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Procopio N, Bonicelli A. From flesh to bones: Multi-omics approaches in forensic science. Proteomics 2024; 24:e2200335. [PMID: 38683823 DOI: 10.1002/pmic.202200335] [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: 10/28/2023] [Revised: 03/12/2024] [Accepted: 03/26/2024] [Indexed: 05/02/2024]
Abstract
Recent advancements in omics techniques have revolutionised the study of biological systems, enabling the generation of high-throughput biomolecular data. These innovations have found diverse applications, ranging from personalised medicine to forensic sciences. While the investigation of multiple aspects of cells, tissues or entire organisms through the integration of various omics approaches (such as genomics, epigenomics, metagenomics, transcriptomics, proteomics and metabolomics) has already been established in fields like biomedicine and cancer biology, its full potential in forensic sciences remains only partially explored. In this review, we have presented a comprehensive overview of state-of-the-art analytical platforms employed in omics research, with specific emphasis on their application in the forensic field for the identification of the cadaver and the cause of death. Moreover, we have conducted a critical analysis of the computational integration of omics approaches, and highlighted the latest advancements in employing multi-omics techniques for forensic investigations.
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Affiliation(s)
- Noemi Procopio
- Research Centre for Field Archaeology and Experimental Taphonomy, School of Law and Policing, University of Central Lancashire, Preston, UK
| | - Andrea Bonicelli
- Research Centre for Field Archaeology and Experimental Taphonomy, School of Law and Policing, University of Central Lancashire, Preston, UK
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2
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Huang W, Zhao S, Liu H, Pan M, Dong H. The Role of Protein Degradation in Estimation Postmortem Interval and Confirmation of Cause of Death in Forensic Pathology: A Literature Review. Int J Mol Sci 2024; 25:1659. [PMID: 38338938 PMCID: PMC10855206 DOI: 10.3390/ijms25031659] [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: 12/10/2023] [Revised: 01/04/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024] Open
Abstract
It is well known that proteins are important bio-macromolecules in human organisms, and numerous proteins are widely used in the clinical practice, whereas their application in forensic science is currently limited. This limitation is mainly attributed to the postmortem degradation of targeted proteins, which can significantly impact final conclusions. In the last decade, numerous methods have been established to detect the protein from a forensic perspective, and some of the postmortem proteins have been applied in forensic practice. To better understand the emerging issues and challenges in postmortem proteins, we have reviewed the current application of protein technologies at postmortem in forensic practice. Meanwhile, we discuss the application of proteins in identifying the cause of death, and postmortem interval (PMI). Finally, we highlight the interpretability and limitations of postmortem protein challenges. We believe that utilizing the multi-omics method can enhance the comprehensiveness of applying proteins in forensic practice.
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Affiliation(s)
- Weisheng Huang
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, No. 13 Hangkong Road, Hankou, Wuhan 430030, China; (W.H.)
| | - Shuquan Zhao
- Faculty of Forensic Pathology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China;
| | - Huine Liu
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, No. 13 Hangkong Road, Hankou, Wuhan 430030, China; (W.H.)
| | - Meichen Pan
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, No. 13 Hangkong Road, Hankou, Wuhan 430030, China; (W.H.)
| | - Hongmei Dong
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, No. 13 Hangkong Road, Hankou, Wuhan 430030, China; (W.H.)
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3
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Woess C, Huck CW, Badzoka J, Kappacher C, Arora R, Lindtner RA, Zelger P, Schirmer M, Rabl W, Pallua J. Raman spectroscopy for postmortem interval estimation of human skeletal remains: A scoping review. JOURNAL OF BIOPHOTONICS 2023; 16:e202300189. [PMID: 37494000 DOI: 10.1002/jbio.202300189] [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: 05/24/2023] [Revised: 07/19/2023] [Accepted: 07/22/2023] [Indexed: 07/27/2023]
Abstract
Estimating postmortem intervals (PMI) is crucial in forensic investigations, providing insights into criminal cases and determining the time of death. PMI estimation relies on expert experience and a combination of thanatological data and environmental factors but is prone to errors. The lack of reliable methods for assessing PMI in bones and soft tissues necessitates a better understanding of bone decomposition. Several research groups have shown promise in PMI estimation in skeletal remains but lack valid data for forensic cases. Current methods are costly, time-consuming, and unreliable for PMIs over 5 years. Raman spectroscopy (RS) can potentially estimate PMI by studying chemical modifications in bones and teeth correlated with burial time. This review summarizes RS applications, highlighting its potential as an innovative, nondestructive, and fast technique for PMI estimation in forensic medicine.
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Affiliation(s)
- C Woess
- Institute of Forensic Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Christian W Huck
- Institute of Analytical Chemistry and Radiochemistry, University of Innsbruck, Innsbruck, Austria
| | - J Badzoka
- Institute of Analytical Chemistry and Radiochemistry, University of Innsbruck, Innsbruck, Austria
| | - C Kappacher
- Institute of Analytical Chemistry and Radiochemistry, University of Innsbruck, Innsbruck, Austria
| | - R Arora
- Department of Orthopaedics and Traumatology, Medical University of Innsbruck, Innsbruck, Austria
| | - R A Lindtner
- Department of Orthopaedics and Traumatology, Medical University of Innsbruck, Innsbruck, Austria
| | - Philipp Zelger
- University Clinic for Hearing, Voice and Speech Disorders, Medical University of Innsbruck, Innsbruck, Austria
| | - M Schirmer
- Department of Internal Medicine, Clinic II, Medical University of Innsbruck, Innsbruck, Austria
| | - W Rabl
- Institute of Forensic Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Johannes Pallua
- Department of Orthopaedics and Traumatology, Medical University of Innsbruck, Innsbruck, Austria
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Vignali G, Franceschetti L, Attisano GCL, Cattaneo C. Assessing wound vitality in decomposed bodies: a review of the literature. Int J Legal Med 2023; 137:459-470. [PMID: 36550324 DOI: 10.1007/s00414-022-02932-9] [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: 08/16/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022]
Abstract
The capability of discriminating between a vital and a post-mortem injury has always been a central theme in forensic pathology, particularly when the corpse is an advanced state of decomposition. Post-mortem decay of the body can mask or disrupt the classical features of a skin lesion, making it difficult to establish the cause and manner of death. Taphonomically challenging situations pose several interpretative issues of skin lesions which need to be addressed with scientifically recent methods that are still limited in the forensic literature. For that reason, the present research aims at resuming what is currently available in the attempt to provide some insight regarding this topic. This review considers only original researches, in which the markers of vitality were studied a significant amount of time after death, in order to test post-mortem persistency of these markers over time. A number of 132 original articles and reviews were considered, and the most significant results are resumed in an overview table and in two intuitive figures. Though many researchers tried to establish the vitality of lesions in specimen, few analysed samples from bodies when a significant degree of putrefaction or burning had occurred. The most significant marker proved to be GPA, which sowed a satisfying persistence over time (up to 6 months in air putrefaction and 15 days in water). However, what clearly emerged is that further studies are needed to address the challenges of taphonomically transformed specimen and to possibly neutralize the variability of experimental conditions, which affect the reproducibility of results. In conclusion, this study could be a starting point for providing food for thoughts about the most useful markers to search for in unusually tricky autopsy cases.
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Affiliation(s)
- Giulia Vignali
- Institute of Legal Medicine, Department of Biomedical Sciences for Health, University of Milan, Milan, Italy.
| | - Lorenzo Franceschetti
- LABANOF (Laboratorio Di Antropologia E Odontologia Forense), Institute of Legal Medicine, Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Giuseppe Carlo Lanza Attisano
- LABANOF (Laboratorio Di Antropologia E Odontologia Forense), Institute of Legal Medicine, Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Cristina Cattaneo
- LABANOF (Laboratorio Di Antropologia E Odontologia Forense), Institute of Legal Medicine, Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
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Application of artificial intelligence and machine learning technology for the prediction of postmortem interval: A systematic review of preclinical and clinical studies. Forensic Sci Int 2022; 340:111473. [PMID: 36166880 DOI: 10.1016/j.forsciint.2022.111473] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 06/28/2022] [Accepted: 09/18/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND /PURPOSE Establishing an accurate postmortem interval (PMI) is exceptionally crucial in forensic investigation. Artificial intelligence (AI) and Machine learning (ML) models are widely employed in forensic practice. ML is a part of AI, both terms are highly associated and sometimes used interchangeably. This systematic review aims to evaluate the application and performance of AI technology for the prediction of PMI. METHODS Systematic literature search across different electronic databases using PubMed/Google Scholar/EMBASE/Scopus/CINAHL/Web of Science/Cochrane library was conducted from inception to 3 December 2021 for preclinical and clinical studies reported ML models for PMI estimation. RESULTS We identified 18 studies (12 preclinical and 06 clinical) that met the inclusion criteria in the qualitative analysis. Most of the studies employed supervised learning (N = 15), and others employed unsupervised learning (N = 3). Due to the heterogeneity of the samples, quantitative analysis was not performed. CONCLUSION In this systematic review, we discussed the performance of AI-based automated systems in PMI estimation. ML models have demonstrated accuracy and precision and the ability to overcome human errors and bias. However, the research is limited, conducted in primarily small, selected human populations. In addition, we suggest further research in larger population-based studies is needed to fully understand the extent of integrated ML models.
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Forensic proteomics. Forensic Sci Int Genet 2021; 54:102529. [PMID: 34139528 DOI: 10.1016/j.fsigen.2021.102529] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 12/19/2022]
Abstract
Protein is a major component of all biological evidence, often the matrix that embeds other biomolecules such as polynucleotides, lipids, carbohydrates, and small molecules. The proteins in a sample reflect the transcriptional and translational program of the originating cell types. Because of this, proteins can be used to identify body fluids and tissues, as well as convey genetic information in the form of single amino acid polymorphisms, the result of non-synonymous SNPs. This review explores the application and potential of forensic proteomics. The historical role that protein analysis played in the development of forensic science is examined. This review details how innovations in proteomic mass spectrometry have addressed many of the historical limitations of forensic protein science, and how the application of forensic proteomics differs from proteomics in the life sciences. Two more developed applications of forensic proteomics are examined in detail: body fluid and tissue identification, and proteomic genotyping. The review then highlights developing areas of proteomics that have the potential to impact forensic science in the near future: fingermark analysis, species identification, peptide toxicology, proteomic sex estimation, and estimation of post-mortem intervals. Finally, the review highlights some of the newer innovations in proteomics that may drive further development of the field. In addition to potential impact, this review also attempts to evaluate the stage of each application in the development, validation and implementation process. This review is targeted at investigators who are interested in learning about proteomics in a forensic context and expanding the amount of information they can extract from biological evidence.
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Abstract
Proteomics, the large-scale study of all proteins of an organism or system, is a powerful tool for studying biological systems. It can provide a holistic view of the physiological and biochemical states of given samples through identification and quantification of large numbers of peptides and proteins. In forensic science, proteomics can be used as a confirmatory and orthogonal technique for well-built genomic analyses. Proteomics is highly valuable in cases where nucleic acids are absent or degraded, such as hair and bone samples. It can be used to identify body fluids, ethnic group, gender, individual, and estimate post-mortem interval using bone, muscle, and decomposition fluid samples. Compared to genomic analysis, proteomics can provide a better global picture of a sample. It has been used in forensic science for a wide range of sample types and applications. In this review, we briefly introduce proteomic methods, including sample preparation techniques, data acquisition using liquid chromatography-tandem mass spectrometry, and data analysis using database search, spectral library search, and de novo sequencing. We also summarize recent applications in the past decade of proteomics in forensic science with a special focus on human samples, including hair, bone, body fluids, fingernail, muscle, brain, and fingermark, and address the challenges, considerations, and future developments of forensic proteomics.
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8
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Mass spectrometry-based proteomics for the forensic identification of vomit traces. J Proteomics 2019; 209:103524. [DOI: 10.1016/j.jprot.2019.103524] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 08/19/2019] [Accepted: 09/12/2019] [Indexed: 02/06/2023]
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9
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Applications and challenges of forensic proteomics. Forensic Sci Int 2019; 297:350-363. [DOI: 10.1016/j.forsciint.2019.01.022] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 01/09/2019] [Accepted: 01/13/2019] [Indexed: 12/23/2022]
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10
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Sterling S, Mason KE, Anex DS, Parker GJ, Hart B, Prinz M. Combined
DNA
Typing and Protein Identification from Unfired Brass Cartridges,,,. J Forensic Sci 2019; 64:1475-1481. [DOI: 10.1111/1556-4029.14042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 02/15/2019] [Accepted: 02/15/2019] [Indexed: 12/25/2022]
Affiliation(s)
| | - Katelyn E. Mason
- Lawrence Livermore National Laboratory 7000 East Avenue Livermore CA 94550
| | - Deon S. Anex
- Lawrence Livermore National Laboratory 7000 East Avenue Livermore CA 94550
| | | | - Bradley Hart
- Lawrence Livermore National Laboratory 7000 East Avenue Livermore CA 94550
| | - Mechthild Prinz
- John Jay College of Criminal Justice 524 W. 59th St. New York NY 10019
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11
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Kushner IK, Clair G, Purvine SO, Lee JY, Adkins JN, Payne SH. Individual Variability of Protein Expression in Human Tissues. J Proteome Res 2018; 17:3914-3922. [PMID: 30300549 DOI: 10.1021/acs.jproteome.8b00580] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Human tissues are known to exhibit interindividual variability, but a deeper understanding of the different factors affecting protein expression is necessary to further apply this knowledge. Our goal was to explore the proteomic variability between individuals as well as between healthy and diseased samples, and to test the efficacy of machine learning classifiers. In order to investigate whether disparate proteomics data sets may be combined, we performed a retrospective analysis of proteomics data from 9 different human tissues. These data sets represent several different sample prep methods, mass spectrometry instruments, and tissue health. Using these data, we examined interindividual and intertissue variability in peptide expression, and analyzed the methods required to build accurate tissue classifiers. We also evaluated the limits of tissue classification by downsampling the peptide data to simulate situations where less data is available, such as clinical biopsies, laser capture microdissection or potentially single-cell proteomics. Our findings reveal the strong potential for utilizing proteomics data to build robust tissue classifiers, which has many prospective clinical applications for evaluating the applicability of model clinical systems.
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Affiliation(s)
- Irena K Kushner
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99336 , United States
| | - Geremy Clair
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99336 , United States
| | - Samuel Owen Purvine
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99336 , United States
| | - Joon-Yong Lee
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99336 , United States
| | - Joshua N Adkins
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99336 , United States
| | - Samuel H Payne
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99336 , United States
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12
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Pieri M, Lombardi A, Basilicata P, Mamone G, Picariello G. Proteomics in Forensic Sciences: Identification of the Nature of the Last Meal at Autopsy. J Proteome Res 2018; 17:2412-2420. [DOI: 10.1021/acs.jproteome.8b00159] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Maria Pieri
- Dipartimento di Scienze Biomediche Avanzate − Sezione di Medicina Legale. University of Naples “Federico II”, Via S. Pansini, 5, 80131 Naples, Italy
| | | | - Pascale Basilicata
- Dipartimento di Scienze Biomediche Avanzate − Sezione di Medicina Legale. University of Naples “Federico II”, Via S. Pansini, 5, 80131 Naples, Italy
| | - Gianfranco Mamone
- Istituto di Scienze dell’Alimentazione − Consiglio Nazionale delle Ricerche (CNR), Via Roma 64, 83100 Avellino, Italy
| | - Gianluca Picariello
- Istituto di Scienze dell’Alimentazione − Consiglio Nazionale delle Ricerche (CNR), Via Roma 64, 83100 Avellino, Italy
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13
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Moini M. Applications of liquid-based separation in conjunction with mass spectrometry to the analysis of forensic evidence. Electrophoresis 2018. [PMID: 29529344 DOI: 10.1002/elps.201700501] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In the past few years, there has been a significant effort by the forensic science community to develop new scientific techniques for the analysis of forensic evidence. Forensic chemists have been spearheaded to develop information-rich confirmatory technologies and techniques and apply them to a broad array of forensic challenges. The purpose of these confirmatory techniques is to provide alternatives to presumptive techniques that rely on data such as color changes, pattern matching, or retention time alone, which are prone to more false positives. To this end, the application of separation techniques in conjunction with mass spectrometry has played an important role in the analysis of forensic evidence. Moreover, in the past few years the role of liquid separation techniques, such as liquid chromatography and capillary electrophoresis in conjunction with mass spectrometry, has gained significant tractions and have been applied to a wide range of chemicals, from small molecules such as drugs and explosives, to large molecules such as proteins. For example, proteomics and peptidomics have been used for identification of humans, organs, and bodily fluids. A wide range of HPLC techniques including reversed phase, hydrophilic interaction, mixed-mode, supercritical fluid, multidimensional chromatography, and nanoLC, as well as several modes of capillary electrophoresis mass spectrometry, including capillary zone electrophoresis, partial filling, full filling, and micellar electrokenetic chromatography have been applied to the analysis drugs, explosives, and questioned documents. In this article, we review recent (2015-2017) applications of liquid separation in conjunction with mass spectrometry to the analysis of forensic evidence.
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Affiliation(s)
- Mehdi Moini
- Department of Forensic Sciences, George Washington University, Washington, D.C., USA
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14
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Hanson E, Ballantyne J. Human Organ Tissue Identification by Targeted RNA Deep Sequencing to Aid the Investigation of Traumatic Injury. Genes (Basel) 2017; 8:genes8110319. [PMID: 29125589 PMCID: PMC5704232 DOI: 10.3390/genes8110319] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 11/03/2017] [Accepted: 11/06/2017] [Indexed: 11/16/2022] Open
Abstract
Molecular analysis of the RNA transcriptome from a putative tissue fragment should permit the assignment of its source to a specific organ, since each will exhibit a unique pattern of gene expression. Determination of the organ source of tissues from crime scenes may aid in shootings and other investigations. We have developed a prototype massively parallel sequencing (MPS) mRNA profiling assay for organ tissue identification that is designed to definitively identify 10 organ/tissue types using a targeted panel of 46 mRNA biomarkers. The identifiable organs and tissues include brain, lung, liver, heart, kidney, intestine, stomach, skeletal muscle, adipose, and trachea. The biomarkers were chosen after iterative specificity testing of numerous candidate genes in various tissue types. The assay is very specific, with little cross-reactivity with non-targeted tissue, and can detect RNA mixtures from different tissues. We also demonstrate the ability of the assay to successful identify the tissue source of origin using a single blind study.
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Affiliation(s)
- Erin Hanson
- National Center for Forensic Science, University of Central Florida, Orlando, FL 32816, USA.
| | - Jack Ballantyne
- National Center for Forensic Science, University of Central Florida, Orlando, FL 32816, USA.
- Department of Chemistry, University of Central Florida, Orlando, FL 32816, USA.
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15
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Merkley ED, Sego LH, Lin A, Leiser OP, Kaiser BLD, Adkins JN, Keim PS, Wagner DM, Kreuzer HW. Protein abundances can distinguish between naturally-occurring and laboratory strains of Yersinia pestis, the causative agent of plague. PLoS One 2017; 12:e0183478. [PMID: 28854255 PMCID: PMC5576697 DOI: 10.1371/journal.pone.0183478] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 08/05/2017] [Indexed: 11/19/2022] Open
Abstract
The rapid pace of bacterial evolution enables organisms to adapt to the laboratory environment with repeated passage and thus diverge from naturally-occurring environmental ("wild") strains. Distinguishing wild and laboratory strains is clearly important for biodefense and bioforensics; however, DNA sequence data alone has thus far not provided a clear signature, perhaps due to lack of understanding of how diverse genome changes lead to convergent phenotypes, difficulty in detecting certain types of mutations, or perhaps because some adaptive modifications are epigenetic. Monitoring protein abundance, a molecular measure of phenotype, can overcome some of these difficulties. We have assembled a collection of Yersinia pestis proteomics datasets from our own published and unpublished work, and from a proteomics data archive, and demonstrated that protein abundance data can clearly distinguish laboratory-adapted from wild. We developed a lasso logistic regression classifier that uses binary (presence/absence) or quantitative protein abundance measures to predict whether a sample is laboratory-adapted or wild that proved to be ~98% accurate, as judged by replicated 10-fold cross-validation. Protein features selected by the classifier accord well with our previous study of laboratory adaptation in Y. pestis. The input data was derived from a variety of unrelated experiments and contained significant confounding variables. We show that the classifier is robust with respect to these variables. The methodology is able to discover signatures for laboratory facility and culture medium that are largely independent of the signature of laboratory adaptation. Going beyond our previous laboratory evolution study, this work suggests that proteomic differences between laboratory-adapted and wild Y. pestis are general, potentially pointing to a process that could apply to other species as well. Additionally, we show that proteomics datasets (even archived data collected for different purposes) contain the information necessary to distinguish wild and laboratory samples. This work has clear applications in biomarker detection as well as biodefense.
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Affiliation(s)
- Eric D. Merkley
- Chemical and Biological Signature Sciences, Pacific Northwest National Laboratory, Richland, Washington, United States of America
- * E-mail:
| | - Landon H. Sego
- Applied Statistics and Computational Modeling, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Andy Lin
- Chemical and Biological Signature Sciences, Pacific Northwest National Laboratory, Richland, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Owen P. Leiser
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Brooke L. Deatherage Kaiser
- Chemical and Biological Signature Sciences, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Joshua N. Adkins
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Paul S. Keim
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - David M. Wagner
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Helen W. Kreuzer
- Chemical and Biological Signature Sciences, Pacific Northwest National Laboratory, Richland, Washington, United States of America
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