA; Department of Chemistry and Biochemistry, International Forensic Research Institute, Florida International University, Miami, FL, USA.
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43
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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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44
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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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45
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Elghamry HA, Hassan FM, Mohamed MI, Abdelfattah DS, Abdelaal AG. Estimation of the postmortem interval using GAPDH mRNA in skin and heart tissues of albino rats at different environmental conditions. EGYPTIAN JOURNAL OF FORENSIC SCIENCES 2018. [DOI: 10.1186/s41935-018-0102-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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46
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Age Determination of Blood-Stained Fingerprints Using Visible Wavelength Reflectance Hyperspectral Imaging. J Imaging 2018. [DOI: 10.3390/jimaging4120141] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The ability to establish the exact time a crime was committed is one of the fundamental aims of forensic science. The analysis of recovered evidence can provide information to assist in age determination, such as blood, which is one of the most commonly encountered types of biological evidence and the most common fingerprint contaminant. There are currently no accepted methods to establish the age of a blood-stained fingerprint, so progress in this area would be of considerable benefit for forensic investigations. A novel application of visible wavelength reflectance, hyperspectral imaging (HSI), is used for the detection and age determination of blood-stained fingerprints on white ceramic tiles. Both identification and age determination are based on the unique visible absorption spectrum of haemoglobin between 400 and 680 nm and the presence of the Soret peak at 415 nm. In this study, blood-stained fingerprints were aged over 30 days and analysed using HSI. False colour aging scales were produced from a 30-day scale and a 24 h scale, allowing for a clear visual method for age estimations for deposited blood-stained fingerprints. Nine blood-stained fingerprints of varying ages deposited on one white ceramic tile were easily distinguishable using the 30-day false colour scale.
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47
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"The acid test"-validation of the ParaDNA® Body Fluid ID Test for routine forensic casework. Int J Legal Med 2018; 133:751-757. [PMID: 30460509 DOI: 10.1007/s00414-018-1971-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 11/12/2018] [Indexed: 01/18/2023]
Abstract
The identification of the cellular origin and composition of crime scene-related traces can provide crucial insight into a crime scene reconstruction. In the last decade, especially mRNA-based body fluid and tissue identification (BFI) has been vigorously examined. Besides capillary electrophoretic (CE) and real-time quantitative PCR (RT-qPCR)-based approaches for mRNA detection, melt curve analysis bears potential as a simple-to-use method for BFI. The ParaDNA® Body Fluid ID Test relies on HyBeacon® probes and was developed as a rapid test for mRNA-based BFI of six different body fluids: vaginal fluid, seminal fluid, sperm cells, saliva, menstrual, and peripheral blood. The herein presented work was performed as an "acid test" of the system and should clarify whether the approach matches the requirements of forensic routine casework in German police departments. Tested samples consisted of single source as well as of mixed samples.
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48
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Blackman S, Stafford-Allen B, Hanson EK, Panasiuk M, Brooker AL, Rendell P, Ballantyne J, Wells S. Developmental validation of the ParaDNA® Body Fluid ID System—A rapid multiplex mRNA-profiling system for the forensic identification of body fluids. Forensic Sci Int Genet 2018; 37:151-161. [DOI: 10.1016/j.fsigen.2018.08.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 06/01/2018] [Accepted: 08/22/2018] [Indexed: 11/28/2022]
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49
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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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50
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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: 152] [Impact Index Per Article: 25.3] [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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