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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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Common Ground between Biological Rhythms and Forensics. BIOLOGY 2022; 11:biology11071071. [PMID: 36101448 PMCID: PMC9312156 DOI: 10.3390/biology11071071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/12/2022] [Accepted: 07/14/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary Biological clocks regulate the timing of numerous body functions in adaption to daily repeating cycles in the environment, such as the sleep–wake phases that are trained by the cycling changes of night and day light. The identification of a deceased victim is a critical component in a forensic investigation, but it can be significantly hampered by the condition of the dead body and the lack of personal records and documents. This review links current knowledge on the molecular mechanisms of biological rhythms to forensically relevant aspects, including the time period since death, cause of death, the use of insects for forensics, sex and age of a person, ethnic background and development. Putting these findings in context demonstrates how the analysis of molecular clock analysis could be used as tool for future personal identification in forensic investigations. Abstract Biological clocks set the timing for a large number of essential processes in the living human organism. After death, scientific evidence is required in forensic investigations in order to collect as much information as possible on the death circumstances and personal identifiers of the deceased victim. We summarize the associations between the molecular mechanisms of biological rhythms and forensically relevant aspects, including post-mortem interval and cause of death, entomological findings, sex, age, ethnicity and development. Given their importance during lifetime, biological rhythms could be potential tools to draw conclusions on the death circumstances and the identity of a deceased person by mechanistic investigations of the different biological clocks in a forensic context. This review puts the known effects of biological rhythms on the functions of the human organism in context with potential applications in forensic fields of interest, such as personal identification, entomology as well as the determination of the post-mortem interval and cause of death.
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Janjić K, Agis H. Chronodentistry: the role & potential of molecular clocks in oral medicine. BMC Oral Health 2019; 19:32. [PMID: 30760278 PMCID: PMC6375164 DOI: 10.1186/s12903-019-0720-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 01/23/2019] [Indexed: 12/14/2022] Open
Abstract
Molecular clocks help organisms to adapt important physiological functions to periodically changing conditions in the environment. These include the adaption of the 24 h sleep-wake rhythm to changes of day and night. The circadian clock is known to act as a key regulator in processes of health and disease in different organs. The knowledge on the circadian clock led to the development of chronopharmacology and chronotherapy. These fields aim to investigate how efficiency of medication and therapies can be improved based on circadian clock mechanisms. In this review we aim to highlight the role of the circadian clock in oral tissues and its potential in the different fields of dentistry including oral and maxillofacial surgery, restorative dentistry, endodontics, periodontics and orthodontics to trigger the evolving field of chronodentistry.
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Affiliation(s)
- Klara Janjić
- Department of Conservative Dentistry and Periodontology, University Clinic of Dentistry, Medical University of Vienna, Sensengasse 2a, 1090, Vienna, Austria.,Austrian Cluster for Tissue Regeneration, Vienna, Austria
| | - Hermann Agis
- Department of Conservative Dentistry and Periodontology, University Clinic of Dentistry, Medical University of Vienna, Sensengasse 2a, 1090, Vienna, Austria. .,Austrian Cluster for Tissue Regeneration, Vienna, Austria.
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Mahna D, Puri S, Sharma S. DNA methylation signatures: Biomarkers of drug and alcohol abuse. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2018; 777:19-28. [DOI: 10.1016/j.mrrev.2018.06.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 05/22/2018] [Accepted: 06/18/2018] [Indexed: 01/08/2023]
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Abstract
Self-sustained and synchronized to environmental stimuli, circadian clocks are under genetic and epigenetic regulation. Recent findings have greatly increased our understanding of epigenetic plasticity governed by circadian clock. Thus, the link between circadian clock and epigenetic machinery is reciprocal. Circadian clock can affect epigenetic features including genomic DNA methylation, noncoding RNA, mainly miRNA expression, and histone modifications resulted in their 24-h rhythms. Concomitantly, these epigenetic events can directly modulate cyclic system of transcription and translation of core circadian genes and indirectly clock output genes. Significant findings interlocking circadian clock, epigenetics, and cancer have been revealed, particularly in breast, colorectal, and blood cancers. Aberrant methylation of circadian gene promoter regions and miRNA expression affected circadian gene expression, together with 24-h expression oscillation pace have been frequently observed.
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Marie-Claire C, Jourdaine C, Lépine JP, Bellivier F, Bloch V, Vorspan F. Pharmacoepigenomics of opiates and methadone maintenance treatment: current data and perspectives. Pharmacogenomics 2017; 18:1359-1372. [DOI: 10.2217/pgs-2017-0040] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Current treatments of opioid addiction include primarily maintenance medications such as methadone. Chronic exposure to opiate and/or long-lasting maintenance treatment induce modulations of gene expression in brain and peripheral tissues. There is increasing evidence that epigenetic modifications underlie these modulations. This review summarizes published results on opioid-induced epigenetic changes in animal models and in patients. The epigenetic modifications observed with other drugs of abuse often used by opiate abusers are also outlined. Specific methadone maintenance treatment induced epigenetic modifications at different treatment stages may be combined with the ones resulting from patients’ substance use history. Therefore, research comparing groups of addicts with similar history and substances use disorders but contrasting for well-characterized treatment phenotypes should be encouraged.
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Affiliation(s)
- Cynthia Marie-Claire
- Variabilité de réponse aux psychotropes, INSERMU1144/Faculté de Pharmacie de Paris/Université Paris Descartes/Université ParisDiderot/Université Sorbonne Paris Cité, Paris, France
| | - Clément Jourdaine
- AP-HP, GH Saint-Louis – Lariboisière – F. Widal, Pôle de Psychiatrie et de Médecine Addictologique, 75475 Paris cedex 10, France
| | - Jean-Pierre Lépine
- AP-HP, GH Saint-Louis – Lariboisière – F. Widal, Pôle de Psychiatrie et de Médecine Addictologique, 75475 Paris cedex 10, France
| | - Frank Bellivier
- Variabilité de réponse aux psychotropes, INSERMU1144/Faculté de Pharmacie de Paris/Université Paris Descartes/Université ParisDiderot/Université Sorbonne Paris Cité, Paris, France
- AP-HP, GH Saint-Louis – Lariboisière – F. Widal, Pôle de Psychiatrie et de Médecine Addictologique, 75475 Paris cedex 10, France
| | - Vanessa Bloch
- Variabilité de réponse aux psychotropes, INSERMU1144/Faculté de Pharmacie de Paris/Université Paris Descartes/Université ParisDiderot/Université Sorbonne Paris Cité, Paris, France
| | - Florence Vorspan
- Variabilité de réponse aux psychotropes, INSERMU1144/Faculté de Pharmacie de Paris/Université Paris Descartes/Université ParisDiderot/Université Sorbonne Paris Cité, Paris, France
- AP-HP, GH Saint-Louis – Lariboisière – F. Widal, Pôle de Psychiatrie et de Médecine Addictologique, 75475 Paris cedex 10, France
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Cronin P, McCarthy MJ, Lim ASP, Salmon DP, Galasko D, Masliah E, De Jager PL, Bennett DA, Desplats P. Circadian alterations during early stages of Alzheimer's disease are associated with aberrant cycles of DNA methylation in BMAL1. Alzheimers Dement 2017; 13:689-700. [PMID: 27883893 PMCID: PMC5785929 DOI: 10.1016/j.jalz.2016.10.003] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 09/16/2016] [Accepted: 10/10/2016] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Circadian alterations are prevalent in Alzheimer's disease (AD) and may contribute to cognitive impairment, behavioral symptoms, and neurodegeneration. Epigenetic mechanisms regulate the circadian clock, and changes in DNA methylation have been reported in AD brains, but the pathways that mediate circadian deregulation in AD are incompletely understood. We hypothesized that aberrant DNA methylation may affect circadian rhythms in AD. METHODS We investigated DNA methylation, transcription, and expression of BMAL1, a positive regulator of the circadian clock, in cultured fibroblasts and brain samples from two independent cohorts of aging and AD. RESULTS DNA methylation modulated rhythmic expression of clock genes in cultured fibroblasts. Moreover, rhythmic methylation of BMAL1 was altered in AD brains and fibroblasts and correlated with transcription cycles. DISCUSSION Our results indicate that cycles of DNA methylation contribute to the regulation of BMAL1 rhythms in the brain. Hence, aberrant epigenetic patterns may be linked to circadian alterations in AD.
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Affiliation(s)
- Peter Cronin
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
| | - Michael J McCarthy
- Psychiatry Service, Veterans Affairs San Diego Health Care System, San Diego, CA, USA; Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Andrew S P Lim
- Division of Neurology, Department of Medicine, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, ON, Canada
| | - David P Salmon
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
| | - Douglas Galasko
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
| | - Eliezer Masliah
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA; Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Philip L De Jager
- Departments of Neurology, Brigham and Women's Hospital, Boston, MA, USA; Department of Psychiatry, Brigham and Women's Hospital, Boston, MA, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Paula Desplats
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA; Department of Pathology, University of California San Diego, La Jolla, CA, USA.
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Abstract
The circadian clock choreographs fundamental biological rhythms. This system is comprised of the master circadian pacemaker in the suprachiasmatic nucleus and associated pacemakers in other tissues that coordinate complex physiological processes and behaviors, such as sleep, feeding, and metabolism. The molecular circuitry that underlies these clocks and orchestrates circadian gene expression has been the focus of intensive investigation, and it is becoming clear that epigenetic factors are highly integrated into these networks. In this review, we draw attention to the fundamental roles played by epigenetic mechanisms in transcriptional and post-transcriptional regulation within the circadian clock system. We also highlight how alterations in epigenetic factors and mechanisms are being linked with sleep-wake disorders. These observations provide important insights into the pathogenesis and potential treatment of these disorders and implicate epigenetic deregulation in the significant but poorly understood interconnections now emerging between circadian processes and neurodegeneration, metabolic diseases, cancer, and aging.
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Affiliation(s)
- Irfan A. Qureshi
- Roslyn and Leslie Goldstein Laboratory for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Institute for Brain Disorders and Neural Regeneration, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Neurology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Rose F. Kennedy Center for Research on Intellectual and Developmental Disabilities, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Mark F. Mehler
- Roslyn and Leslie Goldstein Laboratory for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Institute for Brain Disorders and Neural Regeneration, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Neurology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Rose F. Kennedy Center for Research on Intellectual and Developmental Disabilities, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Ruth S. and David L. Gottesman Stem Cell Institute, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Center for Epigenomics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Institute for Aging Research, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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Vidaki A, Daniel B, Court DS. Forensic DNA methylation profiling—Potential opportunities and challenges. Forensic Sci Int Genet 2013; 7:499-507. [DOI: 10.1016/j.fsigen.2013.05.004] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 05/14/2013] [Indexed: 11/26/2022]
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Gršković B, Zrnec D, Vicković S, Popović M, Mršić G. DNA methylation: the future of crime scene investigation? Mol Biol Rep 2013; 40:4349-60. [DOI: 10.1007/s11033-013-2525-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Accepted: 04/27/2013] [Indexed: 12/31/2022]
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