1
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Charlier P, Bourdin V, N'Dah D, Kielbasa M, Pible O, Armengaud J. Metaproteomic analysis of King Ghezo tomb wall (Abomey, Benin) confirms 19th century voodoo sacrifices. Proteomics 2024; 24:e2400048. [PMID: 38807532 DOI: 10.1002/pmic.202400048] [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: 02/04/2024] [Revised: 05/01/2024] [Accepted: 05/13/2024] [Indexed: 05/30/2024]
Abstract
The palace of King Ghezo in Abomey, capital of the ancient kingdom of Dahomey (present-day Benin), houses two sacred huts which are specific funerary structures. It is claimed that the binder in their walls is made of human blood. In the study presented here, we conceived an original strategy to analyze the proteins present on minute amounts of the cladding sampled from the inner facade of the cenotaph wall and establish their origin. The extracted proteins were proteolyzed and the resulting peptides were characterized by high-resolution tandem mass spectrometry. Over 6397 distinct molecular entities were identified using cascading searches. Starting from without a priori searches of an extended generic database, the peptide repertoire was narrowed down to the most representative organisms-identified by means of taxon-specific peptides. A wide diversity of bacteria, fungi, plants, and animals were detected through the available protein material. This inventory was used to archaeologically reconstruct the voodoo rituals of consecration and maintenance of vitality. Several indicators attested to the presence of traces of human and poultry blood in the material taken. This study shows the essential advantages of paleoproteomics and metaproteomics for the study of ancient residues from archaeological excavations or historical monuments.
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Affiliation(s)
- Philippe Charlier
- Department of research and higher education, musée du quai Branly - Jacques Chirac, Paris, France
- Laboratory Anthropology, Archaeology, Biology (LAAB), UFR of Health Sciences (UVSQ/Paris-Saclay University), Montigny-Le-Bretonneux, France
- Foundation Anthropology, Archaeology, Biology (FAAB) - Institut de France, Paris, France
| | - Virginie Bourdin
- Laboratory Anthropology, Archaeology, Biology (LAAB), UFR of Health Sciences (UVSQ/Paris-Saclay University), Montigny-Le-Bretonneux, France
| | - Didier N'Dah
- Département d'Histoire et d'Archéologie, Institut National des Métiers d'Art, d'Archéologie et de la Culture (INMAAC), Université d'Abomey-Calavi, Boite Postale 04 BP 431 Cotonou, République du Bénin
| | - Mélodie Kielbasa
- Département Médicaments et Technologies pour la Santé (DMTS), CEA, INRAE, SPI, Université Paris-Saclay, Bagnols-sur-Cèze, France
| | - Olivier Pible
- Département Médicaments et Technologies pour la Santé (DMTS), CEA, INRAE, SPI, Université Paris-Saclay, Bagnols-sur-Cèze, France
| | - Jean Armengaud
- Département Médicaments et Technologies pour la Santé (DMTS), CEA, INRAE, SPI, Université Paris-Saclay, Bagnols-sur-Cèze, France
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2
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Zupanič Pajnič I, Kovačič N. DNA preservation in compact and trabecular bone. Forensic Sci Int Genet 2024; 71:103067. [PMID: 38833778 DOI: 10.1016/j.fsigen.2024.103067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 05/30/2024] [Accepted: 05/30/2024] [Indexed: 06/06/2024]
Abstract
Significant variation exists in the molecular structure of compact and trabecular bone. In compact bone full dissolution of the bone powder is required to efficiently release the DNA from hydroxyapatite. In trabecular bone where soft tissues are preserved, we assume that full dissolution of the bone powder is not required to release the DNA from collagen. To investigate this issue, research was performed on 45 Second World War diaphysis (compact bone)-epiphysis (trabecular bone) femur pairs, each processed with a full dissolution (FD) and partial dissolution (PD) extraction method. DNA quality and quantity were assessed using qPCR PowerQuant analyses, and autosomal STRs were typed to confirm the authenticity of isolated DNA. Our results support different mechanisms of DNA preservation in compact and trabecular bone because FD method was more efficient than PD method only in compact bone, and no difference in DNA yield was observed in trabecular bone, showing no need for full dissolution of the bone powder when trabecular bone tissue is processed. In addition, a significant difference in DNA yield was observed between compact and trabecular bone when PD was applied, with more DNA extracted from trabecular bone than compact bone. High suitability of trabecular bone processed with PD method is also supported by the similar quantities of DNA isolated by FD method when applied to both compact and trabecular bone. Additionally similar quantities of DNA were isolated when compact bone was extracted with FD method and trabecular bone was extracted with PD method. Processing trabecular bone with PD method in routine identification of skeletonized human remains shortens the extraction procedure and simplifies the grinding process.
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Affiliation(s)
- Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, Ljubljana 1000, Slovenia.
| | - Nika Kovačič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, Ljubljana 1000, Slovenia
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3
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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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4
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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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5
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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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6
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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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7
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Dekker J, Larson T, Tzvetkov J, Harvey VL, Dowle A, Hagan R, Genever P, Schrader S, Soressi M, Hendy J. Spatial analysis of the ancient proteome of archeological teeth using mass spectrometry imaging. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2023; 37:e9486. [PMID: 36735645 DOI: 10.1002/rcm.9486] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 01/28/2023] [Accepted: 01/29/2023] [Indexed: 06/18/2023]
Abstract
RATIONALE Proteins extracted from archaeological bone and teeth are utilised for investigating the phylogeny of extinct and extant species, the biological sex and age of past individuals, as well as ancient health and physiology. However, variable preservation of proteins in archaeological materials represents a major challenge. METHODS To better understand the spatial distribution of ancient proteins preserved within teeth, we applied matrix assisted laser desorption/ionisation mass spectrometry imaging (MALDI-MSI) for the first time to bioarchaeological samples to visualise the intensity of proteins in archaeological teeth thin sections. We specifically explored the spatial distribution of four proteins (collagen type I, of which the chains alpha-1 and alpha-2, alpha-2-HS-glycoprotein, haemoglobin subunit alpha and myosin light polypeptide 6). RESULTS We successfully identified ancient proteins in archaeological teeth thin sections using mass spectrometry imaging. The data are available via ProteomeXchange with identifier PXD038114. However, we observed that peptides did not always follow our hypotheses for their spatial distribution, with distinct differences observed in the spatial distribution of several proteins, and occasionally between peptides of the same protein. CONCLUSIONS While it remains unclear what causes these differences in protein intensity distribution within teeth, as revealed by MALDI-MSI in this study, we have demonstrated that MALDI-MSI can be successfully applied to mineralised bioarchaeological tissues to detect ancient peptides. In future applications, this technique could be particularly fruitful not just for understanding the preservation of proteins in a range of archaeological materials, but making informed decisions on sampling strategies and the targeting of key proteins of archaeological and biological interest.
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Affiliation(s)
- Joannes Dekker
- BioArCh, Department of Archaeology, University of York, York, UK
- Section for GeoBiology, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Faculty of Archaeology, Leiden University, Leiden, the Netherlands
| | - Tony Larson
- Metabolomics & Proteomics Laboratory, Bioscience Technology Facility, Department of Biology, University of York, York, UK
| | | | - Virginia L Harvey
- BioArCh, Department of Archaeology, University of York, York, UK
- Department of Biological Sciences, University of Chester, Chester, UK
| | - Adam Dowle
- Metabolomics & Proteomics Laboratory, Bioscience Technology Facility, Department of Biology, University of York, York, UK
| | - Richard Hagan
- BioArCh, Department of Archaeology, University of York, York, UK
| | - Paul Genever
- Department of Biology, University of York, York, UK
| | - Sarah Schrader
- Faculty of Archaeology, Leiden University, Leiden, the Netherlands
| | - Marie Soressi
- Faculty of Archaeology, Leiden University, Leiden, the Netherlands
| | - Jessica Hendy
- BioArCh, Department of Archaeology, University of York, York, UK
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8
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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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9
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Examination of human osteoarchaeological remains as a feasible source of polar and apolar metabolites to study past conditions. Sci Rep 2023; 13:696. [PMID: 36639564 PMCID: PMC9839756 DOI: 10.1038/s41598-023-27401-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 01/02/2023] [Indexed: 01/15/2023] Open
Abstract
Metabolomics is a modern tool that aids in our understanding of the molecular changes in organisms. Archaeological science is a branch of archaeology that explores different archaeological materials using modern analytical tools. Human osteoarchaeological material are a frequent finding in archaeological contexts and have the potential to offer information about previous human populations, which can be illuminating about our current condition. Using a set of samples comprising different skeletal elements and bone structures, here we explore for the first time the possibility of extracting metabolites from osteoarchaeological material. Here, a protocol for extraction and measurement of extracted polar and less-polar/apolar metabolites by ultra-high performance liquid chromatography hyphenated to high resolution mass spectrometry is presented to measure the molecules separated after a reversed phase and hydrophilic interaction liquid chromatography column. Molecular information was obtained, showing that osteoarchaeological material is a viable source of molecular information for metabolomic studies.
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10
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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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11
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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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12
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Fretwurst T, Tritschler I, Rothweiler R, Nahles S, Altmann B, Schilling O, Nelson K. Proteomic profiling of human bone from different anatomical sites - A pilot study. Proteomics Clin Appl 2022; 16:e2100049. [PMID: 35462455 DOI: 10.1002/prca.202100049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 04/11/2022] [Accepted: 04/20/2022] [Indexed: 12/30/2022]
Abstract
PURPOSE The study aim is a comparative proteome-based analysis of different autologous bone entities (alveolar bone [AB], iliac cortical [IC] bone, and iliac spongiosa [IS]) used for alveolar onlay grafting. EXPERIMENTAL DESIGN Site-matched bone samples of AB, IC, and IS were harvested during alveolar onlay grafting. Proteins were extracted using a detergent-based (sodium dodecyl sulfate) strategy and trypsinized. Proteome analysis was performed using liquid chromatography-tandem mass spectrometry (LC-MS/MS). MaxQuant was used for peptide-to-spectrum matching, peak detection, and quantitation. Linear models for microarray analysis (LIMMA) were used to detect differentially abundant peptides and proteins. RESULTS A total of 1730 different proteins were identified across the 15 samples at a false discovery rate of 1%. Partial least-squares discriminant analysis approved segregation of AB, IC, and IS protein profiles. LIMMA statistics highlighted 66 proteins that were more abundant in AB then in IC (vs. 92 proteins were enriched in IC over AB). Gene Ontology enrichment analysis revealed a matrisomal versus an immune-related proteome fingerprint in AB versus IC. CONCLUSION AND CLINICAL RELEVANCE This pilot study demonstrates an ECM protein-related proteome fingerprint in AB and an immune-related proteome fingerprint in IS and IC.
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Affiliation(s)
- Tobias Fretwurst
- Department of Oral- and Craniomaxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center, University of Freiburg, Freiburg, Germany
| | | | - René Rothweiler
- Department of Oral- and Craniomaxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center, University of Freiburg, Freiburg, Germany
| | - Susanne Nahles
- Department of Oral and Maxillofacial Surgery, Berlin Institute of Health, Corporate Member of Freie Universität Berlin, Charité - Universitätsmedizin Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Brigitte Altmann
- Department of Prosthetic Dentistry, Center for Dental Medicine, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,G.E.R.N Center for Tissue Replacement, Regeneration & Neogenesis, Department of Prosthetic Dentistry, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Oliver Schilling
- Institute of Surgical Pathology, Faculty of Medicine, Medical Center, University of Freiburg, Freiburg, Germany
| | - Katja Nelson
- Department of Oral- and Craniomaxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center, University of Freiburg, Freiburg, Germany
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13
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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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14
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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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15
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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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16
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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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17
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Abstract
The goal of paleoproteomics is to characterize proteins from specimens that have been subjected to the degrading and obscuring effects of time, thus obtaining biological information about tissues or organisms both unobservable in the present and unobtainable through morphological study. Although the description of sequences from Tyrannosaurus rex and Brachylophosaurus canadensis suggested that proteins may persist over tens of millions of years, the majority of paleoproteomic analyses have focused on historical, archeological, or relatively young paleontological samples that rarely exceed 1 million years in age. However, recent advances in methodology and analyses of diverse tissues types (e.g., fossil eggshell, dental enamel) have begun closing the large window of time that remains unexplored in the fossil history of the Cenozoic. In this perspective, we discuss the history and current state of deep time paleoproteomics (DTPp), here defined as paleoproteomic study of samples ∼1 million years (1 Ma) or more in age. We then discuss the future of DTPp research, including what we see as critical ways the field can expand, advancements in technology that can be utilized, and the types of questions DTPp can address if such a future is realized.
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Affiliation(s)
- Elena R Schroeter
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Timothy P Cleland
- Museum Conservation Institute, Smithsonian Institution, Suitland, Maryland 20746, United States
| | - Mary H Schweitzer
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, United States.,North Carolina Museum of Natural Sciences, Raleigh, North Carolina 27605, United States.,Department of Geology, Lund University, Lund SE-221 00, Sweden
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18
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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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19
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Leskovar T, Zupanič Pajnič I, Jerman I. Dealing with minor differences in bone matrix: can spectra follow the DNA preservation? AUST J FORENSIC SCI 2021. [DOI: 10.1080/00450618.2021.1948102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Tamara Leskovar
- Centre for Interdisciplinary Research in Archaeology, Department of Archaeology, Faculty of Arts, University of Ljubljana, Ljubljana, Slovenia
| | - Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Ivan Jerman
- Department for Materials Chemistry, National Institute of Chemistry, Ljubljana, Slovenia
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20
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Plasma Proteomic Analysis in Morquio A Disease. Int J Mol Sci 2021; 22:ijms22116165. [PMID: 34200496 PMCID: PMC8201332 DOI: 10.3390/ijms22116165] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 06/02/2021] [Accepted: 06/04/2021] [Indexed: 12/18/2022] Open
Abstract
Mucopolysaccharidosis type IVA (MPS IVA) is a lysosomal disease caused by mutations in the gene encoding the enzymeN-acetylgalactosamine-6-sulfate sulfatase (GALNS), and is characterized by systemic skeletal dysplasia due to excessive storage of keratan sulfate (KS) and chondroitin-6-sulfate in chondrocytes. Although improvements in the activity of daily living and endurance tests have been achieved with enzyme replacement therapy (ERT) with recombinant human GALNS, recovery of bone lesions and bone growth in MPS IVA has not been demonstrated to date. Moreover, no correlation has been described between therapeutic efficacy and urine levels of KS, which accumulates in MPS IVA patients. The objective of this study was to assess the validity of potential biomarkers proposed by other authors and to identify new biomarkers. To identify candidate biomarkers of this disease, we analyzed plasma samples from healthy controls (n=6) and from untreated (n=8) and ERT-treated (n=5, sampled before and after treatment) MPS IVA patients using both qualitative and quantitative proteomics analyses. The qualitative proteomics approach analyzed the proteomic profile of the different study groups. In the quantitative analysis, we identified/quantified 215 proteins after comparing healthy control untreated, ERT-treated MPSIVA patients. We selected a group of proteins that were dysregulated in MPS IVA patients. We identified four potential protein biomarkers, all of which may influence bone and cartilage metabolism: fetuin-A, vitronectin, alpha-1antitrypsin, and clusterin. Further studies of cartilage and bone samples from MPS IVA patients will be required to verify the validity of these proteins as potential biomarkers of MPS IVA.
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21
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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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22
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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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23
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Cleland TP, Sarancha JJ, France CAM. Proteomic profile of bone "collagen" extracted for stable isotopes: Implications for bulk and single amino acid analyses. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2021; 35:e9025. [PMID: 33332665 DOI: 10.1002/rcm.9025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/11/2020] [Accepted: 12/12/2020] [Indexed: 06/12/2023]
Abstract
RATIONALE Protein studies in archaeology and paleontology have been dominated by stable isotope studies to understand diet and trophic levels, but recent applications of proteomic techniques have resulted in a more complete understanding of protein diagenesis than stable isotopes alone. In stable isotope analyses, samples are retained or discarded based on their properties. Proteomics can directly determine what proteins are present within the sample and may be able to allow previously discarded samples to be analyzed. METHODS Protein samples that had been previously analyzed for stable isotopes, including those with marginal and poor sample quality, were characterized by liquid chromatography/mass spectrometry using an LTQ Orbitrap Velos mass spectrometer after separation on a Dionex Ultimate 3000 LC system. Data were analyzed using MetaMorpheus and custom R scripts. RESULTS We found a variety of proteins in addition to collagen, although collagen I was found in the majority of the samples (most samples >80%). We also found a positive correlation between total deamidation and wt% N, suggesting that deamidation may impact the overall nitrogen signal in bulk analyses. The amino acid profiles of samples, including those of marginal or poor stable isotope quality, reflect the expected collagen I percentages, allowing their use in single amino acid stable isotope analyses. CONCLUSIONS All the samples regardless of quality were found to have high concentrations of collagen I, making interpretations of dietary routing based on collagen I reasonably valid. The amino acid profiles on the marginal and poor samples reflect an expected collagen I profile and allow these samples to be recovered for single amino acid analyses.
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Affiliation(s)
- Timothy P Cleland
- Museum Conservation Institute, Smithsonian Institution, Suitland, MD, USA
| | - Julianne J Sarancha
- School of Earth and Space Exploration, Arizona State University, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
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24
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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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25
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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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26
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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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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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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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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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Palaeoproteomic identification of breast milk protein residues from the archaeological skeletal remains of a neonatal dog. Sci Rep 2019; 9:12841. [PMID: 31492911 PMCID: PMC6731306 DOI: 10.1038/s41598-019-49183-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 08/19/2019] [Indexed: 01/07/2023] Open
Abstract
Accurate postmortem estimation of breastfeeding status for archaeological or forensic neonatal remains is difficult. Confident identification of milk-specific proteins associated with these remains would provide direct evidence of breast milk consumption. We used liquid chromatography coupled to tandem mass spectrometry (MS) to confidently identify beta-lactoglobulin-1 (LGB1) and whey acidic protein (WAP), major whey proteins associated with a neonatal dog (Canis lupus familiaris) skeleton (430–960 cal AD), from an archaeological site in Hokkaido, Japan. The age at death of the individual was estimated to be approximately two weeks after birth. Protein residues extracted from rib and vertebra fragments were analyzed and identified by matching tandem MS spectra against the dog reference proteome. A total of 200 dog protein groups were detected and at least one peptide from canine LGB1 and two peptides from canine WAP were confidently identified. These milk proteins most probably originated from the mother’s breast milk, ingested by the neonate just before it died. We suggest the milk diffused outside the digestive apparatus during decomposition, and, by being absorbed into the bones, it partially preserved. The result of this study suggests that proteomic analysis can be used for postmortem reconstruction of the breastfeeding status at the time of death of neonatal mammalian, by analyzing their skeletal archaeological remains. This method is also applicable to forensic and wildlife studies.
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31
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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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Prieto-Bonete G, Pérez-Cárceles MD, Maurandi-López A, Pérez-Martínez C, Luna A. Association between protein profile and postmortem interval in human bone remains. J Proteomics 2018; 192:54-63. [PMID: 30145274 DOI: 10.1016/j.jprot.2018.08.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 06/08/2018] [Accepted: 08/07/2018] [Indexed: 12/15/2022]
Abstract
Proteomic techniques in bones forensic samples are increasingly, being applied. The main aim of forensic sciences is the estimation of postmortem interval. Most current techniques are useful for the first post-mortem stages. However, in the case of osseous remains, these techniques may be difficult to use due to the high level of decomposition of the sample. Our objective was to attempt to know whether there is a protein profile in human bone remains that would enable a late postmortem. interval ranging from 5 to 20 years postmortem to be estimated. A total of 40 femur bones from 40 different cadavers (data range 5-20 years) were use. Of the 275 total proteins, we excluded the circulating ones (n = 227), leaving a total of 48 proteins (29 structural and 19 functional) were found. A multiple correspondence analysis was applied on the 48 proteins. Finally selecting 32 proteins that allowed us to discriminate between the. two groups of postmortem interval. Analysis of the protein profile present in bone permits an approximation of the date of death within the studied interval, and could be used to complement other tests for estimating the postmortem interval.
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Affiliation(s)
| | | | - Antonio Maurandi-López
- Department of Didactics of Mathematical and Social Sciences, University of Murcia, Spain
| | | | - Aurelio Luna
- Department of Legal and Forensic Medicine, University of Murcia, Spain
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Mason KE, Anex D, Grey T, Hart B, Parker G. Protein-based forensic identification using genetically variant peptides in human bone. Forensic Sci Int 2018; 288:89-96. [DOI: 10.1016/j.forsciint.2018.04.016] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 04/04/2018] [Accepted: 04/10/2018] [Indexed: 01/17/2023]
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Welker F. Elucidation of cross-species proteomic effects in human and hominin bone proteome identification through a bioinformatics experiment. BMC Evol Biol 2018; 18:23. [PMID: 29463217 PMCID: PMC5819086 DOI: 10.1186/s12862-018-1141-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 02/15/2018] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The study of ancient protein sequences is increasingly focused on the analysis of older samples, including those of ancient hominins. The analysis of such ancient proteomes thereby potentially suffers from "cross-species proteomic effects": the loss of peptide and protein identifications at increased evolutionary distances due to a larger number of protein sequence differences between the database sequence and the analyzed organism. Error-tolerant proteomic search algorithms should theoretically overcome this problem at both the peptide and protein level; however, this has not been demonstrated. If error-tolerant searches do not overcome the cross-species proteomic issue then there might be inherent biases in the identified proteomes. Here, a bioinformatics experiment is performed to test this using a set of modern human bone proteomes and three independent searches against sequence databases at increasing evolutionary distances: the human (0 Ma), chimpanzee (6-8 Ma) and orangutan (16-17 Ma) reference proteomes, respectively. RESULTS Incorrectly suggested amino acid substitutions are absent when employing adequate filtering criteria for mutable Peptide Spectrum Matches (PSMs), but roughly half of the mutable PSMs were not recovered. As a result, peptide and protein identification rates are higher in error-tolerant mode compared to non-error-tolerant searches but did not recover protein identifications completely. Data indicates that peptide length and the number of mutations between the target and database sequences are the main factors influencing mutable PSM identification. CONCLUSIONS The error-tolerant results suggest that the cross-species proteomics problem is not overcome at increasing evolutionary distances, even at the protein level. Peptide and protein loss has the potential to significantly impact divergence dating and proteome comparisons when using ancient samples as there is a bias towards the identification of conserved sequences and proteins. Effects are minimized between moderately divergent proteomes, as indicated by almost complete recovery of informative positions in the search against the chimpanzee proteome (≈90%, 6-8 Ma). This provides a bioinformatic background to future phylogenetic and proteomic analysis of ancient hominin proteomes, including the future description of novel hominin amino acid sequences, but also has negative implications for the study of fast-evolving proteins in hominins, non-hominin animals, and ancient bacterial proteins in evolutionary contexts.
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Affiliation(s)
- F Welker
- Department of Human Evolution, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany.
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
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Procopio N, Chamberlain AT, Buckley M. Exploring Biological and Geological Age-related Changes through Variations in Intra- and Intertooth Proteomes of Ancient Dentine. J Proteome Res 2018; 17:1000-1013. [PMID: 29356547 DOI: 10.1021/acs.jproteome.7b00648] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Proteomic analyses are becoming more widely used in archeology not only due to the greater preservation of proteins in ancient specimens than DNA but also because they can offer different information, particularly relating to compositional preservation and potentially a means to estimate biological and geological age. However, it remains unclear to what extent different burial environments impact these aspects of proteome decay. Teeth have to date been much less studied than bone but are ideal to explore how proteins decay with time due to the negligible turnover that occurs in dentine relative to bone. We investigated the proteome variability and deamidation levels of different sections of molar teeth from archeological bovine mandibles as well as their mandibular bone. We obtained a greater yield of proteins from the crown of the teeth but did not find differences between the different molars analyzed within each mandible. We also obtained the best variety of protein from a well-preserved mandible that was not the youngest one in terms of chronological age, showing the influence of the preservation conditions on the final proteomic outcome. Intriguingly, we also noticed an increase in abundance levels of fetuin-A in biologically younger mandibles as reported previously, but the opposite trend in tooth dentine. Interestingly, we observed higher glutamine deamidation levels in teeth from the geologically oldest mandible despite it being the biologically youngest specimen, showing that the archeological age strongly impacts on the level of deamidations observed, much more so than biological aging. This indicates that the glutamine deamidation ratio of selected peptides may act as a good predictor of the relative geochronological age of archeological specimens.
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Affiliation(s)
- Noemi Procopio
- Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Andrew T Chamberlain
- School of Earth and Environmental Sciences, The University of Manchester , Stopford Building, 99 Oxford Road, Manchester M13 9PG, United Kingdom
| | - Michael Buckley
- Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
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36
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Procopio N, Williams A, Chamberlain AT, Buckley M. Forensic proteomics for the evaluation of the post-mortem decay in bones. J Proteomics 2018; 177:21-30. [PMID: 29407476 DOI: 10.1016/j.jprot.2018.01.016] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 01/25/2018] [Accepted: 01/29/2018] [Indexed: 12/31/2022]
Abstract
Current methods for evaluation the of post-mortem interval (PMI) of skeletal remains suffer from poor accuracy due to the great number of variables that affect the diagenetic process and to the lack of specific guidelines to address this issue. During decomposition, proteins can undergo cumulative decay over the time, resulting in a decrease in the range and abundance of proteins present (i.e., the proteome) in different tissues as well as in an increase of post-translational modifications occurring in these proteins. In this study, we investigate the applicability of bone proteomic analyses to simulated forensic contexts, looking for specific biomarkers that may help the estimation of PMI, as well as evaluate a previously discovered marker for the estimation of biological age. We noticed a reduction of particular plasma and muscle proteins with increasing PMIs, as well as an increased deamidation of biglycan, a protein with a role in modulating bone growth and mineralization. We also corroborated our previous results regarding the use of fetuin-A as a potential biomarker for the estimation of age-at-death, demonstrating the applicability and the great potential that proteomics may have towards forensic sciences. SIGNIFICANCE The estimation of the post-mortem interval has a key role in forensic investigations, however nowadays it still suffers from poor reliability, especially when body tissues are heavily decomposed. Here we propose for the first time the application of bone proteomics to the estimation of the time elapsed since death and found several new potential biomarkers to address this, demonstrating the applicability of proteomic analyses to forensic sciences.
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Affiliation(s)
- Noemi Procopio
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Anna Williams
- School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - Andrew T Chamberlain
- School of Earth and Environmental Sciences, The University of Manchester, Stopford Building, 99 Oxford Road, Manchester, M13 9PG, UK
| | - Michael Buckley
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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Mackie M, Hendy J, Lowe AD, Sperduti A, Holst M, Collins MJ, Speller CF. Preservation of the metaproteome: variability of protein preservation in ancient dental calculus. SCIENCE AND TECHNOLOGY OF ARCHAEOLOGICAL RESEARCH 2017; 3:74-86. [PMID: 29098079 PMCID: PMC5633013 DOI: 10.1080/20548923.2017.1361629] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 07/16/2017] [Indexed: 05/25/2023]
Abstract
Proteomic analysis of dental calculus is emerging as a powerful tool for disease and dietary characterisation of archaeological populations. To better understand the variability in protein results from dental calculus, we analysed 21 samples from three Roman-period populations to compare: 1) the quantity of extracted protein; 2) the number of mass spectral queries; and 3) the number of peptide spectral matches and protein identifications. We found little correlation between the quantity of calculus analysed and total protein identifications, as well as no systematic trends between site location and protein preservation. We identified a wide range of individual variability, which may be associated with the mechanisms of calculus formation and/or post-depositional contamination, in addition to taphonomic factors. Our results suggest dental calculus is indeed a stable, long-term reservoir of proteins as previously reported, but further systematic studies are needed to identify mechanisms associated with protein entrapment and survival in dental calculus.
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Affiliation(s)
- Meaghan Mackie
- BioArCh, Department of Archaeology, University of York, York, UK
| | - Jessica Hendy
- BioArCh, Department of Archaeology, University of York, York, UK
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Abigail D. Lowe
- BioArCh, Department of Archaeology, University of York, York, UK
- Department of Earth Sciences, Natural History Museum, London, UK
| | | | - Malin Holst
- BioArCh, Department of Archaeology, University of York, York, UK
- York Osteoarchaeology Ltd
| | - Matthew J. Collins
- BioArCh, Department of Archaeology, University of York, York, UK
- EvoGenomics Section, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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