1
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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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Gent L, Chiappetta ME, Hesketh S, Palmowski P, Porter A, Bonicelli A, Schwalbe EC, Procopio N. Bone Proteomics Method Optimization for Forensic Investigations. J Proteome Res 2024; 23:1844-1858. [PMID: 38621258 PMCID: PMC11077585 DOI: 10.1021/acs.jproteome.4c00151] [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: 02/28/2024] [Revised: 03/30/2024] [Accepted: 04/03/2024] [Indexed: 04/17/2024]
Abstract
The application of proteomic analysis to forensic skeletal remains has gained significant interest in improving biological and chronological estimations in medico-legal investigations. To enhance the applicability of these analyses to forensic casework, it is crucial to maximize throughput and proteome recovery while minimizing interoperator variability and laboratory-induced post-translational protein modifications (PTMs). This work compared different workflows for extracting, purifying, and analyzing bone proteins using liquid chromatography with tandem mass spectrometry (LC-MS)/MS including an in-StageTip protocol previously optimized for forensic applications and two protocols using novel suspension-trap technology (S-Trap) and different lysis solutions. This study also compared data-dependent acquisition (DDA) with data-independent acquisition (DIA). By testing all of the workflows on 30 human cortical tibiae samples, S-Trap workflows resulted in increased proteome recovery with both lysis solutions tested and in decreased levels of induced deamidations, and the DIA mode resulted in greater sensitivity and window of identification for the identification of lower-abundance proteins, especially when open-source software was utilized for data processing in both modes. The newly developed S-Trap protocol is, therefore, suitable for forensic bone proteomic workflows and, particularly when paired with DIA mode, can offer improved proteomic outcomes and increased reproducibility, showcasing its potential in forensic proteomics and contributing to achieving standardization in bone proteomic analyses for forensic applications.
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Affiliation(s)
- Luke Gent
- School
of Law and Policing, Research Centre for Field Archaeology and Forensic
Taphonomy, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | - Maria Elena Chiappetta
- School
of Law and Policing, Research Centre for Field Archaeology and Forensic
Taphonomy, University of Central Lancashire, Preston PR1 2HE, United Kingdom
- Department
of Biology, Ecology and Earth Sciences (DiBEST), University of Calabria, Arcavacata
di Rende 87036, Italy
| | - Stuart Hesketh
- School
of Medicine, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | - Pawel Palmowski
- NUPPA
Facility, Medical School, Newcastle University, Newcastle Upon Tyne NE1
7RU, United Kingdom
| | - Andrew Porter
- NUPPA
Facility, Medical School, Newcastle University, Newcastle Upon Tyne NE1
7RU, United Kingdom
| | - Andrea Bonicelli
- School
of Law and Policing, Research Centre for Field Archaeology and Forensic
Taphonomy, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | - Edward C. Schwalbe
- Department
of Applied Sciences, Northumbria University, Newcastle Upon Tyne NE1
8ST, United Kingdom
| | - Noemi Procopio
- School
of Law and Policing, Research Centre for Field Archaeology and Forensic
Taphonomy, University of Central Lancashire, Preston PR1 2HE, United Kingdom
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3
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Topitsch A, Halstenbach T, Rothweiler R, Fretwurst T, Nelson K, Schilling O. Mass Spectrometry-Based Proteomics of Poly(methylmethacrylate)-Embedded Bone. J Proteome Res 2024; 23:1810-1820. [PMID: 38634750 DOI: 10.1021/acs.jproteome.4c00046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is a widely employed technique in proteomics research for studying the proteome biology of various clinical samples. Hard tissues, such as bone and teeth, are routinely preserved using synthetic poly(methyl methacrylate) (PMMA) embedding resins that enable histological, immunohistochemical, and morphological examination. However, the suitability of PMMA-embedded hard tissues for large-scale proteomic analysis remained unexplored. This study is the first to report on the feasibility of PMMA-embedded bone samples for LC-MS/MS analysis. Conventional workflows yielded merely limited coverage of the bone proteome. Using advanced strategies of prefractionation by high-pH reversed-phase liquid chromatography in combination with isobaric tandem mass tag labeling resulted in proteome coverage exceeding 1000 protein identifications. The quantitative comparison with cryopreserved samples revealed that each sample preparation workflow had a distinct impact on the proteomic profile. However, workflow replicates exhibited a high reproducibility for PMMA-embedded samples. Our findings further demonstrate that decalcification prior to protein extraction, along with the analysis of solubilization fractions, is not preferred for PMMA-embedded bone. The biological applicability of the proposed workflow was demonstrated using samples of human PMMA-embedded alveolar bone and the iliac crest, which revealed anatomical site-specific proteomic profiles. Overall, these results establish a crucial foundation for large-scale proteomics studies contributing to our knowledge of bone biology.
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Affiliation(s)
- Annika Topitsch
- Institute for Surgical Pathology, Faculty of Medicine, Medical Center - University of Freiburg, Breisacher Straße 115a, 79106 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstraße 19a, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Tim Halstenbach
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - René Rothweiler
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Tobias Fretwurst
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Katja Nelson
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Oliver Schilling
- Institute for Surgical Pathology, Faculty of Medicine, Medical Center - University of Freiburg, Breisacher Straße 115a, 79106 Freiburg, Germany
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Schmidt VM, Zelger P, Wöss C, Fodor M, Hautz T, Schneeberger S, Huck CW, Arora R, Brunner A, Zelger B, Schirmer M, Pallua JD. Handheld hyperspectral imaging as a tool for the post-mortem interval estimation of human skeletal remains. Heliyon 2024; 10:e25844. [PMID: 38375262 PMCID: PMC10875450 DOI: 10.1016/j.heliyon.2024.e25844] [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: 07/31/2023] [Revised: 01/30/2024] [Accepted: 02/02/2024] [Indexed: 02/21/2024] Open
Abstract
In forensic medicine, estimating human skeletal remains' post-mortem interval (PMI) can be challenging. Following death, bones undergo a series of chemical and physical transformations due to their interactions with the surrounding environment. Post-mortem changes have been assessed using various methods, but estimating the PMI of skeletal remains could still be improved. We propose a new methodology with handheld hyperspectral imaging (HSI) system based on the first results from 104 human skeletal remains with PMIs ranging between 1 day and 2000 years. To differentiate between forensic and archaeological bone material, the Convolutional Neural Network analyzed 65.000 distinct diagnostic spectra: the classification accuracy was 0.58, 0.62, 0.73, 0.81, and 0.98 for PMIs of 0 week-2 weeks, 2 weeks-6 months, 6 months-1 year, 1 year-10 years, and >100 years, respectively. In conclusion, HSI can be used in forensic medicine to distinguish bone materials >100 years old from those <10 years old with an accuracy of 98%. The model has adequate predictive performance, and handheld HSI could serve as a novel approach to objectively and accurately determine the PMI of human skeletal remains.
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Affiliation(s)
- Verena-Maria Schmidt
- Institute of Forensic Medicine, Medical University of Innsbruck, Muellerstraße 44, 6020 Innsbruck, Austria
| | - Philipp Zelger
- University Clinic for Hearing, Voice and Speech Disorders, Medical University of Innsbruck, Anichstrasse 35, 6020 Innsbruck, Austria
| | - Claudia Wöss
- Institute of Forensic Medicine, Medical University of Innsbruck, Muellerstraße 44, 6020 Innsbruck, Austria
| | - Margot Fodor
- OrganLifeTM, Department of Visceral, Transplant and Thoracic Surgery, Medical University of Innsbruck, Innsbruck, Austria
| | - Theresa Hautz
- OrganLifeTM, Department of Visceral, Transplant and Thoracic Surgery, Medical University of Innsbruck, Innsbruck, Austria
| | - Stefan Schneeberger
- OrganLifeTM, Department of Visceral, Transplant and Thoracic Surgery, Medical University of Innsbruck, Innsbruck, Austria
| | - Christian Wolfgang Huck
- Institute of Analytical Chemistry and Radiochemistry, University of Innsbruck, 6020 Innsbruck, Austria
| | - Rohit Arora
- Department of Orthopaedics and Traumatology, Medical University of Innsbruck, Anichstraße 35, 6020 Innsbruck, Austria
| | - Andrea Brunner
- Institute of Pathology, Neuropathology, and Molecular Pathology, Medical University of Innsbruck, Muellerstrasse 44, 6020 Innsbruck, Austria
| | - Bettina Zelger
- Institute of Pathology, Neuropathology, and Molecular Pathology, Medical University of Innsbruck, Muellerstrasse 44, 6020 Innsbruck, Austria
| | - Michael Schirmer
- Department of Internal Medicine, Clinic II, Medical University of Innsbruck, Anichstrasse 35, 6020 Innsbruck, Austria
| | - Johannes Dominikus Pallua
- Department of Orthopaedics and Traumatology, Medical University of Innsbruck, Anichstraße 35, 6020 Innsbruck, Austria
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5
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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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6
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Battistini A, Capitanio D, Bailo P, Moriggi M, Tambuzzi S, Gelfi C, Piccinini A. Proteomic analysis by mass spectrometry of postmortem muscle protein degradation for PMI estimation: A pilot study. Forensic Sci Int 2023; 349:111774. [PMID: 37399773 DOI: 10.1016/j.forsciint.2023.111774] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/24/2023] [Accepted: 06/26/2023] [Indexed: 07/05/2023]
Abstract
The determination of the postmortem interval is a topic of great forensic interest. The possibility of using new technologies has allowed the study of postmortem decay of biomolecules in the determination of PMI. Skeletal muscle proteins are promising candidates because skeletal muscle exhibits slower postmortem decay compared to other internal organs and nervous tissues, while its degradation is faster than cartilage and bone. In this pilot study, skeletal muscle tissue from pigs was degraded at two different controlled temperatures, 21 °C and 6 °C, and analysed at predefined times points: 0, 24, 48, 72, 96, and 120 h. The obtained samples were analysed by mass spectrometry proteomics approach for qualitative and quantitative evaluation of proteins and peptides. Immunoblotting validation was performed for the candidate proteins. The results obtained appeared significant and identified several proteins useful for possible postmortem interval estimation. Of these proteins, PDLIM7, TPM1, and ATP2A2 were validated by immunoblotting at a larger number of experimental points and at different temperatures. The results obtained are in agreement with those observed in similar works. In addition, the use of a mass spectrometry approach increased the number of protein species identified, providing a larger panel of proteins for PMI assessment.
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Affiliation(s)
- Alessio Battistini
- Sezione di Medicina Legale e delle Assicurazioni, Department of Biomedical Sciences for Health, University of Milan, Via Luigi Mangiagalli, 37, 20133 Milan, Italy.
| | | | - Paolo Bailo
- Section of Legal Medicine, School of Law, University of Camerino, 62032 Camerino, Italy
| | - Manuela Moriggi
- University of Milan, Via Luigi Mangiagalli 31, 20133 Milan, Italy
| | - Stefano Tambuzzi
- Sezione di Medicina Legale e delle Assicurazioni, Department of Biomedical Sciences for Health, University of Milan, Via Luigi Mangiagalli, 37, 20133 Milan, Italy
| | - Cecilia Gelfi
- University of Milan, Via Luigi Mangiagalli 31, 20133 Milan, Italy; IRCCS Istituto Ortopedico Galeazzi, Via Riccardo Galeazzi 4, 20161 Milan, Italy
| | - Andrea Piccinini
- Sezione di Medicina Legale e delle Assicurazioni, Department of Biomedical Sciences for Health, University of Milan, Via Luigi Mangiagalli, 37, 20133 Milan, Italy
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7
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Johnston E, Buckley M. Age-Related Changes in Post-Translational Modifications of Proteins from Whole Male and Female Skeletal Elements. Molecules 2023; 28:4899. [PMID: 37446562 DOI: 10.3390/molecules28134899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/30/2023] [Accepted: 06/08/2023] [Indexed: 07/15/2023] Open
Abstract
One of the key questions in forensic cases relates to some form of age inference, whether this is how old a crime scene is, when in time a particular crime was committed, or how old the victim was at the time of the crime. These age-related estimations are currently achieved through morphological methods with varying degrees of accuracy. As a result, biomolecular approaches are considered of great interest, with the relative abundances of several protein markers already recognized for their potential forensic significance; however, one of the greatest advantages of proteomic investigations over genomics ones is the wide range of post-translational modifications (PTMs) that make for a complex but highly dynamic resource of information. Here, we explore the abundance of several PTMs including the glycosylation, deamidation, and oxidation of several key proteins (collagen, fetuin A, biglycan, serum albumin, fibronectin and osteopontin) as being of potential value to the development of an age estimation tool worthy of further evaluation in forensic contexts. We find that glycosylations lowered into adulthood but deamidation and oxidation increased in the same age range.
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Affiliation(s)
- Elizabeth Johnston
- School of Natural Sciences, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Michael Buckley
- School of Natural Sciences, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
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Franceschetti L, Amadasi A, Bugelli V, Bolsi G, Tsokos M. Estimation of Late Postmortem Interval: Where Do We Stand? A Literature Review. BIOLOGY 2023; 12:783. [PMID: 37372068 DOI: 10.3390/biology12060783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 05/26/2023] [Accepted: 05/27/2023] [Indexed: 06/29/2023]
Abstract
Estimating time since death can be challenging for forensic experts, and is one of the most challenging activities concerning the forensic world. Various methods have been assessed to calculate the postmortem interval on dead bodies in different stages of decomposition and are currently widely used. Nowadays, the only well-recognized dating technique is carbon-14 radioisotope measurement, whereas other methods have been tested throughout the years involving different disciplines with different and sometimes not univocal results. Today, there is no precise and secure method to precisely determine time since death, and late postmortem interval estimation remains one of the most debated topics in forensic pathology. Many proposed methods have shown promising results, and it is desirable that with further studies some of them might become acknowledged techniques to resolve such a difficult and important challenge. The present review aims at presenting studies about the different techniques that have been tested in order to find a valuable method for estimating time since death for skeletal remains. By providing a comprehensive overview, the purpose of this work is to offer readers new perspectives on postmortem interval estimation and to improve current practice in the management of skeletal remains and decomposed bodies.
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Affiliation(s)
- Lorenzo Franceschetti
- Istituto di Medicina Legale, Dipartimento di Scienze Biomediche per la Salute, Università degli Studi di Milano, via Luigi Mangiagalli 37, 20133 Milan, Italy
| | - Alberto Amadasi
- Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin Berlin, Turmstr. 21 (Haus M), 10559 Berlin, Germany
| | - Valentina Bugelli
- South-East Tuscany Local Health Unit, Department of Legal Medicine, via Cimabue 109, 58100 Grosseto, Italy
| | - Giulia Bolsi
- Istituto di Medicina Legale, Dipartimento di Scienze Biomediche per la Salute, Università degli Studi di Milano, via Luigi Mangiagalli 37, 20133 Milan, Italy
| | - Michael Tsokos
- Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin Berlin, Turmstr. 21 (Haus M), 10559 Berlin, Germany
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Toma L, Vignali G, Maffioli E, Tambuzzi S, Giaccari R, Mattarozzi M, Nonnis S, Milioli M, Franceschetti L, Paredi G, Negri A, Riccardi B, Cattaneo C, Careri M, Tedeschi G, Bruno S. Mass spectrometry-based proteomic strategy for ecchymotic skin examination in forensic pathology. Sci Rep 2023; 13:6116. [PMID: 37059833 PMCID: PMC10104867 DOI: 10.1038/s41598-023-32520-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 03/28/2023] [Indexed: 04/16/2023] Open
Abstract
Mass spectrometry (MS)-based proteomics has recently attracted the attention from forensic pathologists. This work is the first report of the development of a shotgun bottom-up proteomic approach based on rapid protein extraction and nano-liquid chromatography/high-resolution mass spectrometry applied to full-thickness human skin for the differential analysis of normal and ecchymotic tissues to identify new biomarkers for bruise characterization and dating. We identified around 2000 proteins from each pooled extract. The method showed excellent precision on independent replicates, with Pearson correlation coefficients always higher than 95%. Glycophorin A, a known biomarker of vital wounds from immunochemical studies, was identified only in ecchymotic tissues, as confirmed by Western blotting analysis. This finding suggests that this protein can be used as a MS-detectable biomarker of wound vitality. By focusing on skin samples from individuals with known wound dating, besides Glycophorin A, other proteins differentially expressed in ecchymotic samples and dependant on wound age were identified, although further analysis on larger datasets are needed to validate these findings. This study paves the way for an in-depth investigation of the potential of MS-based techniques for wound examination in forensic pathology, overcoming the limitations of immunochemical assays.
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Affiliation(s)
- Lorenzo Toma
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124, Parma, Italy
| | - Giulia Vignali
- Institute of Legal Medicine, Department of Biomedical Sciences for Health, University of Milan, 20133, Milan, Italy
| | - Elisa Maffioli
- Department of Veterinary Medicine and Animal Science, University of Milan, 26900, Lodi, Italy
| | - Stefano Tambuzzi
- Institute of Legal Medicine, Department of Biomedical Sciences for Health, University of Milan, 20133, Milan, Italy
| | - Roberta Giaccari
- Food and Drug Department, University of Parma, 43124, Parma, Italy
| | - Monica Mattarozzi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124, Parma, Italy.
| | - Simona Nonnis
- Department of Veterinary Medicine and Animal Science, University of Milan, 26900, Lodi, Italy.
- CRC Innovation for Well-Being and Environment (I-WE), University of Milan, 20133, Milan, Italy.
| | - Marco Milioli
- Department of Pharmacokinetic, Biochemistry and Metabolism, Global Research and Preclinical Development, Chiesi Farmaceutici Spa, 43122, Parma, Italy
| | - Lorenzo Franceschetti
- Institute of Legal Medicine, Department of Biomedical Sciences for Health, University of Milan, 20133, Milan, Italy
| | - Gianluca Paredi
- Food and Drug Department, University of Parma, 43124, Parma, Italy
| | - Armando Negri
- Department of Veterinary Medicine and Animal Science, University of Milan, 26900, Lodi, Italy
| | - Benedetta Riccardi
- Department of Pharmacokinetic, Biochemistry and Metabolism, Global Research and Preclinical Development, Chiesi Farmaceutici Spa, 43122, Parma, Italy
| | - Cristina Cattaneo
- Institute of Legal Medicine, Department of Biomedical Sciences for Health, University of Milan, 20133, Milan, Italy
| | - Maria Careri
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124, Parma, Italy
| | - Gabriella Tedeschi
- Department of Veterinary Medicine and Animal Science, University of Milan, 26900, Lodi, Italy
- CRC Innovation for Well-Being and Environment (I-WE), University of Milan, 20133, Milan, Italy
| | - Stefano Bruno
- Food and Drug Department, University of Parma, 43124, Parma, Italy
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10
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Locci E, Stocchero M, Gottardo R, Chighine A, De-Giorgio F, Ferino G, Nioi M, Demontis R, Tagliaro F, d'Aloja E. PMI estimation through metabolomics and potassium analysis on animal vitreous humour. Int J Legal Med 2023; 137:887-895. [PMID: 36799966 PMCID: PMC10085955 DOI: 10.1007/s00414-023-02975-6] [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: 10/23/2022] [Accepted: 02/08/2023] [Indexed: 02/18/2023]
Abstract
INTRODUCTION The estimation of post-mortem interval (PMI) remains a major challenge in forensic science. Most of the proposed approaches lack the reliability required to meet the rigorous forensic standards. OBJECTIVES We applied 1H NMR metabolomics to estimate PMI on ovine vitreous humour comparing the results with the actual scientific gold standard, namely vitreous potassium concentrations. METHODS Vitreous humour samples were collected in a time frame ranging from 6 to 86 h after death. Experiments were performed by using 1H NMR metabolomics and ion capillary analysis. Data were submitted to multivariate statistical data analysis. RESULTS A multivariate calibration model was built to estimate PMI based on 47 vitreous humour samples. The model was validated with an independent test set of 24 samples, obtaining a prediction error on the entire range of 6.9 h for PMI < 24 h, 7.4 h for PMI between 24 and 48 h, and 10.3 h for PMI > 48 h. Time-related modifications of the 1H NMR vitreous metabolomic profile could predict PMI better than potassium up to 48 h after death, whilst a combination of the two is better than the single approach for higher PMI estimation. CONCLUSION The present study, although in a proof-of-concept animal model, shows that vitreous metabolomics can be a powerful tool to predict PMI providing a more accurate estimation compared to the widely studied approach based on vitreous potassium concentrations.
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Affiliation(s)
- Emanuela Locci
- Department of Medical Sciences and Public Health, Section of Legal Medicine, University of Cagliari, Cittadella Universitaria di Monserrato, 09042, Monserrato, Cagliari, Italy
| | - Matteo Stocchero
- Department of Women's and Children's Health, University of Padova, Padua, Italy
| | - Rossella Gottardo
- Department of Diagnostics and Public Health, Unit of Forensic Medicine, University of Verona, Verona, Italy
| | - Alberto Chighine
- Department of Medical Sciences and Public Health, Section of Legal Medicine, University of Cagliari, Cittadella Universitaria di Monserrato, 09042, Monserrato, Cagliari, Italy.
| | - Fabio De-Giorgio
- Department of Health Surveillance and Bioethics, Section of Legal Medicine, Catholic University of Rome, Rome, Italy.,Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Giulio Ferino
- Department of Medical Sciences and Public Health, Section of Legal Medicine, University of Cagliari, Cittadella Universitaria di Monserrato, 09042, Monserrato, Cagliari, Italy
| | - Matteo Nioi
- Department of Medical Sciences and Public Health, Section of Legal Medicine, University of Cagliari, Cittadella Universitaria di Monserrato, 09042, Monserrato, Cagliari, Italy
| | - Roberto Demontis
- Department of Medical Sciences and Public Health, Section of Legal Medicine, University of Cagliari, Cittadella Universitaria di Monserrato, 09042, Monserrato, Cagliari, Italy
| | - Franco Tagliaro
- Department of Diagnostics and Public Health, Unit of Forensic Medicine, University of Verona, Verona, Italy
| | - Ernesto d'Aloja
- Department of Medical Sciences and Public Health, Section of Legal Medicine, University of Cagliari, Cittadella Universitaria di Monserrato, 09042, Monserrato, Cagliari, Italy
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11
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Gent L, Schwalbe EC, Procopio N. The impact of maceration on the 'Osteo-ome'; a pilot investigation. J Proteomics 2023; 271:104754. [PMID: 36243311 DOI: 10.1016/j.jprot.2022.104754] [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: 03/15/2022] [Revised: 10/03/2022] [Accepted: 10/07/2022] [Indexed: 11/05/2022]
Abstract
The bone proteome, i.e., the 'osteo-ome', is a rich source of information for forensic studies. There have been advances in the study of biomolecule biomarkers for age-at-death (AAD) and post-mortem interval (PMI) estimations, by looking at changes in protein abundance and post-translational modifications (PTMs) at the peptide level. However, the extent to which other post-mortem factors alter the proteome, including 'maceration' procedures adopted in human taphonomy facilities (HTFs) to clean bones for osteological collections, is poorly understood. This pilot study aimed to characterise the impact of these 'cleaning' methods for de-fleshing skeletons on bone biomolecules, and therefore, what further impact this may have on putative biomarkers in future investigations. Three specific maceration procedures, varying in submersion time (one week or two days) and water temperature (55 °C or 87 °C) were conducted on six bovid tibiae from three individual bovines; the proteome of fresh and macerated bones of each individual was compared. The maceration at 87 °C for two days had the greatest proteomic impact, decreasing protein relative abundances and inducing specific PTMs. Overall, these results suggest that routinely-employed maceration procedures are harsh, variable and potentially threaten the viability of discovering new forensic biomarkers in macerated skeletal remains. SIGNIFICANCE: For the first time, the application of bone proteomics in understanding maceration procedures was conducted to help address the risks for experimental confounding associated with this post-mortem cleaning technique. This pilot study demonstrates that recent advances in biomarker discovery for post-mortem interval and age-at-death estimation using bone proteomics has potential for confounding by differing and destructive bone-cleaning methods.
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Affiliation(s)
- Luke Gent
- Forensic Science Research Group, Faculty of Health and Life Sciences, Applied Sciences, Northumbria University, NE1 8ST Newcastle Upon Tyne, UK; School of Natural Sciences, University of Central Lancashire, PR1 2HE Preston, UK
| | - Edward C Schwalbe
- Forensic Science Research Group, Faculty of Health and Life Sciences, Applied Sciences, Northumbria University, NE1 8ST Newcastle Upon Tyne, UK
| | - Noemi Procopio
- Forensic Science Research Group, Faculty of Health and Life Sciences, Applied Sciences, Northumbria University, NE1 8ST Newcastle Upon Tyne, UK; School of Natural Sciences, University of Central Lancashire, PR1 2HE Preston, UK.
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12
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Bonicelli A, Mickleburgh HL, Chighine A, Locci E, Wescott DJ, Procopio N. The 'ForensOMICS' approach for postmortem interval estimation from human bone by integrating metabolomics, lipidomics, and proteomics. eLife 2022; 11:e83658. [PMID: 36583441 PMCID: PMC9803353 DOI: 10.7554/elife.83658] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/09/2022] [Indexed: 12/31/2022] Open
Abstract
The combined use of multiple omics allows to study complex interrelated biological processes in their entirety. We applied a combination of metabolomics, lipidomics and proteomics to human bones to investigate their combined potential to estimate time elapsed since death (i.e., the postmortem interval [PMI]). This 'ForensOMICS' approach has the potential to improve accuracy and precision of PMI estimation of skeletonized human remains, thereby helping forensic investigators to establish the timeline of events surrounding death. Anterior midshaft tibial bone was collected from four female body donors before their placement at the Forensic Anthropology Research Facility owned by the Forensic Anthropological Center at Texas State (FACTS). Bone samples were again collected at selected PMIs (219-790-834-872days). Liquid chromatography mass spectrometry (LC-MS) was used to obtain untargeted metabolomic, lipidomic, and proteomic profiles from the pre- and post-placement bone samples. The three omics blocks were investigated independently by univariate and multivariate analyses, followed by Data Integration Analysis for Biomarker discovery using Latent variable approaches for Omics studies (DIABLO), to identify the reduced number of markers describing postmortem changes and discriminating the individuals based on their PMI. The resulting model showed that pre-placement metabolome, lipidome and proteome profiles were clearly distinguishable from post-placement ones. Metabolites in the pre-placement samples suggested an extinction of the energetic metabolism and a switch towards another source of fuelling (e.g., structural proteins). We were able to identify certain biomolecules with an excellent potential for PMI estimation, predominantly the biomolecules from the metabolomics block. Our findings suggest that, by targeting a combination of compounds with different postmortem stability, in the future we could be able to estimate both short PMIs, by using metabolites and lipids, and longer PMIs, by using proteins.
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Affiliation(s)
- Andrea Bonicelli
- The Forensic Science Unit, Faculty of Health and Life Sciences, Northumbria UniversityNewcastle upon TyneUnited Kingdom
| | - Hayley L Mickleburgh
- Amsterdam Centre for Ancient Studies and Archaeology (ACASA) – Department of Archaeology, Faculty of Humanities, University of AmsterdamAmsterdamNetherlands
- Forensic Anthropology Center, Texas State UniversitySan MarcosUnited States
| | - Alberto Chighine
- Department of Medical Science and Public Health, Section of Legal Medicine, University of CagliariMonserratoItaly
| | - Emanuela Locci
- Department of Medical Science and Public Health, Section of Legal Medicine, University of CagliariMonserratoItaly
| | - Daniel J Wescott
- Forensic Anthropology Center, Texas State UniversitySan MarcosUnited States
| | - Noemi Procopio
- The Forensic Science Unit, Faculty of Health and Life Sciences, Northumbria UniversityNewcastle upon TyneUnited Kingdom
- Forensic Anthropology Center, Texas State UniversitySan MarcosUnited States
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13
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Pittner S, Merold V, Anders S, Lohner L, Amendt J, Klinger M, Hausmann R, Kissling S, Monticelli F, Geissenberger J, Zissler A, Steinbacher P. A standard protocol for the analysis of postmortem muscle protein degradation: process optimization and considerations for the application in forensic PMI estimation. Int J Legal Med 2022; 136:1913-1923. [PMID: 35710956 PMCID: PMC9576658 DOI: 10.1007/s00414-022-02849-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 05/27/2022] [Indexed: 12/14/2022]
Abstract
The analysis of postmortem protein degradation has become of large interest for the estimation of the postmortem interval (PMI). Although several techniques have been published in recent years, protein degradation-based techniques still largely did not exceed basic research stages. Reasons include impractical and complex sampling procedures, as well as highly variable protocols in the literature, making it difficult to compare results. Following a three-step procedure, this study aimed to establish an easily replicable standardized procedure for sampling and processing, and further investigated the reliability and limitations for routine application. Initially, sampling and processing were optimized using a rat animal model. In a second step, the possible influences of sample handling and storage on postmortem protein degradation dynamics were assessed on a specifically developed human extracorporeal degradation model. Finally, the practical application was simulated by the collection of tissue in three European forensic institutes and an international transfer to our forensic laboratory, where the samples were processed and analyzed according to the established protocol.
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Affiliation(s)
- Stefan Pittner
- Department of Forensic Medicine, Paris-Lodron University of Salzburg, Salzburg, Austria.
| | - Veronika Merold
- Department of Environment and Biodiversity, Paris-Lodron University of Salzburg, Salzburg, Austria
| | - Sven Anders
- Department of Legal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Larissa Lohner
- Department of Legal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jens Amendt
- Institute of Legal Medicine, Goethe-University, Frankfurt, Frankfurt, Germany
| | - Miriam Klinger
- Institute of Legal Medicine, Goethe-University, Frankfurt, Frankfurt, Germany
| | - Roland Hausmann
- Institute of Legal Medicine, Cantonal Hospital St, Gallen, St. Gallen, Switzerland
| | - Steffen Kissling
- Institute of Legal Medicine, Cantonal Hospital St, Gallen, St. Gallen, Switzerland
| | - Fabio Monticelli
- Department of Forensic Medicine, Paris-Lodron University of Salzburg, Salzburg, Austria
| | - Janine Geissenberger
- Department of Environment and Biodiversity, Paris-Lodron University of Salzburg, Salzburg, Austria
| | - Angela Zissler
- Department of Environment and Biodiversity, Paris-Lodron University of Salzburg, Salzburg, Austria
| | - Peter Steinbacher
- Department of Environment and Biodiversity, Paris-Lodron University of Salzburg, Salzburg, Austria
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14
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Bonicelli A, Cheung W, Hughes S, Wescott DJ, Procopio N. Preliminary Investigation of the Effect of Maceration Procedures on Bone Metabolome and Lipidome. Metabolites 2022; 12:1020. [PMID: 36355103 PMCID: PMC9693520 DOI: 10.3390/metabo12111020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/20/2022] [Accepted: 10/22/2022] [Indexed: 11/16/2022] Open
Abstract
The study of post-mortem changes is a crucial component of forensic investigation. Human forensic taphonomic facilities (HFTFs) are the only institutions allowing the design and execution of controlled human decomposition experiments. When bodies are skeletonized, bones are normally stored in skeletal collections and used for anthropological studies. However, HFTFs apply chemical and/or thermal treatments to the remains prior bone long-term storage. These treatments are believed to alter heavily the original biochemical and molecular signature of bone material. The present study aims to evaluate the effect of these procedures on the bone metabolome and lipidome by using an animal bone model. Three intact bovine tibiae were processed using three protocols routinely applied at HFTFs, and their three counterparts were used as non-treated controls. Bone powder samples were subjected to biphasic extraction and both metabolites and lipids were analysed via liquid chromatography tandem mass-spectrometry. Results showed severe reductions in the abundances of both metabolites and lipids, and the presence of contamination introduced by cleaning agents. Despite the preliminary nature of the study, we demonstrated that the biochemical profile of bone is heavily affected by the maceration procedures. Ideally, these treatments should be avoided, or replaced by minimally invasive procedures agreed across HFTFs.
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Affiliation(s)
- Andrea Bonicelli
- The Forensic Science Unit, Faculty of Health and Life Sciences, Ellison Building, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - William Cheung
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Sheree Hughes
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, Huntsville, TX 773402525, USA
| | - Daniel J. Wescott
- Forensic Anthropology Center at Texas State, Department of Anthropology, Texas State University, San Marcos, TX 78666, USA
| | - Noemi Procopio
- The Forensic Science Unit, Faculty of Health and Life Sciences, Ellison Building, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
- Forensic Anthropology Center at Texas State, Department of Anthropology, Texas State University, San Marcos, TX 78666, USA
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15
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Abstract
Paleoproteomics, the study of ancient proteins, is a rapidly growing field at the intersection of molecular biology, paleontology, archaeology, paleoecology, and history. Paleoproteomics research leverages the longevity and diversity of proteins to explore fundamental questions about the past. While its origins predate the characterization of DNA, it was only with the advent of soft ionization mass spectrometry that the study of ancient proteins became truly feasible. Technological gains over the past 20 years have allowed increasing opportunities to better understand preservation, degradation, and recovery of the rich bioarchive of ancient proteins found in the archaeological and paleontological records. Growing from a handful of studies in the 1990s on individual highly abundant ancient proteins, paleoproteomics today is an expanding field with diverse applications ranging from the taxonomic identification of highly fragmented bones and shells and the phylogenetic resolution of extinct species to the exploration of past cuisines from dental calculus and pottery food crusts and the characterization of past diseases. More broadly, these studies have opened new doors in understanding past human-animal interactions, the reconstruction of past environments and environmental changes, the expansion of the hominin fossil record through large scale screening of nondiagnostic bone fragments, and the phylogenetic resolution of the vertebrate fossil record. Even with these advances, much of the ancient proteomic record still remains unexplored. Here we provide an overview of the history of the field, a summary of the major methods and applications currently in use, and a critical evaluation of current challenges. We conclude by looking to the future, for which innovative solutions and emerging technology will play an important role in enabling us to access the still unexplored "dark" proteome, allowing for a fuller understanding of the role ancient proteins can play in the interpretation of the past.
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Affiliation(s)
- Christina Warinner
- Department
of Anthropology, Harvard University, Cambridge, Massachusetts 02138, United States
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Kristine Korzow Richter
- Department
of Anthropology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Matthew J. Collins
- Department
of Archaeology, Cambridge University, Cambridge CB2 3DZ, United Kingdom
- Section
for Evolutionary Genomics, Globe Institute,
University of Copenhagen, Copenhagen 1350, Denmark
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16
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Schmidt VM, Zelger P, Woess C, Pallua AK, Arora R, Degenhart G, Brunner A, Zelger B, Schirmer M, Rabl W, Pallua JD. Application of Micro-Computed Tomography for the Estimation of the Post-Mortem Interval of Human Skeletal Remains. BIOLOGY 2022; 11:biology11081105. [PMID: 35892961 PMCID: PMC9331256 DOI: 10.3390/biology11081105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/22/2022] [Accepted: 07/22/2022] [Indexed: 12/02/2022]
Abstract
It is challenging to estimate the post-mortem interval (PMI) of skeletal remains within a forensic context. As a result of their interactions with the environment, bones undergo several chemical and physical changes after death. So far, multiple methods have been used to follow up on post-mortem changes. There is, however, no definitive way to estimate the PMI of skeletal remains. This research aimed to propose a methodology capable of estimating the PMI using micro-computed tomography measurements of 104 human skeletal remains with PMIs between one day and 2000 years. The present study indicates that micro-computed tomography could be considered an objective and precise method of PMI evaluation in forensic medicine. The measured parameters show a significant difference regarding the PMI for Cort Porosity p < 0.001, BV/TV p > 0.001, Mean1 p > 0.001 and Mean2 p > 0.005. Using a machine learning approach, the neural network showed an accuracy of 99% for distinguishing between samples with a PMI of less than 100 years and archaeological samples.
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Affiliation(s)
- Verena-Maria Schmidt
- Institute of Legal Medicine, Medical University of Innsbruck, Muellerstraße 44, 6020 Innsbruck, Austria; (V.-M.S.); (C.W.); (W.R.)
| | - Philipp Zelger
- University Clinic for Hearing, Voice and Speech Disorders, Medical University of Innsbruck, Anichstrasse 35, 6020 Innsbruck, Austria;
| | - Claudia Woess
- Institute of Legal Medicine, Medical University of Innsbruck, Muellerstraße 44, 6020 Innsbruck, Austria; (V.-M.S.); (C.W.); (W.R.)
| | - Anton K. Pallua
- Former Institute for Computed Tomography-Neuro CT, Medical University of Innsbruck, Anichstraße 35, 6020 Innsbruck, Austria;
| | - Rohit Arora
- University Hospital for Orthopaedics and Traumatology, Medical University of Innsbruck, Anichstraße 35, 6020 Innsbruck, Austria;
| | - Gerald Degenhart
- Department of Radiology, Medical University of Innsbruck, Anichstraße 35, 6020 Innsbruck, Austria;
| | - Andrea Brunner
- Institute of Pathology, Neuropathology, Molecular Pathology, Medical University of Innsbruck, Muellerstrasse 44, 6020 Innsbruck, Austria; (A.B.); (B.Z.)
| | - Bettina Zelger
- Institute of Pathology, Neuropathology, Molecular Pathology, Medical University of Innsbruck, Muellerstrasse 44, 6020 Innsbruck, Austria; (A.B.); (B.Z.)
| | - Michael Schirmer
- Department of Internal Medicine, Clinic II, Medical University of Innsbruck, Anichstrasse 35, 6020 Innsbruck, Austria;
| | - Walter Rabl
- Institute of Legal Medicine, Medical University of Innsbruck, Muellerstraße 44, 6020 Innsbruck, Austria; (V.-M.S.); (C.W.); (W.R.)
| | - Johannes D. Pallua
- University Hospital for Orthopaedics and Traumatology, Medical University of Innsbruck, Anichstraße 35, 6020 Innsbruck, Austria;
- Correspondence:
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17
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Post-Mortem Interval of Human Skeletal Remains Estimated with Handheld NIR Spectrometry. BIOLOGY 2022; 11:biology11071020. [PMID: 36101401 PMCID: PMC9312135 DOI: 10.3390/biology11071020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/30/2022] [Accepted: 07/04/2022] [Indexed: 11/17/2022]
Abstract
Estimating the post-mortem interval (PMI) of human skeletal remains is a critical issue of forensic analysis, with important limitations such as sample preparation and practicability. In this work, NIR spectroscopy (NIRONE® Sensor X; Spectral Engines, 61449, Germany) was applied to estimate the PMI of 104 human bone samples between 1 day and 2000 years. Reflectance data were repeatedly collected from eight independent spectrometers between 1950 and 1550 nm with a spectral resolution of 14 nm and a step size of 2 nm, each from the external and internal bone. An Artificial Neural Network was used to analyze the 66,560 distinct diagnostic spectra, and clearly distinguished between forensic and archaeological bone material: the classification accuracies for PMIs of 0−2 weeks, 2 weeks−6 months, 6 months−1 year, 1 year−10 years, and >100 years were 0.90, 0.94, 0.94, 0.93, and 1.00, respectively. PMI of archaeological bones could be determined with an accuracy of 100%, demonstrating the adequate predictive performance of the model. Applying a handheld NIR spectrometer to estimate the PMI of human skeletal remains is rapid and extends the repertoire of forensic analyses as a distinct, novel approach.
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18
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Systematic Review on Post-Mortem Protein Alterations: Analysis of Experimental Models and Evaluation of Potential Biomarkers of Time of Death. Diagnostics (Basel) 2022; 12:diagnostics12061490. [PMID: 35741301 PMCID: PMC9222196 DOI: 10.3390/diagnostics12061490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/06/2022] [Accepted: 06/13/2022] [Indexed: 11/16/2022] Open
Abstract
Estimating the post-mortem interval (PMI) is a very complex issue due to numerous variables that may affect the calculation. Several authors have investigated the quantitative and qualitative variations of protein expression on post-mortem biological samples in certain time intervals, both in animals and in humans. However, the literature data are very numerous and often inhomogeneous, with different models, tissues and proteins evaluated, such that the practical application of these methods is limited to date. The aim of this paper was to offer an organic view of the state of the art about post-mortem protein alterations for the calculation of PMI through the analysis of the various experimental models proposed. The purpose was to investigate the validity of some proteins as “molecular clocks” candidates, focusing on the evidence obtained in the early, intermediate and late post-mortem interval. This study demonstrates how the study of post-mortem protein alterations may be useful for estimating the PMI, although there are still technical limits, especially in the experimental models performed on humans. We suggest a protocol to homogenize the study of future experimental models, with a view to the next concrete application of these methods also at the crime scene.
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19
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Ntasi G, Palomo IR, Marino G, Piaz FD, Sirano F, Cappellini E, Birolo L, Petrone P. Molecular signatures written in bone proteins of 79 AD victims from Herculaneum and Pompeii. Sci Rep 2022; 12:8401. [PMID: 35624181 PMCID: PMC9142588 DOI: 10.1038/s41598-022-12042-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 04/18/2022] [Indexed: 11/09/2022] Open
Abstract
An extensive proteomic analysis was performed on a set of 12 bones of human victims of the eruption that in AD 79 rapidly buried Pompeii and Herculaneum, allowing the detection of molecular signatures imprinted in the surviving protein components. Bone collagen survived the heat of the eruption, bearing a piece of individual biological history encoded in chemical modifications. Here we show that the human bone proteomes from Pompeii are more degraded than those from the inhabitants of Herculaneum, despite the latter were exposed to temperatures much higher than those experienced in Pompeii. The analysis of the specimens from Pompeii shows lower content of non-collagenous proteins, higher deamidation level and higher extent of collagen modification. In Pompeii, the slow decomposition of victims' soft tissues in the natural dry-wet hydrogeological soil cycles damaged their bone proteome more than what was experienced at Herculaneum by the rapid vanishing of body tissues from intense heat, under the environmental condition of a permanent waterlogged burial context. Results herein presented are the first proteomic analyses of bones exposed to eruptive conditions, but also delivered encouraging results for potential biomarkers that might also impact future development of forensic bone proteomics.
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Affiliation(s)
- Georgia Ntasi
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Ismael Rodriguez Palomo
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Gennaro Marino
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy.,Department of Humanities, University Suor Orsola Benincasa, Naples, Italy
| | - Fabrizio Dal Piaz
- Department of Medicine, Surgery and Dentistry, University of Salerno, Fisciano, Salerno, Italy
| | | | - Enrico Cappellini
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Leila Birolo
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy. .,Task Force Di Ateneo "Metodologie Analitiche per la Salvaguardia dei Beni Culturali", University of Naples Federico II, Naples, Italy.
| | - Pierpaolo Petrone
- Task Force Di Ateneo "Metodologie Analitiche per la Salvaguardia dei Beni Culturali", University of Naples Federico II, Naples, Italy.,Department of Advanced Biomedical Sciences, Departmental Section of Legal Medicine, Anatomy and Histology, University of Naples Federico II, Naples, Italy
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20
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Bonicelli A, Di Nunzio A, Di Nunzio C, Procopio N. Insights into the Differential Preservation of Bone Proteomes in Inhumed and Entombed Cadavers from Italian Forensic Caseworks. J Proteome Res 2022; 21:1285-1298. [PMID: 35316604 PMCID: PMC9087355 DOI: 10.1021/acs.jproteome.1c00904] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Indexed: 01/30/2023]
Abstract
Bone is a hard biological tissue and a precious reservoir of information in forensic investigations as it retains key biomolecules commonly used for identification purposes. Bone proteins have recently attracted significant interest for their potential in estimating post-mortem interval (PMI) and age at death (AAD). However, the preservation of such proteins is highly dependent on intrinsic and extrinsic factors that can hinder the potential application of molecular techniques to forensic sciences. The present study aims at investigating the effects that two commonly used types of burial practices (entombment and inhumation) have on bone protein survival. The sample consists of 14 exhumed individuals from cemeteries in Southern Italy with different AADs (29-85 years) and PMIs (1-37 years). LC-MS/MS analyses show that 16 proteins are better preserved under the entombed conditions and 4 proteins are better preserved under the inhumed conditions, whereas no clear differences are detected for post-translational protein modifications. Furthermore, several potential "stable" protein markers (i.e., proteins not affected by the burial environment) are identified for PMI and AAD estimation. Overall, these results show that the two burial environments play a role in the differential preservation of noncollagenous proteins, confirming the potential of LC-MS/MS-based proteomics in forensic sciences.
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Affiliation(s)
- Andrea Bonicelli
- Forensic
Science Research Group, Faculty of Health and Life Sciences, Applied
Sciences, Northumbria University, NE1 8ST Newcastle
Upon Tyne, United Kingdom
| | - Aldo Di Nunzio
- Chemical
Sciences Department, University of Naples
Federico II, 80126 Naples, Italy
| | - Ciro Di Nunzio
- Legal
Medicine Department, University of Catanzaro
Magna Graecia, 88100 Germaneto, Italy
| | - Noemi Procopio
- Forensic
Science Research Group, Faculty of Health and Life Sciences, Applied
Sciences, Northumbria University, NE1 8ST Newcastle
Upon Tyne, United Kingdom
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21
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Boudier-Lemosquet A, Mahler A, Bobo C, Dufossée M, Priault M. Introducing protein deamidation: Landmark discoveries, societal outreach, and tentative priming workflow to address deamidation. Methods 2021; 200:3-14. [PMID: 34843979 DOI: 10.1016/j.ymeth.2021.11.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 11/15/2021] [Accepted: 11/18/2021] [Indexed: 12/17/2022] Open
Abstract
Our current knowledge on protein deamidation results from a journey that started almost 100 years ago, when a handful of researchers first described the non-enzymatic "desamidation" of glutamine, and the effect of different anions on the catalytic rate of the reaction. Since then, the field has tremendously expended and now finds outreach in very diverse areas. In light of all the recent articles published in these areas, it seemed timely to propose an integrated review on the subject, including a short historical overview of the landmark discoveries in the field, highlighting the current global positioning of protein deamidation in biology and non-biology fields, and concluding with a workflow for those asking if a protein can deamidate, and identify the residues involved. This review is essentially intended to provide newcomers in the field with an overview of how deamidation has penetrated our society and what tools are currently at hand to identify and quantify protein deamidation.
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Affiliation(s)
| | - Adrien Mahler
- Univ. Bordeaux, CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France
| | - Claude Bobo
- Univ. Bordeaux, CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France
| | - Mélody Dufossée
- Univ. Bordeaux, CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France
| | - Muriel Priault
- Univ. Bordeaux, CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France.
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22
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Ortiz-Herrero L, Uribe B, Armas LH, Alonso ML, Sarmiento A, Irurita J, Alonso RM, Maguregui MI, Etxeberria F, Bartolomé L. Estimation of the post-mortem interval of human skeletal remains using Raman spectroscopy and chemometrics. Forensic Sci Int 2021; 329:111087. [PMID: 34736052 DOI: 10.1016/j.forsciint.2021.111087] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 09/20/2021] [Accepted: 10/25/2021] [Indexed: 12/11/2022]
Abstract
An important demand exists in the field of forensic analysis to objectively determine the post-mortem interval (PMI) when human skeletal remains are discovered. It is widely known that bones undergo different chemical and physical processes after death, mainly due to their interaction with the environment in which they are found, although it is not known exactly what these processes consist of. Multiple techniques have been used so far to follow up these and other post-mortem changes and thus establish the time elapsed since the individual's death, but they present important drawbacks in terms of reliability and accuracy. The aim of this research was to propose an analytical methodology capable of determining the PMI by using non-destructive Raman spectroscopy measurements of human skeletal remains. The recorded Raman spectra provided valuable and potentially useful information from which a multivariate study was performed by means of orthogonal partial least squares regression (OPLSR) in order to correlate the PMI with the detected spectral modifications. A collection of 53 real human skeletal remains with known PMI (15 years ≤ PMI ≤ 87 years) was analysed and used for building and validating the OPLS model. The PMI of 10 out of 14 validation samples could be determined with an accuracy error of less than 30%, demonstrating the adequate predictive performance of the OPLS model even in spite of the large inter-individual variability it handled. This opens up the possibility of applying the OPLS model in combination with non-destructive techniques to the determination of the PMI of human skeletal remains that have been buried in conditions similar or equal to those of cemetery niches and in a geographic location with a Mediterranean climate, which is an important achievement for forensic medicine and anthropology.
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Affiliation(s)
- L Ortiz-Herrero
- Analytical Chemistry Department, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena S/N, 48940 Leioa, Bizkaia, Spain.
| | - B Uribe
- Analytical Chemistry Department, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena S/N, 48940 Leioa, Bizkaia, Spain.
| | - L Hidalgo Armas
- Advances Research Facilities (SGIker), Martina Casiano Technology Platform, University of the Basque Country (UPV/EHU), Barrio Sarriena S/N, 48940 Leioa, Bizkaia, Spain.
| | - M L Alonso
- Analytical Chemistry Department, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena S/N, 48940 Leioa, Bizkaia, Spain.
| | - A Sarmiento
- Advances Research Facilities (SGIker), Coupled Multispectroscopy Singular Laboratory (Raman-LASPEA), Faculty of Medicine and Odontology, University of the Basque Country (UPV/EHU), Barrio Sarriena S/N, 48940 Leioa, Bizkaia, Spain.
| | - J Irurita
- Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, University of Granada, Parque Tecnológico de la Salud, Av. de la Investigación 11, 18016 Granada, Spain.
| | - R M Alonso
- Analytical Chemistry Department, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena S/N, 48940 Leioa, Bizkaia, Spain.
| | - M I Maguregui
- Painting Department, Faculty of Fine Arts, University of the Basque Country (UPV/EHU), Barrio Sarriena S/N, 48940 Leioa, Bizkaia, Spain.
| | - F Etxeberria
- Department of Physical Anthropology, Aranzadi Science Society, Zorroagagaina 11, 20014 Donostia, Gipuzkoa, Spain; Department of Legal and Forensic Medicine, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Paseo Dr. J. Beguiristain 105, 20014 Donostia, Gipuzkoa, Spain.
| | - L Bartolomé
- Advances Research Facilities (SGIker), Martina Casiano Technology Platform, University of the Basque Country (UPV/EHU), Barrio Sarriena S/N, 48940 Leioa, Bizkaia, Spain.
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23
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Sangwan A, Singh SP, Singh P, Gupta OP, Manas A, Gupta S. Role of molecular techniques in PMI estimation: An update. J Forensic Leg Med 2021; 83:102251. [PMID: 34592482 DOI: 10.1016/j.jflm.2021.102251] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 08/19/2021] [Accepted: 09/12/2021] [Indexed: 10/20/2022]
Abstract
The time frames between death and reporting of the cadaver, known as post Mortem interval (PMI), is essential in investigation of homicide deaths, suspicious deaths, or other untimely deaths as well as natural deaths. Such information helps to connect the missing links in homicide or other relevant cases. Over the time several methods are developed which depends upon factors as several methods physiological, biochemical, entomological, and archaeological for the estimation of degradation of body with time. These methods lack precision, require expertise to achieve worthy results or authentic estimate. Although these methods are currently in use but, these evaluations are still unreliable and imprecise. Hence, we still need new methods for better estimation of PMI. Initially, the predictable morphological and chemical changes in cadaver are used as PMI indicators but, as the time since death increases, the above methods become less useful for as they can't pin point the time of death rather give a ballpark idea. With the advent of the field of molecular biology, the estimation of PMI is proposed to be executed by evaluating the degradation pattern of the biological markers (DNA, RNA, and Proteins). It is now proved that the DNA is fairly unwavering over long post-mortem phases, RNA is much more labile in nature, and sensitive to degradation in a tissue-specific manner. Thus, the main purpose (aim, agenda) of this document is to provide review that mainly focuses on potential use of RNA markers in estimation of PMI. For this Critical Review, the systematic evaluation of 47 studies is executed according to the chosen inclusion and exclusion criteria.
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Affiliation(s)
- Amita Sangwan
- Department of Oral Pathology & Microbiology, King George's Medical University, Lucknow, India
| | - Saurabh Pratap Singh
- Department of Oral Pathology & Microbiology, King George's Medical University, Lucknow, India
| | - Prerna Singh
- Department of Oral Pathology & Microbiology, King George's Medical University, Lucknow, India
| | - O P Gupta
- Department of General Surgery, Career Institute of Medical Sciences, Lucknow, India
| | - Abhigyan Manas
- Department of General Surgery, Career Institute of Medical Sciences, Lucknow, India
| | - Shalini Gupta
- Department of Oral Pathology & Microbiology, King George's Medical University, Lucknow, India.
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24
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Trends in deamidation across archaeological bones, ceramics and dental calculus. Methods 2021; 200:67-79. [PMID: 34450289 DOI: 10.1016/j.ymeth.2021.08.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 06/04/2021] [Accepted: 08/14/2021] [Indexed: 11/23/2022] Open
Abstract
The accumulation of post-translational modifications (PTMs) in proteins throughout the lifecycle has been studied for decades, particularly more so with the advent of soft-ionization mass spectrometry-based proteomic techniques. However, particular PTMs, such as the deamidations of asparagine and glutamine residues, continue to accumulate in proteins that remain into the forensic, archaeological, and palaeontological records. The accurate measurement of these ancient 'molecular timers' has been proposed as a method to not only differentiate between exogenous and endogenous proteins within complex mixtures (i.e., contamination), but also as a method of providing relative age estimations into geological time. In this study we explored the extent to which deamidation varies with chronological age across different proteins in bones, as well as investigated differences between proteins across dental calculus and archaeological ceramics. We also analysed the relationships between the observed extent of deamidation and the protein primary structure. We found that collagen obtained from archaeological bones showed a chronological dependence on the extent of deamidation observed, but only when they were from similar environments, supporting prior suggestions about 'thermal age' being a major influence on the deamidation observed. Our study on non-collagenous proteins (NCPs) in archaeological bones showed that while biglycan, and to a lesser extent chondroadherin, showed positive correlations between geological age and the extent of deamidation, others including fetuin-A and serum albumin did not. However, despite the well-known dependence of deamidation on the three-dimensional structure of the peptides, we were unable to find any clear correlation between the structural motifs of the peptides in archaeological bones and the extent of deamidation observed. Our analysis of a set of food proteins obtained from Neolithic archaeological ceramics in Çatalhöyük also showed similar deamidation levels irrespective of the protein structure. Overall, our results suggest that deamidation in archaeological samples could be useful for obtaining additional information beyond identification of species and tissue type, be that as a measure of protein endogeneity and potential contamination, or a measure of protein degradation, or as an indicator of thermal age and for relative dating; however, further research needs to be undertaken to understand why particular proteins are better for this than others, going beyond simple consideration of their secondary structure.
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25
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Geissenberger J, Ehrenfellner B, Monticelli FC, Pittner S, Steinbacher P. Dismembered porcine limbs as a proxy for postmortem muscle protein degradation. Int J Legal Med 2021; 135:1627-1636. [PMID: 33956198 PMCID: PMC8205874 DOI: 10.1007/s00414-021-02571-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/11/2021] [Indexed: 12/14/2022]
Abstract
The estimation of the postmortem interval (PMI) is of critical importance in forensic routine. The most frequently applied methods, however, are all restricted to specific time periods or must be excluded under certain circumstances. In the last years it has been shown that the analysis of muscle protein degradation has the potential to contribute to according delimitations in practice. In particular, upon biochemical analysis, the specific time points of degradation events provide reasonable markers for PMI delimitation. Nevertheless, considerable research is yet required to increase the understanding of protein decomposition and how it is affected by individual and environmental influencing factors. This is best investigated under standardized conditions, however, a considerate selection of proxies, regarding costs, effort, and expected outcome is required. Here, we use pigs to compare muscle protein decomposition in whole bodies and dismembered body parts (amputated hind limbs). Not only do experiments on body parts reduce the costs and allow easier handling in basic research, but also they aid to investigate the practical application of PMI estimation in dismembered body parts, or other extensive injuries, which are not unusual scenarios in crime investigation. Specifically, we investigated whether there are differences in the degradation rates of selected muscle proteins, sampled from dismembered legs and from hind limbs attached to whole pig bodies. Our results show distinct time-dependent degradation patterns of muscle proteins in a predictable manner regardless of sample origin. We are able to demonstrate that amputated hind limbs are suitable proxies for the analysis of muscle protein degradation, especially to investigate certain influencing factors and establish according standardized models.
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Affiliation(s)
- J Geissenberger
- Department of Biosciences, University of Salzburg, Hellbrunner Str. 34, 5020, Salzburg, Austria
| | - B Ehrenfellner
- Department of Biosciences, University of Salzburg, Hellbrunner Str. 34, 5020, Salzburg, Austria
| | - F C Monticelli
- Department of Forensic Medicine and Forensic Neuropsychiatry, University of Salzburg, Salzburg, Austria
| | - Stefan Pittner
- Department of Forensic Medicine and Forensic Neuropsychiatry, University of Salzburg, Salzburg, Austria
| | - Peter Steinbacher
- Department of Biosciences, University of Salzburg, Hellbrunner Str. 34, 5020, Salzburg, Austria.
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26
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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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27
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Bone Diagenesis in Short Timescales: Insights from an Exploratory Proteomic Analysis. BIOLOGY 2021; 10:biology10060460. [PMID: 34071025 PMCID: PMC8224596 DOI: 10.3390/biology10060460] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/20/2021] [Accepted: 05/20/2021] [Indexed: 11/16/2022]
Abstract
The evaluation of bone diagenetic phenomena in archaeological timescales has a long history; however, little is known about the origins of the microbes driving bone diagenesis, nor about the extent of bone diagenesis in short timeframes-such as in forensic contexts. Previously, the analysis of non-collagenous proteins (NCPs) through bottom-up proteomics revealed the presence of potential biomarkers useful in estimating the post-mortem interval (PMI). However, there is still a great need for enhancing the understanding of the diagenetic processes taking place in forensic timeframes, and to clarify whether proteomic analyses can help to develop better models for estimating PMI reliably. To address these knowledge gaps, we designed an experiment based on whole rat carcasses, defleshed long rat bones, and excised but still-fleshed rat limbs, which were either buried in soil or exposed on a clean plastic surface, left to decompose for 28 weeks, and retrieved at different time intervals. This study aimed to assess differences in bone protein relative abundances for the various deposition modalities and intervals. We further evaluated the effects that extrinsic factors, autolysis, and gut and soil bacteria had on bone diagenesis via bottom-up proteomics. Results showed six proteins whose abundance was significantly different between samples subjected to either microbial decomposition (gut or soil bacteria) or to environmental factors. In particular, muscle- and calcium-binding proteins were found to be more prone to degradation by bacterial attack, whereas plasma and bone marrow proteins were more susceptible to exposure to extrinsic agents. Our results suggest that both gut and soil bacteria play key roles in bone diagenesis and protein decay in relatively short timescales, and that bone proteomics is a proficient resource with which to identify microbially-driven versus extrinsically-driven diagenesis.
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28
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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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29
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Mickleburgh HL, Schwalbe EC, Bonicelli A, Mizukami H, Sellitto F, Starace S, Wescott DJ, Carter DO, Procopio N. Human Bone Proteomes before and after Decomposition: Investigating the Effects of Biological Variation and Taphonomic Alteration on Bone Protein Profiles and the Implications for Forensic Proteomics. J Proteome Res 2021; 20:2533-2546. [PMID: 33683123 PMCID: PMC8155572 DOI: 10.1021/acs.jproteome.0c00992] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
![]()
Bone proteomic studies
using animal proxies and skeletonized human
remains have delivered encouraging results in the search for potential
biomarkers for precise and accurate post-mortem interval (PMI) and
the age-at-death (AAD) estimation in medico-legal investigations.
The development of forensic proteomics for PMI and AAD estimation
is in critical need of research on human remains throughout decomposition,
as currently the effects of both inter-individual biological differences
and taphonomic alteration on the survival of human bone protein profiles
are unclear. This study investigated the human bone proteome in four
human body donors studied throughout decomposition outdoors. The effects
of ageing phenomena (in vivo and post-mortem) and
intrinsic and extrinsic variables on the variety and abundancy of
the bone proteome were assessed. Results indicate that taphonomic
and biological variables play a significant role in the survival of
proteins in bone. Our findings suggest that inter-individual and inter-skeletal
differences in bone mineral density (BMD) are important variables
affecting the survival of proteins. Specific proteins survive better
within the mineral matrix due to their mineral-binding properties.
The mineral matrix likely also protects these proteins by restricting
the movement of decomposer microbes. New potential biomarkers for
PMI estimation and AAD estimation were identified. Future development
of forensic bone proteomics should include standard measurement of
BMD and target a combination of different biomarkers.
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Affiliation(s)
- Hayley L Mickleburgh
- Department of Cultural Sciences, Linnaeus University, Kalmar 352 52, Sweden.,Forensic Anthropology Center, Texas State University, San Marcos 78666, Texas, United States
| | - Edward C Schwalbe
- Forensic Science Research Group, Faculty of Health and Life Sciences, Northumbria University, Ellison Building, Northumbria University Newcastle, Newcastle Upon Tyne NE1 8ST, U. K
| | - Andrea Bonicelli
- Forensic Science Research Group, Faculty of Health and Life Sciences, Northumbria University, Ellison Building, Northumbria University Newcastle, Newcastle Upon Tyne NE1 8ST, U. K
| | - Haruka Mizukami
- Forensic Science Research Group, Faculty of Health and Life Sciences, Northumbria University, Ellison Building, Northumbria University Newcastle, Newcastle Upon Tyne NE1 8ST, U. K
| | - Federica Sellitto
- Forensic Science Research Group, Faculty of Health and Life Sciences, Northumbria University, Ellison Building, Northumbria University Newcastle, Newcastle Upon Tyne NE1 8ST, U. K
| | - Sefora Starace
- Dipartimento di Chimica, University of Turin, Via P. Giuria 7, 10125 Turin, Italy
| | - Daniel J Wescott
- Forensic Anthropology Center, Texas State University, San Marcos 78666, Texas, United States
| | - David O Carter
- Forensic Sciences Unit, School of Natural Sciences and Mathematics, Chaminade University of Honolulu, Honolulu 96816, Hawaii, United States
| | - Noemi Procopio
- Forensic Science Research Group, Faculty of Health and Life Sciences, Northumbria University, Ellison Building, Northumbria University Newcastle, Newcastle Upon Tyne NE1 8ST, U. K
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30
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Procopio N, Hopkins RJ, Harvey VL, Buckley M. Proteome Variation with Collagen Yield in Ancient Bone. J Proteome Res 2021; 20:1754-1769. [PMID: 33529527 PMCID: PMC7944572 DOI: 10.1021/acs.jproteome.0c01014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Indexed: 11/30/2022]
Abstract
Isotope analyses are some of the most common analytical methods applied to ancient bone, aiding the interpretation of past diets and chronology. For this, the evaluation of "collagen yield" (as defined in radiocarbon dating and stable isotope research) is a routine step that allows for the selection of specimens that are deemed adequate for subsequent analyses, with samples containing less than ∼1% "collagen yield" normally being used for isotopic analysis but discounted for radiocarbon dating. The aims of this study were to use proteomic methods of MALDI-TOF (matrix assisted laser desorption ionization time-of-fligh mass spectrometry) and LC-ESI-MS/MS (liquid chromatography electrospray ionization tandem mass spectrometry) to investigate the endogeneity of the dominant proteinaceous biomolecules within samples that are typically considered to contain poorly preserved protein. Taking 29 archaeological samples, we evaluated the proteome variability between different acid-soluble fractions removed prior to protein gelatinization and considered waste as part of the radiocarbon dating process. We then correlated these proteomes against the commonly used "collagen yield" proxy for preservation. We found that these waste fractions contained a significant amount of both collagenous and noncollagenous proteins (NCPs) but that the abundance of these was not correlated with the acquired "collagen yield". Rather than a depleted protein load as would be expected from a low "collagen yield", the variety of the extracted NCPs was comparable with that commonly obtained from ancient samples and included informative proteins useful for species identification, phylogenetic studies, and potentially even for isotopic analyses, given further method developments. Additionally, we did not observe any correlation between "collagen yield" and peptide mass fingerprint success or between the different fractions taken from the same sample but at different radiocarbon pretreatment stages. Overall, these findings highlight the value in retaining and analyzing sample fractions that are otherwise discarded as waste during the radiocarbon dating process but more importantly, that low "collagen yield" specimens that are often misinterpreted by archaeologists as being devoid of protein can still yield useful molecular sequence-based information.
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Affiliation(s)
- Noemi Procopio
- Forensic
Science Research Group, Faculty of Health and Life Sciences, Northumbria University, Northumbria University Newcastle, Ellison Building, Newcastle Upon Tyne NE1 8ST, U.K.
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Rachel J.A. Hopkins
- Department
of Anthropology, University of New Mexico, MSC01-1040, 1 University of New
Mexico, Albuquerque, New
Mexico 87131-0001, United States
- Research
Laboratory for Archaeology and the History of Art (RLAHA), School
of Archaeology, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, U.K.
| | - Virginia L. Harvey
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
- Interdisciplinary
Centre for Ancient Life, School of Natural Sciences, University of Manchester, Manchester, U.K.
| | - Michael Buckley
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
- Interdisciplinary
Centre for Ancient Life, School of Natural Sciences, University of Manchester, Manchester, U.K.
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31
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Fischer B, Hofmann A, Kurz S, Edel M, Zajonz DJ, Roth A, Schleifenbaum S. Influence of the fixation technique on the mechanical properties of human cancellous bone of the femoral head. Clin Biomech (Bristol, Avon) 2021; 82:105280. [PMID: 33582564 DOI: 10.1016/j.clinbiomech.2021.105280] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/16/2021] [Accepted: 01/19/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND The femoral head is of central importance for the force transmission from the suprapelvic body mass to the lower extremity. However, the condition of the subcortical bone and its mechanical properties in case of pathological changes due to coxarthrosis or femoral head necrosis differ from the healthy condition. METHODS Fresh femoral heads were gathered during hip total endoprosthesis surgeries and cylindrical cancellous bone samples were extracted with a hollow drill. By means of a uniaxial tensile-compression test system, the compressive strength was determined for two different specimen types (fresh and 24 h storage in acetone). Exemplary tests on an exceptionally large femoral head were performed to compare properties of fresh, fresh-deep-frozen and acetone-stored samples. FINDINGS The deformation behaviour and the material parameters determined were very heterogeneous. For most of the specimens, a destructive material test was successfully carried out, i.e. the compressive strength was determined. The average strength of fresh specimens was slightly higher than that of acetone specimens. On the other hand, the average Young's modulus of the acetone specimens was higher than that of the fresh specimens. INTERPRETATION The lower Young's moodulus of the fresh samples compared to the acetone samples could indicate a causal effect of the degreasing influence of the acetone. The partly considerable individual differences in compressive strength and failure compression can have patient-specific influencing factors such as constitution and physical fitness as well as causes in the initial pathological condition.
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Affiliation(s)
- Benjamin Fischer
- ZESBO - Center for Research on Musculoskeletal Systems, Leipzig University, Semmelweisstrasse 14, D-04103 Leipzig, Germany; Department of Orthopaedic Surgery, Traumatology and Plastic Surgery, University of Leipzig Medical Center, Liebigstrasse 20, D-04103 Leipzig, Germany.
| | - Alexander Hofmann
- Department of Orthopaedic Surgery, Traumatology and Plastic Surgery, University of Leipzig Medical Center, Liebigstrasse 20, D-04103 Leipzig, Germany
| | - Sascha Kurz
- ZESBO - Center for Research on Musculoskeletal Systems, Leipzig University, Semmelweisstrasse 14, D-04103 Leipzig, Germany; Department of Orthopaedic Surgery, Traumatology and Plastic Surgery, University of Leipzig Medical Center, Liebigstrasse 20, D-04103 Leipzig, Germany
| | - Melanie Edel
- ZESBO - Center for Research on Musculoskeletal Systems, Leipzig University, Semmelweisstrasse 14, D-04103 Leipzig, Germany; Department of Orthopaedic Surgery, Traumatology and Plastic Surgery, University of Leipzig Medical Center, Liebigstrasse 20, D-04103 Leipzig, Germany
| | - Dirk Jörg Zajonz
- Department of Orthopaedic Surgery, Traumatology and Plastic Surgery, University of Leipzig Medical Center, Liebigstrasse 20, D-04103 Leipzig, Germany
| | - Andreas Roth
- Department of Orthopaedic Surgery, Traumatology and Plastic Surgery, University of Leipzig Medical Center, Liebigstrasse 20, D-04103 Leipzig, Germany
| | - Stefan Schleifenbaum
- ZESBO - Center for Research on Musculoskeletal Systems, Leipzig University, Semmelweisstrasse 14, D-04103 Leipzig, Germany; Department of Orthopaedic Surgery, Traumatology and Plastic Surgery, University of Leipzig Medical Center, Liebigstrasse 20, D-04103 Leipzig, Germany
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32
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Wang J, Chen G, Qian H, Shang Q, Xiao J, Liang M, Gao B, Li T, Liu X. PP2A-C may be a promising candidate for postmortem interval estimation. Int J Legal Med 2021; 135:837-844. [PMID: 33409557 DOI: 10.1007/s00414-020-02466-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 11/12/2020] [Indexed: 01/16/2023]
Abstract
Determining the postmortem interval (PMI) is an important task in forensic pathology. However, a reliable means of determining the PMI between 24 h and approximately 7 days after death has not yet been established. A previous study demonstrated that subunit A of protein phosphatase 2A (PP2A-A) is a promising candidate to estimate the PMI during the first 96 h. However, more detailed work is still needed to investigate PP2A's function in PMI estimation. PP2A is a serine/threonine phosphatase consisting of three subunits (PP2A-A, PP2A-B, and PP2A-C), and its activation is reflected by Tyr-307 phosphorylation of the catalytic subunit (P-PP2A-C). In this study, we speculated that the other two subunits of PP2A and the activation of PP2A may play different roles in estimating the PMI. For this purpose, mice were euthanized and stored at different temperatures (4, 15, and 25 °C). At each temperature, the musculus vastus lateralis was collected at different time points (0, 24, 48, and 96 h) to investigate the degradation of PP2A-B, PP2A-C, and P-PP2A-C (Tyr-307). Homocysteine (Hcy) was used to establish a hyperhomocysteinemia animal model to explore the effects of plasma Hcy on PMI estimation. The data showed not only that PP2A-C was more stable than PP2A-B, but also that it was not affected by homocysteine (Hcy). These characteristics make PP2A-C a promising candidate for short-term (24 h to 48 h) PMI estimation.
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Affiliation(s)
- Jing Wang
- College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Yanta Road W.76, Xi'an, Shaanxi, 710061, People's Republic of China.,The Key Laboratory of Health Ministry for Forensic Science, Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Gang Chen
- College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Yanta Road W.76, Xi'an, Shaanxi, 710061, People's Republic of China.,The Key Laboratory of Health Ministry for Forensic Science, Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Hongyan Qian
- College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Yanta Road W.76, Xi'an, Shaanxi, 710061, People's Republic of China.,The Key Laboratory of Health Ministry for Forensic Science, Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Qing Shang
- College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Yanta Road W.76, Xi'an, Shaanxi, 710061, People's Republic of China.,The Key Laboratory of Health Ministry for Forensic Science, Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Jing Xiao
- College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Yanta Road W.76, Xi'an, Shaanxi, 710061, People's Republic of China.,The Key Laboratory of Health Ministry for Forensic Science, Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Min Liang
- College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Yanta Road W.76, Xi'an, Shaanxi, 710061, People's Republic of China.,The Key Laboratory of Health Ministry for Forensic Science, Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Baoyao Gao
- College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Yanta Road W.76, Xi'an, Shaanxi, 710061, People's Republic of China.,The Key Laboratory of Health Ministry for Forensic Science, Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Tao Li
- College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Yanta Road W.76, Xi'an, Shaanxi, 710061, People's Republic of China. .,The Key Laboratory of Health Ministry for Forensic Science, Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China.
| | - Xinshe Liu
- College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Yanta Road W.76, Xi'an, Shaanxi, 710061, People's Republic of China. .,The Key Laboratory of Health Ministry for Forensic Science, Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China.
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Zissler A, Stoiber W, Steinbacher P, Geissenberger J, Monticelli FC, Pittner S. Postmortem Protein Degradation as a Tool to Estimate the PMI: A Systematic Review. Diagnostics (Basel) 2020; 10:E1014. [PMID: 33256203 PMCID: PMC7760775 DOI: 10.3390/diagnostics10121014] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/22/2020] [Accepted: 11/23/2020] [Indexed: 12/12/2022] Open
Abstract
Objectives: We provide a systematic review of the literature to evaluate the current research status of protein degradation-based postmortem interval (PMI) estimation. Special attention is paid to the applicability of the proposed approaches/methods in forensic routine practice. Method: A systematic review of the literature on protein degradation in tissues and organs of animals and humans was conducted. Therefore, we searched the scientific databases Pubmed and Ovid for publications until December 2019. Additional searches were performed in Google Scholar and the reference lists of eligible articles. Results: A total of 36 studies were included. This enabled us to consider the degradation pattern of over 130 proteins from 11 different tissues, studied with different methods including well-established and modern approaches. Although comparison between studies is complicated by the heterogeneity of study designs, tissue types, methods, proteins and outcome measurement, there is clear evidence for a high explanatory power of protein degradation analysis in forensic PMI analysis. Conclusions: Although only few approaches have yet exceeded a basic research level, the current research status provides strong evidence in favor of the applicability of a protein degradation-based PMI estimation method in routine forensic practice. Further targeted research effort towards specific aims (also addressing influencing factors and exclusion criteria), especially in human tissue will be required to obtain a robust, reliable laboratory protocol, and collect sufficient data to develop accurate multifactorial mathematical decomposition models.
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Affiliation(s)
- Angela Zissler
- Department of Biosciences, University of Salzburg, 5020 Salzburg, Austria; (A.Z.); (W.S.); (P.S.); (J.G.)
| | - Walter Stoiber
- Department of Biosciences, University of Salzburg, 5020 Salzburg, Austria; (A.Z.); (W.S.); (P.S.); (J.G.)
| | - Peter Steinbacher
- Department of Biosciences, University of Salzburg, 5020 Salzburg, Austria; (A.Z.); (W.S.); (P.S.); (J.G.)
| | - Janine Geissenberger
- Department of Biosciences, University of Salzburg, 5020 Salzburg, Austria; (A.Z.); (W.S.); (P.S.); (J.G.)
| | - Fabio C. Monticelli
- Department of Forensic Medicine, University of Salzburg, 5020 Salzburg, Austria;
| | - Stefan Pittner
- Department of Forensic Medicine, University of Salzburg, 5020 Salzburg, Austria;
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Magni PA, Tingey E, Armstrong NJ, Verduin J. Evaluation of barnacle (Crustacea: Cirripedia) colonisation on different fabrics to support the estimation of the time spent in water by human remains. Forensic Sci Int 2020; 318:110526. [PMID: 33218795 DOI: 10.1016/j.forsciint.2020.110526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 09/14/2020] [Accepted: 09/22/2020] [Indexed: 11/18/2022]
Abstract
The estimation of the time since death (minimum Post Mortem Interval, minPMI) is an essential aspect of forensic investigations. This is particularly complex when a human body is found submerged, floating or beached in a marine environment. When a cadaver is found in a terrestrial environment the minPMI estimation is generally based on the presence of carrion insects. However, when a cadaver is found in an aquatic environment, a correct crime scene reconstruction is more complex and requires the consideration of the time the remains spent submerged underwater (minimum Post Mortem Submersion Interval, minPMSI) and/or floating (Floating Interval, FI). In marine crime scene scenarios, the use of barnacles (Crustacea: Cirripedia) has recently received some attention, due to their permanent settlement on human remains and their accompanying clothing. Previous research considered barnacle growth on human shoes, but the present research is the first to focus on the colonisation of barnacles on clothing materials (fabrics). Polystyrene floats were covered by either cotton, velvet, satin or neoprene and submerged underwater over a period of six months off the coast of Perth, Western Australia. The aims of this research were 1) the identification of marine species colonising the fabrics, with special attention to barnacles; 2) the identification of which fabric type provides the most desirable environment for colonisation; and 3) the identification of factors that affect the growth rate of the different species. Three species of barnacles, Balanus trigonus Darwin, Amphibalanus reticulatus (Utinomi) and A. variegatus (Darwin), were present in varying numbers and sizes. The colonisation process of the barnacles occurred rapidly, with the first sighting of barnacles observed within the first month on neoprene and control floats. The surface that attracted the largest number of barnacles was neoprene, followed by satin and cotton, while velvet showed an inconsistent colonisation rate. The largest size barnacles were observed on the control floats, while all fabrics showed a similar smaller size. Overall, time spent in water and water temperature had a significant positive relationship with both number and size of the colonising barnacles. This study is the first to provide information that will aid in the investigation of human remains recovered from Western Australian marine waters, using the barnacle colonisation on different fabric types.
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Affiliation(s)
- Paola A Magni
- Discipline of Medical, Molecular & Forensic Sciences, Murdoch University, 90 South Street, Murdoch, Western Australia, 6150, Australia; Murdoch University Singapore, King's Centre, 390 Havelock Road, 169662, Singapore.
| | - Elysia Tingey
- Discipline of Medical, Molecular & Forensic Sciences, Murdoch University, 90 South Street, Murdoch, Western Australia, 6150, Australia.
| | - Nicola J Armstrong
- Centre for Sustainable Aquatic Ecosystems, Murdoch University, 90 South Street, Murdoch, Western Australia, 6150, Australia; Mathematics and Statistics, Murdoch University, 90 South Street, Murdoch, Western Australia, 6150, Australia.
| | - Jennifer Verduin
- Centre for Sustainable Aquatic Ecosystems, Murdoch University, 90 South Street, Murdoch, Western Australia, 6150, Australia.
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35
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Johnston E, Buckley M. Relative Protein Abundances and Biological Ageing in Whole Skeletal Elements. J Proteome Res 2020; 20:538-548. [PMID: 33089684 DOI: 10.1021/acs.jproteome.0c00555] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Establishing biological age is an integral part of forensic investigations, currently achieved through morphological methods with varying degrees of accuracy. Furthermore, biological ageing is much easier in juveniles than in adults, at which point traditional ageing methods struggle. Therefore, biomolecular approaches are considered of great interest, with several protein markers already recognized for their potential forensic significance. However, previous studies have typically relied on subsampling different parts of skeletal elements. Here, we attempt to evaluate the proteome of complete elements using a rat model. In the analysis of specimens spanning beyond adulthood (1 week to 1.5 years), we observed 729 unique proteins across 33 samples (three for each sex for each of the five (female) or six (male)), five of which represent newly identified proteins in relation to age estimation: vimentin, osteopontin, matrilin-1, apolipoprotein A-I, and prothrombin. Most of these follow the trend of decreasing abundance through age, with the exception of prothrombin that increases. We consider the combined use of these relative abundances, along with those of previously noted fetuin-A, biglycan, albumin, and chromogranin-A signatures, as being of potential value to the development of an age estimation tool worthy of further evaluation in forensic contexts.
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Affiliation(s)
- Elizabeth Johnston
- Department of Earth and Environmental Sciences, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Michael Buckley
- Department of Earth and Environmental Sciences, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
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36
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Proteomics in Deaths by Drowning: Diagnostic Efficacy of Apolipoprotein A1 and α-1Antitrypsin, Pilot Study. Diagnostics (Basel) 2020; 10:diagnostics10100747. [PMID: 32987960 PMCID: PMC7650832 DOI: 10.3390/diagnostics10100747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 09/18/2020] [Accepted: 09/23/2020] [Indexed: 12/19/2022] Open
Abstract
Drowning is one of the leading causes of death worldwide. The pathophysiology of drowning is complex and, sometimes, interpretation of the circumstances of death in the autopsy becomes the main source of information in its diagnosis. New advances in medical research, such as proteomics, especially in forensic pathology, are still in the development. We proposed to investigate the application of Mass Spectrometry-based technologies, to identify differentially expressed proteins that may act as potential biomarkers in the postmortem diagnosis of drowning. We performed a pilot proteomic experiment with the inclusion of two drowned and two control forensic cases. After applying restrictive parameters, we identified apolipoprotein A1 (ApoA1) and α-1 antitrypsin as differentially expressed between the two diagnostic groups. A validation experiment, with the determination of both proteins in 25 forensic cases (16 drowned and 9 controls) was performed, and we corroborated ApoA1 higher values in the drowning group, whereas α-1 antitrypsin showed lower levels. After adjusting by confounder factors, both remained as predictive independent factors for diagnosis of drowning (p = 0.010 and p = 0.022, respectively). We constructed ROC curves for biomarkers’ levels attending at the origin of death and established an ApoA1 cut-off point of 100 mg/dL. Correct classification based on the diagnosis criteria was reached for 73.9% of the cases in a discriminant analysis. We propose apolipoprotein A1 (with our cutoff value for correct classification) and α-1 antitrypsin as valuable biomarkers of drowning. Our study, based on forensic cases, reveals our proteomic approach as a new complementary tool in the forensic diagnosis of drowning and, perhaps, in clinical future implications in drowned patients. However, this is a pilot approach, and future studies are necessary to consolidate our promising preliminary data.
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37
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Pittner S, Gotsmy W, Zissler A, Ehrenfellner B, Baumgartner D, Schrüfer A, Steinbacher P, Monticelli F. Intra- and intermuscular variations of postmortem protein degradation for PMI estimation. Int J Legal Med 2020; 134:1775-1782. [PMID: 32632798 PMCID: PMC7417396 DOI: 10.1007/s00414-020-02355-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 06/22/2020] [Indexed: 02/07/2023]
Abstract
In recent years, protein decomposition has become of increasing interest for the use in forensic estimation of the postmortem interval (PMI). Especially skeletal muscle tissue has proven to be a prime target tissue, among other reasons, due to its large abundance in the human body. In this regard, it is important to know whether there are any intra- and intermuscular differences in the behavior of protein degradation. Thus, samples from different locations within several skeletal muscles as well as from cardiac and smooth muscle tissue samples were collected from three autopsy cases with varying degree of decomposition. Samples were analyzed by SDS-PAGE and Western blotting and compared for protein degradation patterns. Intramuscular variations turned out to be minimal and without major influence for the use of the method. Observed intermuscular differences provide possibilities for future improvement of the precision and temporal application range. The results of this study show the strengths and current limitations of protein degradation-based PMI estimation and provide a deeper understanding of intraindividual postmortem protein degradation processes.
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Affiliation(s)
- Stefan Pittner
- Department of Forensic Medicine, University of Salzburg, Salzburg, Austria.
| | - Walther Gotsmy
- Department of Forensic Medicine, University of Salzburg, Salzburg, Austria
| | - Angela Zissler
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | | | | | - Anna Schrüfer
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Peter Steinbacher
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Fabio Monticelli
- Department of Forensic Medicine, University of Salzburg, Salzburg, Austria
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38
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Akçan R, Taştekin B, Yildirim MŞ, Aydogan HC, Sağlam N. Omics era in forensic medicine: towards a new age. Turk J Med Sci 2020; 50:1480-1490. [PMID: 32283897 PMCID: PMC7491271 DOI: 10.3906/sag-1912-197] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 04/11/2020] [Indexed: 02/06/2023] Open
Abstract
Background/aim Forensic medicine and sciences is a multidisciplinary branch of science, which frequently benefit from novel technologies. State of the art omics technologies have begun to be performed in forensic medicine and sciences, particularly in postmortem interval, intoxication, drugs of abuse, diagnosis of diseases and cause of death. This review aims to discuss the role and use of great omics (metabolomics, proteomics, genomics and transcriptomics) in forensic sciences, in detail. Materials and methods A detailed review of related literature was performed, and studies were subdivided as per the type of omics. Results and conclusion Omics seems as a revolutionary step in forensic science and sure carries it towards a new age. The number of forensic studies utilizing omics steadily increases in last years. Omics strategies should be used together in order to gather more accurate and certain data. Additional studies need to be performed to incorporate omics into routine forensic methodology.
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Affiliation(s)
- Ramazan Akçan
- Department of Forensic Medicine, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Burak Taştekin
- Department of Forensic Medicine, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Mahmut Şerif Yildirim
- Department of Forensic Medicine, Faculty of Medicine, Afyonkarahisar Health Sciences University, Afyonkarahisar, Turkey
| | - Halit Canberk Aydogan
- Department of Forensic Medicine, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Necdet Sağlam
- Department of Nanotechnology and Nanomedicine, Graduate School of Science and Engineering, Hacettepe University, Ankara, Turkey
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39
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Na JY. Estimation of the post-mortem interval using microRNA in the bones. J Forensic Leg Med 2020; 75:102049. [PMID: 32861958 DOI: 10.1016/j.jflm.2020.102049] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/29/2020] [Accepted: 08/20/2020] [Indexed: 12/20/2022]
Abstract
MicroRNAs (miRNAs) can be useful in forensic science because of their numerous characteristics, especially stability. Post-mortem interval (PMI) is crucial for death scene investigations. However, estimating PMI is challenging in cases involving significantly decomposed or destroyed bodies, such as those involving skeletonized remains. In this study, 71 bones (patella) were collected from the bodies during autopsies (PMI ranging from 1 day to 2 years). As the let-7e and miR-16 miRNAs were used as internal controls for the bone tissue in previous studies, these miRNAs were selected as targets to estimate PMI. The miRNA Ce_miR-39_1 was used as a spike-in internal control to normalize the target miRNA levels. Real-time quantitative reverse transcription polymerase chain reaction was performed to correlate the expression levels of let-7e and miR-16 with increasing PMI. A negative correlation was observed between miRNA expression and increasing PMI. The expression of both let-7e and miR-16 was observed to be significantly different between group A and the other PMI groups (group A < 1 month; 1 month < group B < 3 months; 3 months < group C < 6 months; group D > 6 months). In conclusion, these data suggest that the expression level of specific miRNAs (let-7e and miR-16) in the bone tissue could be used to estimate PMI. However, more studies using long-term PMI samples are required to further corroborate these findings.
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Affiliation(s)
- Joo-Young Na
- Department of Pathology, Pusan National University Yangsan Hospital, 20, Geumo-ro, Mulgeum-eup, Yangsan, 50612, Republic of Korea.
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40
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Jayathirtha M, Dupree EJ, Manzoor Z, Larose B, Sechrist Z, Neagu AN, Petre BA, Darie CC. Mass Spectrometric (MS) Analysis of Proteins and Peptides. Curr Protein Pept Sci 2020; 22:92-120. [PMID: 32713333 DOI: 10.2174/1389203721666200726223336] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 05/12/2020] [Accepted: 05/28/2020] [Indexed: 01/09/2023]
Abstract
The human genome is sequenced and comprised of ~30,000 genes, making humans just a little bit more complicated than worms or flies. However, complexity of humans is given by proteins that these genes code for because one gene can produce many proteins mostly through alternative splicing and tissue-dependent expression of particular proteins. In addition, post-translational modifications (PTMs) in proteins greatly increase the number of gene products or protein isoforms. Furthermore, stable and transient interactions between proteins, protein isoforms/proteoforms and PTM-ed proteins (protein-protein interactions, PPI) add yet another level of complexity in humans and other organisms. In the past, all of these proteins were analyzed one at the time. Currently, they are analyzed by a less tedious method: mass spectrometry (MS) for two reasons: 1) because of the complexity of proteins, protein PTMs and PPIs and 2) because MS is the only method that can keep up with such a complex array of features. Here, we discuss the applications of mass spectrometry in protein analysis.
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Affiliation(s)
- Madhuri Jayathirtha
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Emmalyn J Dupree
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Zaen Manzoor
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Brianna Larose
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Zach Sechrist
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, "Alexandru Ioan Cuza" University of Iasi, Iasi, Romania
| | - Brindusa Alina Petre
- Laboratory of Biochemistry, Department of Chemistry, Al. I. Cuza University of Iasi, Iasi, Romania, Center for Fundamental Research and Experimental Development in Translation Medicine - TRANSCEND, Regional Institute of Oncology, Iasi, Romania
| | - Costel C Darie
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
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41
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Procopio N, Ghignone S, Voyron S, Chiapello M, Williams A, Chamberlain A, Mello A, Buckley M. Soil Fungal Communities Investigated by Metabarcoding Within Simulated Forensic Burial Contexts. Front Microbiol 2020; 11:1686. [PMID: 32793158 PMCID: PMC7393272 DOI: 10.3389/fmicb.2020.01686] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 06/29/2020] [Indexed: 01/01/2023] Open
Abstract
Decomposition of animal bodies in the burial environment plays a key role in the biochemistry of the soil, altering the balance of the local microbial populations present before the introduction of the carcass. Despite the growing number of studies on decomposition and soil bacterial populations, less is known on its effects on fungal communities. Shifts in the fungal populations at different post-mortem intervals (PMIs) could provide insights for PMI estimation and clarify the role that specific fungal taxa have at specific decomposition stages. In this study, we buried pig carcasses over a period of 1- to 6-months, and we sampled the soil in contact with each carcass at different PMIs. We performed metabarcoding analysis of the mycobiome targeting both the internal transcribed spacer (ITS) 1 and 2, to elucidate which one was more suitable for this purpose. Our results showed a decrease in the fungal taxonomic richness associated with increasing PMIs, and the alteration of the soil fungal signature even after 6 months post-burial, showing the inability of soil communities to restore their original composition within this timeframe. The results highlighted taxonomic trends associated with specific PMIs, such as the increase of the Mortierellomycota after 4- and 6-months and of Ascomycota particularly after 2 months, and the decrease of Basidiomycota from the first to the last time point. We have found a limited number of taxa specifically associated with the carrion and not present in the control soil, showing that the major contributors to the recorded changes are originated from the soil and were not introduced by the carrion. As this is the first study conducted on burial graves, it sets the baseline for additional studies to investigate the role of fungal communities on prolonged decomposition periods and to identify fungal biomarkers to improve the accuracy of PMI prediction for forensic applications.
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Affiliation(s)
- Noemi Procopio
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
| | - Stefano Ghignone
- Istituto per la Protezione Sostenibile delle Piante, CNR, Turin, Italy
| | - Samuele Voyron
- Istituto per la Protezione Sostenibile delle Piante, CNR, Turin, Italy
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università degli Studi di Torino, Turin, Italy
| | - Marco Chiapello
- Istituto per la Protezione Sostenibile delle Piante, CNR, Turin, Italy
| | - Anna Williams
- School of Applied Sciences, University of Huddersfield, Huddersfield, United Kingdom
| | - Andrew Chamberlain
- School of Natural Sciences, The University of Manchester, Manchester, United Kingdom
| | - Antonietta Mello
- Istituto per la Protezione Sostenibile delle Piante, CNR, Turin, Italy
| | - Michael Buckley
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
- School of Natural Sciences, The University of Manchester, Manchester, United Kingdom
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42
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Mizukami H, Hathway B, Procopio N. Aquatic Decomposition of Mammalian Corpses: A Forensic Proteomic Approach. J Proteome Res 2020; 19:2122-2135. [DOI: 10.1021/acs.jproteome.0c00060] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Haruka Mizukami
- The Forensic Science Unit, Faculty of Health and Life Sciences, Ellison Building, Northumbria University, Newcastle upon Tyne NE1 8ST, U.K
| | - Bella Hathway
- The Forensic Science Unit, Faculty of Health and Life Sciences, Ellison Building, Northumbria University, Newcastle upon Tyne NE1 8ST, U.K
| | - Noemi Procopio
- The Forensic Science Unit, Faculty of Health and Life Sciences, Ellison Building, Northumbria University, Newcastle upon Tyne NE1 8ST, U.K
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43
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Nolan AN, Maker G, Mead RJ, Bringans S, Speers SJ. Peptide analysis of mammalian decomposition fluid in relation to the post-mortem interval. Forensic Sci Int 2020; 311:110269. [PMID: 32259675 DOI: 10.1016/j.forsciint.2020.110269] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 03/19/2020] [Accepted: 03/23/2020] [Indexed: 01/04/2023]
Abstract
We report the results of a semi-quantitative peptide analysis of decomposition fluid under field-based conditions in the absence of a soil matrix. Sixteen domestic pig (Sus scrofa domesticus) cadavers were used to model human decomposition in trials conducted in the summer and winter months in Western Australia. Physical characteristics were recorded and targeted peptide components of decomposition fluid were analysed using high performance liquid chromatography-triple quadrupole mass spectrometry. Principal component analysis identified 29 peptides, originating from haemoglobin subunits alpha and beta, creatine kinase, beta-enolase and lactate dehydrogenase, that contributed to differences in the mean peak areas of samples collected during the early period of decomposition (days 6-12 and day 2 in winter and summer, respectively) and during the later period (days 24-34 and days 8-10 in winter and summer, respectively). Fold changes for 8 peptides between these periods were significantly different. Three peptides derived from haemoglobin subunit beta, one from beta-enolase and two from lactate dehydrogenase displayed consistent trends, in that a notable increase in mean peak area was followed by a marked decrease in both the summer and winter samples. When temperature was accounted for, these trends occurred at different time points in summer and winter, indicating that factors other than temperature had impacted the rate of degradation of the proteins involved. The single peptides derived from haemoglobin subunit alpha and creatine kinase displayed consistent increases in mean peak area for the summer samples, suggesting that temperature played the most significant role in their degradation. Further analyses revealed that 7 peptides (one originating from haemoglobin subunit alpha, three from haemoglobin subunit beta and three from lactate dehydrogenase) displayed consistent trends that could be correlated with total body score and with the early stages of decomposition. The consistent trends (mean peak area versus time) for peptides derived from several proteins during decomposition trials conducted under different temperature regimes further emphasised the potential of peptide analysis in time since death estimation.
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Affiliation(s)
- Ashley-N'Dene Nolan
- Medical, Molecular and Forensic Sciences, Murdoch University Western Australia, 6150, Australia.
| | - Garth Maker
- Medical, Molecular and Forensic Sciences, Murdoch University Western Australia, 6150, Australia.
| | - Robert J Mead
- Medical, Molecular and Forensic Sciences, Murdoch University Western Australia, 6150, Australia.
| | - Scott Bringans
- Proteomics International. PO Box 3009, Broadway, Nedlands, Western Australia, 6009, Australia.
| | - Samuel J Speers
- Medical, Molecular and Forensic Sciences, Murdoch University Western Australia, 6150, Australia.
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Catlin LA, Chou RM, Goecker ZC, Mullins LA, Silva DSBSS, Spurbeck RR, Parker GJ, Bartling CM. Demonstration of a mitochondrial DNA-compatible workflow for genetically variant peptide identification from human hair samples. Forensic Sci Int Genet 2019; 43:102148. [DOI: 10.1016/j.fsigen.2019.102148] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 07/29/2019] [Accepted: 08/14/2019] [Indexed: 12/01/2022]
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45
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Díaz-Martín RD, Ambrosio JR, Flores RM, Gonzáles-Pozos S, Valencia-Caballero L. Cytoskeletal and extracellular matrix proteins resist the burning of bones. Forensic Sci Int 2019; 305:110027. [PMID: 31704515 DOI: 10.1016/j.forsciint.2019.110027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 09/07/2019] [Accepted: 10/27/2019] [Indexed: 02/07/2023]
Abstract
Due the proteins from bone remains are highly resistant to pass of time and environmental conditions, they could tell us about the events that probably happened in the past. In the forensic and physical anthropology context, burnt bone remains are one of the most common pieces of recovered evidence and, generally, they are associated with funerary practices, criminal scenes or massive catastrophic events. In the present study, bone pieces of pigs were calcined at different calcination temperatures, and proteins were searched using biochemical, immunochemical and ultrastructure visualization under these experimentally conditions. For this purpose, it was successfully developed a non-demineralizing protein extraction method from burnt bone remains and the use of specific antibodies permitted the identification of different extracellular matrix and intracellular proteins. While collagen proteins type I and IV were identified and detected under middle and high calcination temperatures (300°C and 600°C); cytoskeletal proteins as actin, tubulin and, the microtubule associated protein Tau, were found under calcination process, even up high calcination temperatures. Under ultrastructural analysis, fibrous materials with a classical disposition of collagens were observed even at high calcination temperatures of the burnt bone remains. The protein identification and characterization in burnt bones as performed in present studies, is clearly demonstrating that using specific strategies for protein characterizations it is possible to found protein biomarkers in burnt bone remains and this strategy could be useful for forensic and anthropological purposes.
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Affiliation(s)
- Rubén Darío Díaz-Martín
- Departamento de Innovación en Material Biológico Humano (DIMBIH), Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México; Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México
| | - Javier R Ambrosio
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México
| | - Ricardo Mondragón Flores
- Departamento de Bioquímica, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), México
| | | | - Lorena Valencia-Caballero
- Departamento de Innovación en Material Biológico Humano (DIMBIH), Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México.
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Choi KM, Zissler A, Kim E, Ehrenfellner B, Cho E, Lee SI, Steinbacher P, Yun KN, Shin JH, Kim JY, Stoiber W, Chung H, Monticelli FC, Kim JY, Pittner S. Postmortem proteomics to discover biomarkers for forensic PMI estimation. Int J Legal Med 2019; 133:899-908. [PMID: 30864069 PMCID: PMC6469664 DOI: 10.1007/s00414-019-02011-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 01/24/2019] [Indexed: 11/18/2022]
Abstract
The assessment of postmortem degradation of skeletal muscle proteins has emerged as a novel approach to estimate the time since death in the early to mid-postmortem phase (approximately 24 h postmortem (hpm) to 120 hpm). Current protein-based methods are limited to a small number of skeletal muscle proteins, shown to undergo proteolysis after death. In this study, we investigated the usability of a target-based and unbiased system-wide protein analysis to gain further insights into systemic postmortem protein alterations and to identify additional markers for postmortem interval (PMI) delimitation. We performed proteomic profiling to globally analyze postmortem alterations of the rat and mouse skeletal muscle proteome at defined time points (0, 24, 48, 72, and 96 hpm), harnessing a mass spectrometry-based quantitative proteomics approach. Hierarchical clustering analysis for a total of 579 (rat) and 896 (mouse) quantified proteins revealed differentially expressed proteins during the investigated postmortem period. We further focused on two selected proteins (eEF1A2 and GAPDH), which were shown to consistently degrade postmortem in both rat and mouse, suggesting conserved intra- and interspecies degradation behavior, and thus preserved association with the PMI and possible transferability to humans. In turn, we validated the usefulness of these new markers by classical Western blot experiments in a rat model and in human autopsy cases. Our results demonstrate the feasibility of mass spectrometry-based analysis to discover novel protein markers for PMI estimation and show that the proteins eEF1A2 and GAPDH appear to be valuable markers for PMI estimation in humans.
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Affiliation(s)
- Kyoung-Min Choi
- Graduate School of Analytical Science and Technology (GRAST), Chungnam National University, Daejeon, South Korea
| | - Angela Zissler
- Dept. of Biosciences, University of Salzburg, Salzburg, Austria
| | - Eunjung Kim
- Dept. of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | | | - Eunji Cho
- Graduate School of Analytical Science and Technology (GRAST), Chungnam National University, Daejeon, South Korea
| | - Se-In Lee
- Graduate School of Analytical Science and Technology (GRAST), Chungnam National University, Daejeon, South Korea
| | | | - Ki Na Yun
- Dept. of Chemistry, Sogang University, Seoul, South Korea
- Biomedical Omics Center, Korea Basic Science Institute, Ochang, South Korea
| | - Jong Hwan Shin
- Graduate School of Analytical Science and Technology (GRAST), Chungnam National University, Daejeon, South Korea
- Biomedical Omics Center, Korea Basic Science Institute, Ochang, South Korea
| | - Jin Young Kim
- Biomedical Omics Center, Korea Basic Science Institute, Ochang, South Korea
| | - Walter Stoiber
- Dept. of Biosciences, University of Salzburg, Salzburg, Austria
| | - Heesun Chung
- Graduate School of Analytical Science and Technology (GRAST), Chungnam National University, Daejeon, South Korea
| | | | - Jae-Young Kim
- Graduate School of Analytical Science and Technology (GRAST), Chungnam National University, Daejeon, South Korea.
- Division of Bioconvergence Analysis, Korea Basic Science Institute, Ochang, South Korea.
| | - Stefan Pittner
- Dept. of Forensic Medicine, University of Salzburg, Salzburg, Austria.
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47
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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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48
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Procopio N, Ghignone S, Williams A, Chamberlain A, Mello A, Buckley M. Metabarcoding to investigate changes in soil microbial communities within forensic burial contexts. Forensic Sci Int Genet 2019; 39:73-85. [DOI: 10.1016/j.fsigen.2018.12.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 11/17/2018] [Accepted: 12/10/2018] [Indexed: 02/02/2023]
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49
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Buckley M, Lawless C, Rybczynski N. Collagen sequence analysis of fossil camels, Camelops and c.f. Paracamelus, from the Arctic and sub-Arctic of Plio-Pleistocene North America. J Proteomics 2019; 194:218-225. [DOI: 10.1016/j.jprot.2018.11.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 11/02/2018] [Accepted: 11/19/2018] [Indexed: 11/27/2022]
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50
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Neagu AN. Proteome Imaging: From Classic to Modern Mass Spectrometry-Based Molecular Histology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:55-98. [PMID: 31347042 DOI: 10.1007/978-3-030-15950-4_4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In order to overcome the limitations of classic imaging in Histology during the actually era of multiomics, the multi-color "molecular microscope" by its emerging "molecular pictures" offers quantitative and spatial information about thousands of molecular profiles without labeling of potential targets. Healthy and diseased human tissues, as well as those of diverse invertebrate and vertebrate animal models, including genetically engineered species and cultured cells, can be easily analyzed by histology-directed MALDI imaging mass spectrometry. The aims of this review are to discuss a range of proteomic information emerging from MALDI mass spectrometry imaging comparative to classic histology, histochemistry and immunohistochemistry, with applications in biology and medicine, concerning the detection and distribution of structural proteins and biological active molecules, such as antimicrobial peptides and proteins, allergens, neurotransmitters and hormones, enzymes, growth factors, toxins and others. The molecular imaging is very well suited for discovery and validation of candidate protein biomarkers in neuroproteomics, oncoproteomics, aging and age-related diseases, parasitoproteomics, forensic, and ecotoxicology. Additionally, in situ proteome imaging may help to elucidate the physiological and pathological mechanisms involved in developmental biology, reproductive research, amyloidogenesis, tumorigenesis, wound healing, neural network regeneration, matrix mineralization, apoptosis and oxidative stress, pain tolerance, cell cycle and transformation under oncogenic stress, tumor heterogeneity, behavior and aggressiveness, drugs bioaccumulation and biotransformation, organism's reaction against environmental penetrating xenobiotics, immune signaling, assessment of integrity and functionality of tissue barriers, behavioral biology, and molecular origins of diseases. MALDI MSI is certainly a valuable tool for personalized medicine and "Eco-Evo-Devo" integrative biology in the current context of global environmental challenges.
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Affiliation(s)
- Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, "Alexandru Ioan Cuza" University of Iasi, Iasi, Romania.
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