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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] [What about the content of this article? (0)] [Affiliation(s)] [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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2
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Procopio N, Bonicelli A. From flesh to bones: Multi-omics approaches in forensic science. Proteomics 2024:e2200335. [PMID: 38683823 DOI: 10.1002/pmic.202200335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [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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3
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Huang W, Zhao S, Liu H, Pan M, Dong H. The Role of Protein Degradation in Estimation Postmortem Interval and Confirmation of Cause of Death in Forensic Pathology: A Literature Review. Int J Mol Sci 2024; 25:1659. [PMID: 38338938 PMCID: PMC10855206 DOI: 10.3390/ijms25031659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 01/04/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024] Open
Abstract
It is well known that proteins are important bio-macromolecules in human organisms, and numerous proteins are widely used in the clinical practice, whereas their application in forensic science is currently limited. This limitation is mainly attributed to the postmortem degradation of targeted proteins, which can significantly impact final conclusions. In the last decade, numerous methods have been established to detect the protein from a forensic perspective, and some of the postmortem proteins have been applied in forensic practice. To better understand the emerging issues and challenges in postmortem proteins, we have reviewed the current application of protein technologies at postmortem in forensic practice. Meanwhile, we discuss the application of proteins in identifying the cause of death, and postmortem interval (PMI). Finally, we highlight the interpretability and limitations of postmortem protein challenges. We believe that utilizing the multi-omics method can enhance the comprehensiveness of applying proteins in forensic practice.
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Affiliation(s)
- Weisheng Huang
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, No. 13 Hangkong Road, Hankou, Wuhan 430030, China; (W.H.)
| | - Shuquan Zhao
- Faculty of Forensic Pathology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China;
| | - Huine Liu
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, No. 13 Hangkong Road, Hankou, Wuhan 430030, China; (W.H.)
| | - Meichen Pan
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, No. 13 Hangkong Road, Hankou, Wuhan 430030, China; (W.H.)
| | - Hongmei Dong
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, No. 13 Hangkong Road, Hankou, Wuhan 430030, China; (W.H.)
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Rose JP, Schurman CA, King CD, Bons J, Patel SK, Burton JB, O’Broin A, Alliston T, Schilling B. Deep coverage and quantification of the bone proteome provides enhanced opportunities for new discoveries in skeletal biology and disease. PLoS One 2023; 18:e0292268. [PMID: 37816044 PMCID: PMC10564166 DOI: 10.1371/journal.pone.0292268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 09/15/2023] [Indexed: 10/12/2023] Open
Abstract
Dysregulation of cell signaling in chondrocytes and in bone cells, such as osteocytes, osteoblasts, osteoclasts, and an elevated burden of senescent cells in cartilage and bone, are implicated in osteoarthritis (OA). Mass spectrometric analyses provides a crucial molecular tool-kit to understand complex signaling relationships in age-related diseases, such as OA. Here we introduce a novel mass spectrometric workflow to promote proteomic studies of bone. This workflow uses highly specialized steps, including extensive overnight demineralization, pulverization, and incubation for 72 h in 6 M guanidine hydrochloride and EDTA, followed by proteolytic digestion. Analysis on a high-resolution Orbitrap Eclipse and Orbitrap Exploris 480 mass spectrometer using Data-Independent Acquisition (DIA) provides deep coverage of the bone proteome, and preserves post-translational modifications, such as hydroxyproline. A spectral library-free quantification strategy, directDIA, identified and quantified over 2,000 protein groups (with ≥ 2 unique peptides) from calcium-rich bone matrices. Key components identified were proteins of the extracellular matrix (ECM), bone-specific proteins (e.g., secreted protein acidic and cysteine rich, SPARC, and bone sialoprotein 2, IBSP), and signaling proteins (e.g., transforming growth factor beta-2, TGFB2), and lysyl oxidase homolog 2 (LOXL2), an important protein in collagen crosslinking. Post-translational modifications (PTMs) were identified without the need for specific enrichment. This includes collagen hydroxyproline modifications, chemical modifications for collagen self-assembly and network formation. Multiple senescence factors were identified, such as complement component 3 (C3) protein of the complement system and many matrix metalloproteinases, that might be monitored during age-related bone disease progression. Our innovative workflow yields in-depth protein coverage and quantification strategies to discover underlying biological mechanisms of bone aging and to provide tools to monitor therapeutic interventions. These novel tools to monitor the bone proteome open novel horizons to investigate bone-specific diseases, many of which are age-related.
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Affiliation(s)
- Jacob P. Rose
- Buck Institute for Research on Aging, Novato, CA, United States of America
| | | | - Christina D. King
- Buck Institute for Research on Aging, Novato, CA, United States of America
| | - Joanna Bons
- Buck Institute for Research on Aging, Novato, CA, United States of America
| | - Sandip K. Patel
- Buck Institute for Research on Aging, Novato, CA, United States of America
| | - Jordan B. Burton
- Buck Institute for Research on Aging, Novato, CA, United States of America
| | - Amy O’Broin
- Buck Institute for Research on Aging, Novato, CA, United States of America
| | - Tamara Alliston
- Department of Orthopaedic Surgery, University of California, San Francisco, CA, Unted States of America
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, United States of America
| | - Birgit Schilling
- Buck Institute for Research on Aging, Novato, CA, United States of America
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Abstract
Fibromodulin (FMOD) is an archetypal member of the class II small leucine-rich proteoglycan family. By directly binding to extracellular matrix structural components, such as collagen and lysyl oxidase, FMOD regulates collagen cross-linking, packing, assembly, and fibril architecture via a multivalent interaction. Meanwhile, as a pluripotent molecule, FMOD acts as a ligand of various cytokines and growth factors, especially those belonging to the transforming growth factor (TGF) β superfamily, by interacting with the corresponding signaling molecules involved in cell adhesion, spreading, proliferation, migration, invasion, differentiation, and metastasis. Consequently, FMOD exhibits promigratory, proangiogenic, anti-inflammatory, and antifibrogenic properties and plays essential roles in cell fate determination and maturation, progenitor cell recruitment, and tissue regeneration. The multifunctional nature of FMOD thus enables it to be a promising therapeutic agent for a broad repertoire of diseases, including but not limited to arthritis, temporomandibular joint disorders, caries, and fibrotic diseases among different organs, as well as to be a regenerative medicine candidate for skin, muscle, and tendon injuries. Moreover, FMOD is also considered a marker for tumor diagnosis and prognosis prediction and a potential target for cancer treatment. Furthermore, FMOD itself is sufficient to reprogram somatic cells into a multipotent state, creating a safe and efficient cell source for various tissue reconstructions and thus opening a new avenue for regenerative medicine. This review focuses on the recent preclinical efforts bringing FMOD research and therapies to the forefront. In addition, a contemporary understanding of the mechanism underlying FMOD's function, particularly its interaction with TGFβ superfamily members, is also discussed at the molecular level to aid the discovery of novel FMOD-based treatments.
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Affiliation(s)
- Z. Zheng
- David Geffen School of Medicine,
University of California, Los Angeles, CA, USA
- School of Dentistry, University of
California, Los Angeles, CA, USA
| | - H.S. Granado
- Department of Orthodontics, School of
Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - C. Li
- Department of Orthodontics, School of
Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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7
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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8
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Li T, Qu H, Ding H, Deng H, Chen Y. Profiling of proteome changes in plasma of HIV-infected patients receiving antiretroviral therapy. Proteomics Clin Appl 2022; 16:e2100099. [PMID: 35920599 DOI: 10.1002/prca.202100099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/16/2022] [Accepted: 07/29/2022] [Indexed: 12/30/2022]
Abstract
PURPOSE Antiretroviral therapy (ART) prevents human immunodeficiency virus (HIV)-1 onward transmission and disease progression, leading to excellent prognosis in people living with HIV-1 (PWH). However, side effects, complications, and impaired immune reconstitution persist in some patients treated with ART. We aimed to profile proteome changes in plasma before and after ART to identify the molecular pathways altered by ART. EXPERIMENTAL DESIGN Quantitative proteomics analysis based on tandem mass tag (TMT) labeling was used to profile proteome changes of paired plasma samples from HIV-1 patients before receiving ART and after ART treatment. RESULTS A total of 1398 protein groups (PGs) were identified, in which 18 proteins were downregulated and 50 were upregulated in plasma from ART treated patients. Based on Ingenuity Pathway analysis (IPA), gap junction signaling and actin cytoskeleton signaling were enriched among upregulated proteins, while downregulated proteins were mainly participated in IL-15 signaling pathway. Patients with the low level of CSF1R and the high levels of MINPP1 and TGM3 showed better CD4+ T-cell recovery. CONCLUSIONS The present study provided plasma proteome changes after ART to elucidate the underlying mechanistic pathways in response to ART, and also identified potential targets to prompt immune reconstitution.
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Affiliation(s)
- Ting Li
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Hong Qu
- Department of Obstetric & Gynecology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Haibo Ding
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Haiteng Deng
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Yuling Chen
- School of Life Sciences, Tsinghua University, Beijing, China
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9
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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