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Gao F, Tom E, Rydz C, Cho W, Kolesnikov AV, Sha Y, Papadam A, Jafari S, Joseph A, Ahanchi A, Saraei NBS, Lyon D, Foik A, Nie Q, Grassmann F, Kefalov VJ, Skowronska-Krawczyk D. Polyunsaturated Fatty Acid - mediated Cellular Rejuvenation for Reversing Age-related Vision Decline. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.01.601592. [PMID: 39005302 PMCID: PMC11244954 DOI: 10.1101/2024.07.01.601592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
The retina is uniquely enriched in polyunsaturated fatty acids (PUFAs), which are primarily localized in cell membranes, where they govern membrane biophysical properties such as diffusion, permeability, domain formation, and curvature generation. During aging, alterations in lipid metabolism lead to reduced content of very long-chain PUFAs (VLC-PUFAs) in the retina, and this decline is associated with normal age-related visual decline and pathological age-related macular degeneration (AMD). ELOVL2 (Elongation of very-long-chain fatty acids-like 2) encodes a transmembrane protein that produces precursors to docosahexaenoic acid (DHA) and VLC-PUFAs, and methylation level of its promoter is currently the best predictor of chronological age. Here, we show that mice lacking ELOVL2-specific enzymatic activity ( Elovl2 C234W ) have impaired contrast sensitivity and slower rod response recovery following bright light exposure. Intravitreal supplementation with the direct product of ELOVL2, 24:5n-3, in aged animals significantly improved visual function and reduced accumulation of ApoE, HTRA1 and complement proteins in sub-RPE deposits. At the molecular level, the gene expression pattern observed in retinas supplemented with 24:5n-3 exhibited a partial rejuvenation profile, including decreased expression of aging-related genes and a transcriptomic signature of younger retina. Finally, we present the first human genetic data showing significant association of several variants in the human ELOVL2 locus with the onset of intermediate AMD, underlying the translational significance of our findings. In sum, our study identifies novel therapeutic opportunities and defines ELOVL2 as a promising target for interventions aimed at preventing age-related vision loss.
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Castagnola MJ, Medina-Paz F, Zapico SC. Uncovering Forensic Evidence: A Path to Age Estimation through DNA Methylation. Int J Mol Sci 2024; 25:4917. [PMID: 38732129 PMCID: PMC11084977 DOI: 10.3390/ijms25094917] [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: 03/25/2024] [Revised: 04/27/2024] [Accepted: 04/28/2024] [Indexed: 05/13/2024] Open
Abstract
Age estimation is a critical aspect of reconstructing a biological profile in forensic sciences. Diverse biochemical processes have been studied in their correlation with age, and the results have driven DNA methylation to the forefront as a promising biomarker. DNA methylation, an epigenetic modification, has been extensively studied in recent years for developing age estimation models in criminalistics and forensic anthropology. Epigenetic clocks, which analyze DNA sites undergoing hypermethylation or hypomethylation as individuals age, have paved the way for improved prediction models. A wide range of biomarkers and methods for DNA methylation analysis have been proposed, achieving different accuracies across samples and cell types. This review extensively explores literature from the past 5 years, showing scientific efforts toward the ultimate goal: applying age prediction models to assist in human identification.
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Affiliation(s)
- María Josefina Castagnola
- Department of Chemistry and Environmental Sciences, New Jersey Institute of Technology, Tiernan Hall 365, Newark, NJ 07102, USA; (M.J.C.); (F.M.-P.)
| | - Francisco Medina-Paz
- Department of Chemistry and Environmental Sciences, New Jersey Institute of Technology, Tiernan Hall 365, Newark, NJ 07102, USA; (M.J.C.); (F.M.-P.)
| | - Sara C. Zapico
- Department of Chemistry and Environmental Sciences, New Jersey Institute of Technology, Tiernan Hall 365, Newark, NJ 07102, USA; (M.J.C.); (F.M.-P.)
- Department of Anthropology and Laboratories of Analytical Biology, National Museum of Natural History, MRC 112, Smithsonian Institution, Washington, DC 20560, USA
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Gutiérrez-Hurtado IA, Sánchez-Méndez AD, Becerra-Loaiza DS, Rangel-Villalobos H, Torres-Carrillo N, Gallegos-Arreola MP, Aguilar-Velázquez JA. Loss of the Y Chromosome: A Review of Molecular Mechanisms, Age Inference, and Implications for Men's Health. Int J Mol Sci 2024; 25:4230. [PMID: 38673816 PMCID: PMC11050192 DOI: 10.3390/ijms25084230] [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: 03/05/2024] [Revised: 03/29/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Until a few years ago, it was believed that the gradual mosaic loss of the Y chromosome (mLOY) was a normal age-related process. However, it is now known that mLOY is associated with a wide variety of pathologies in men, such as cardiovascular diseases, neurodegenerative disorders, and many types of cancer. Nevertheless, the mechanisms that generate mLOY in men have not been studied so far. This task is of great importance because it will allow focusing on possible methods of prophylaxis or therapy for diseases associated with mLOY. On the other hand, it would allow better understanding of mLOY as a possible marker for inferring the age of male samples in cases of human identification. Due to the above, in this work, a comprehensive review of the literature was conducted, presenting the most relevant information on the possible molecular mechanisms by which mLOY is generated, as well as its implications for men's health and its possible use as a marker to infer age.
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Affiliation(s)
- Itzae Adonai Gutiérrez-Hurtado
- Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Guadalajara 44340, Jalisco, Mexico
| | - Astrid Desireé Sánchez-Méndez
- Laboratorio de Ciencias Morfológico Forenses y Medicina Molecular, Departamento de Morfología, Centro Universitario de Ciencias de la Salud, Guadalajara 44340, Jalisco, Mexico
- Doctorado en Genética Humana, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Jalisco, Mexico
| | | | - Héctor Rangel-Villalobos
- Instituto de Investigación en Genética Molecular, Departamento de Ciencias Médicas y de la Vida, Centro Universitario de la Ciénega, Universidad de Guadalajara, Ocotlán 47820, Jalisco, Mexico
| | - Norma Torres-Carrillo
- Departamento de Microbiología y Patología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Jalisco, Mexico
| | - Martha Patricia Gallegos-Arreola
- División de Genética, Centro de Investigación Biomédica de Occidente (CIBO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara 44340, Jalisco, Mexico
| | - José Alonso Aguilar-Velázquez
- Laboratorio de Ciencias Morfológico Forenses y Medicina Molecular, Departamento de Morfología, Centro Universitario de Ciencias de la Salud, Guadalajara 44340, Jalisco, Mexico
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Kampmann ML, Fleckhaus J, Børsting C, Jurtikova H, Piters A, Papin J, Gauthier Q, Ghemrawi M, Doutremepuich C, McCord B, Schneider PM, Drabek J, Morling N. Collaborative exercise: analysis of age estimation using a QIAGEN protocol and the PyroMark Q48 platform. Forensic Sci Res 2024; 9:owad055. [PMID: 38567377 PMCID: PMC10986743 DOI: 10.1093/fsr/owad055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 09/26/2023] [Indexed: 04/04/2024] Open
Abstract
Human age estimation from trace samples may give important leads early in a police investigation by contributing to the description of the perpetrator. Several molecular biomarkers are available for the estimation of chronological age, and currently, DNA methylation patterns are the most promising. In this study, a QIAGEN age protocol for age estimation was tested by five forensic genetic laboratories. The assay comprised bisulfite treatment of the extracted DNA, amplification of five CpG loci (in the genes of ELOVL2, C1orf132, TRIM59, KLF14, and FHL2), and sequencing of the amplicons using the PyroMark Q48 platform. Blood samples from 49 individuals with ages ranging from 18 to 64 years as well as negative and methylation controls were analyzed. An existing age estimation model was applied to display a mean absolute deviation of 3.62 years within the reference data set. Key points Age determination as an intelligence tool during investigations can be a powerful tool in forensic genetics.In this study, five laboratories ran 49 samples and obtained a mean absolute deviation of 3.62 years.Five markers were analyzed on a PyroMark Q48 platform.
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Affiliation(s)
- Marie-Louise Kampmann
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagen, Denmark
| | - Jan Fleckhaus
- Institute of Legal Medicine, Faculty of Medicine and University Clinic, University of Cologne, Cologne, Germany
| | - Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagen, Denmark
| | - Helena Jurtikova
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc and the University Hospital Olomouc, Olomouc, the Czech Republic
| | - Alice Piters
- Laboratoire d’Hématologie Médico-Légale, Bordeaux Cedex, France
| | - Julien Papin
- Laboratoire d’Hématologie Médico-Légale, Bordeaux Cedex, France
| | - Quentin Gauthier
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, USA
| | - Mirna Ghemrawi
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, USA
| | | | - Bruce McCord
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, USA
| | - Peter M Schneider
- Institute of Legal Medicine, Faculty of Medicine and University Clinic, University of Cologne, Cologne, Germany
| | - Jiri Drabek
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc and the University Hospital Olomouc, Olomouc, the Czech Republic
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagen, Denmark
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Yamagishi T, Sakurai W, Watanabe K, Toyomane K, Akutsu T. Development and comparison of forensic interval age prediction models by statistical and machine learning methods based on the methylation rates of ELOVL2 in blood DNA. Forensic Sci Int Genet 2024; 69:103004. [PMID: 38160598 DOI: 10.1016/j.fsigen.2023.103004] [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: 10/05/2023] [Revised: 12/06/2023] [Accepted: 12/18/2023] [Indexed: 01/03/2024]
Abstract
Age estimation can be useful information for narrowing down candidates of unidentified donors in criminal investigations. Various age estimation models based on DNA methylation biomarkers have been developed for forensic usage in the past decade. However, many of these models using ordinary least squares regression cannot generate an appropriate estimation due to the deterioration in prediction accuracy caused by an increased prediction error in older age groups. In the present study, to address this problem, we developed age estimation models that set an appropriate prediction interval for all age groups by two approaches: a statistical method using quantile regression (QR) and a machine learning method using an artificial neural network (ANN). Methylation datasets (n = 1280, age 0-91 years) of the promoter for the gene encoding ELOVL fatty acid elongase 2 were used to develop the QR and ANN models. By validation using several test datasets, both models were shown to enlarge prediction intervals in accordance with aging and have a high level of correct prediction (>90 %) for older age groups. The QR and ANN models also generated a point age prediction with high accuracy. The ANN model enabled a prediction with a mean absolute error (MAE) of 5.3 years and root mean square error (RMSE) of 7.3 years for the test dataset (n = 549), which were comparable to those of the QR model (MAE = 5.6 years, RMSE = 7.8 years). Their applicability to casework was also confirmed using bloodstain samples stored for various periods of time (1-14 years), indicating the stability of the models for aged bloodstain samples. From these results, it was considered that the proposed models can provide more useful and effective age estimation in forensic settings.
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Affiliation(s)
- Takayuki Yamagishi
- National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan.
| | - Wataru Sakurai
- National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Ken Watanabe
- National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Kochi Toyomane
- National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Tomoko Akutsu
- National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
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Bertucci-Richter EM, Shealy EP, Parrott BB. Epigenetic drift underlies epigenetic clock signals, but displays distinct responses to lifespan interventions, development, and cellular dedifferentiation. Aging (Albany NY) 2024; 16:1002-1020. [PMID: 38285616 PMCID: PMC10866415 DOI: 10.18632/aging.205503] [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: 08/03/2023] [Accepted: 12/01/2023] [Indexed: 01/31/2024]
Abstract
Changes in DNA methylation with age are observed across the tree of life. The stereotypical nature of these changes can be modeled to produce epigenetic clocks capable of predicting chronological age with unprecedented accuracy. Despite the predictive ability of epigenetic clocks and their utility as biomarkers in clinical applications, the underlying processes that produce clock signals are not fully resolved, which limits their interpretability. Here, we develop a computational approach to spatially resolve the within read variability or "disorder" in DNA methylation patterns and test if age-associated changes in DNA methylation disorder underlie signals comprising epigenetic clocks. We find that epigenetic clock loci are enriched in regions that both accumulate and lose disorder with age, suggesting a link between DNA methylation disorder and epigenetic clocks. We then develop epigenetic clocks that are based on regional disorder of DNA methylation patterns and compare their performance to other epigenetic clocks by investigating the influences of development, lifespan interventions, and cellular dedifferentiation. We identify common responses as well as critical differences between canonical epigenetic clocks and those based on regional disorder, demonstrating a fundamental decoupling of epigenetic aging processes. Collectively, we identify key linkages between epigenetic disorder and epigenetic clocks and demonstrate the multifaceted nature of epigenetic aging in which stochastic processes occurring at non-random loci produce predictable outcomes.
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Affiliation(s)
- Emily M. Bertucci-Richter
- Savannah River Ecology Laboratory, University of Georgia, Aiken, SC 29802, USA
- Eugene P. Odum School of Ecology, University of Georgia, Athens, GA 30602, USA
| | - Ethan P. Shealy
- Savannah River Ecology Laboratory, University of Georgia, Aiken, SC 29802, USA
- Eugene P. Odum School of Ecology, University of Georgia, Athens, GA 30602, USA
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA 30602, USA
| | - Benjamin B. Parrott
- Savannah River Ecology Laboratory, University of Georgia, Aiken, SC 29802, USA
- Eugene P. Odum School of Ecology, University of Georgia, Athens, GA 30602, USA
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA 30602, USA
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Naue J. Getting the chronological age out of DNA: using insights of age-dependent DNA methylation for forensic DNA applications. Genes Genomics 2023; 45:1239-1261. [PMID: 37253906 PMCID: PMC10504122 DOI: 10.1007/s13258-023-01392-8] [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: 02/28/2023] [Accepted: 04/15/2023] [Indexed: 06/01/2023]
Abstract
BACKGROUND DNA analysis for forensic investigations has a long tradition with important developments and optimizations since its first application. Traditionally, short tandem repeats analysis has been the most powerful method for the identification of individuals. However, in addition, epigenetic changes, i.e., DNA methylation, came into focus of forensic DNA research. Chronological age prediction is one promising application to allow for narrowing the pool of possible individuals who caused a trace, as well as to support the identification of unknown bodies and for age verification of living individuals. OBJECTIVE This review aims to provide an overview of the current knowledge, possibilities, and (current) limitations about DNA methylation-based chronological age prediction with emphasis on forensic application. METHODS The development, implementation and application of age prediction tools requires a deep understanding about the biological background, the analysis methods, the age-dependent DNA methylation markers, as well as the mathematical models for age prediction and their evaluation. Furthermore, additional influences can have an impact. Therefore, the literature was evaluated in respect to these diverse topics. CONCLUSION The numerous research efforts in recent years have led to a rapid change in our understanding of the application of DNA methylation for chronological age prediction, which is now on the way to implementation and validation. Knowledge of the various aspects leads to a better understanding and allows a more informed interpretation of DNAm quantification results, as well as the obtained results by the age prediction tools.
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Affiliation(s)
- Jana Naue
- Institute of Forensic Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
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Refn MR, Kampmann ML, Morling N, Tfelt-Hansen J, Børsting C, Pereira V. Prediction of chronological age and its applications in forensic casework: methods, current practices, and future perspectives. Forensic Sci Res 2023; 8:85-97. [PMID: 37621446 PMCID: PMC10445583 DOI: 10.1093/fsr/owad021] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 04/28/2023] [Indexed: 08/26/2023] Open
Abstract
Estimating an individual's age can be relevant in several areas primarily related to the clinical and forensic fields. In the latter, estimation of an individual's chronological age from biological material left by the perpetrator at a crime scene may provide helpful information for police investigation. Estimation of age is also beneficial in immigration cases, where age can affect the person's protection status under the law, or in disaster victim identification to narrow the list of potential missing persons. In the last decade, research has focused on establishing new approaches for age prediction in the forensic field. From the first forensic age estimations based on morphological inspections of macroscopic changes in bone and teeth, the focus has shifted to molecular methods for age estimation. These methods allow the use of samples from human biological material that does not contain morphological age features and can, in theory, be investigated in traces containing only small amounts of biological material. Molecular methods involving DNA analyses are the primary choice and estimation of DNA methylation levels at specific sites in the genome is the most promising tool. This review aims to provide an overview of the status of forensic age prediction using molecular methods, with particular focus in DNA methylation. The frequent challenges that impact forensic age prediction model development will be addressed, together with the importance of validation efforts within the forensic community.
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Affiliation(s)
- Mie Rath Refn
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marie-Louise Kampmann
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jacob Tfelt-Hansen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Department of Cardiology, The Heart Centre, Copenhagen University Hospital, Rigshospitalet, Copenhagen , Denmark
| | - Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Vania Pereira
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Kayser M, Branicki W, Parson W, Phillips C. Recent advances in Forensic DNA Phenotyping of appearance, ancestry and age. Forensic Sci Int Genet 2023; 65:102870. [PMID: 37084623 DOI: 10.1016/j.fsigen.2023.102870] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/04/2023] [Indexed: 04/09/2023]
Abstract
Forensic DNA Phenotyping (FDP) comprises the prediction of a person's externally visible characteristics regarding appearance, biogeographic ancestry and age from DNA of crime scene samples, to provide investigative leads to help find unknown perpetrators that cannot be identified with forensic STR-profiling. In recent years, FDP has advanced considerably in all of its three components, which we summarize in this review article. Appearance prediction from DNA has broadened beyond eye, hair and skin color to additionally comprise other traits such as eyebrow color, freckles, hair structure, hair loss in men, and tall stature. Biogeographic ancestry inference from DNA has progressed from continental ancestry to sub-continental ancestry detection and the resolving of co-ancestry patterns in genetically admixed individuals. Age estimation from DNA has widened beyond blood to more somatic tissues such as saliva and bones as well as new markers and tools for semen. Technological progress has allowed forensically suitable DNA technology with largely increased multiplex capacity for the simultaneous analysis of hundreds of DNA predictors with targeted massively parallel sequencing (MPS). Forensically validated MPS-based FDP tools for predicting from crime scene DNA i) several appearance traits, ii) multi-regional ancestry, iii) several appearance traits together with multi-regional ancestry, and iv) age from different tissue types, are already available. Despite recent advances that will likely increase the impact of FDP in criminal casework in the near future, moving reliable appearance, ancestry and age prediction from crime scene DNA to the level of detail and accuracy police investigators may desire, requires further intensified scientific research together with technical developments and forensic validations as well as the necessary funding.
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Affiliation(s)
- Manfred Kayser
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
| | - Wojciech Branicki
- Institute of Zoology and Biomedical Research, Jagiellonian University, Kraków, Poland,; Institute of Forensic Research, Kraków, Poland
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, PA, USA
| | - Christopher Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
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Carlsen L, Holländer O, Danzer MF, Vennemann M, Augustin C. DNA methylation-based age estimation for adults and minors: considering sex-specific differences and non-linear correlations. Int J Legal Med 2023; 137:635-643. [PMID: 36811674 PMCID: PMC10085938 DOI: 10.1007/s00414-023-02967-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 01/31/2023] [Indexed: 02/24/2023]
Abstract
DNA methylation patterns change during human lifetime; thus, they can be used to estimate an individual's age. It is known, however, that correlation between DNA methylation and aging might not be linear and that the sex might influence the methylation status. In this study, we conducted a comparative evaluation of linear and several non-linear regressions, as well as sex-specific versus unisex models. Buccal swab samples from 230 donors aged 1 to 88 years were analyzed using a minisequencing multiplex array. Samples were divided into a training set (n = 161) and a validation set (n = 69). The training set was used for a sequential replacement regression and a simultaneous 10-fold cross-validation. The resulting model was improved by including a cut-off of 20 years, dividing the younger individuals with non-linear from the older individuals with linear dependence between age and methylation status. Sex-specific models were developed and improved prediction accuracy in females but not in males, which might be explained by a small sample set. We finally established a non-linear, unisex model combining the markers EDARADD, KLF14, ELOVL2, FHL2, C1orf132, and TRIM59. While age- and sex-adjustments did not generally improve the performance of our model, we discuss how other models and large cohorts might benefit from such adjustments. Our model showed a cross-validated MAD and RMSE of 4.680 and 6.436 years in the training set and of 4.695 and 6.602 years in the validation set, respectively. We briefly explain how to apply the model for age prediction.
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Affiliation(s)
- Laura Carlsen
- Institute of Legal Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Olivia Holländer
- Institute of Legal Medicine, University of Münster, Röntgenstraße 23, 48149, Münster, Germany
| | - Moritz Fabian Danzer
- Institute of Biostatistics and Clinical Research, University of Münster, Münster, Germany
| | - Marielle Vennemann
- Institute of Legal Medicine, University of Münster, Röntgenstraße 23, 48149, Münster, Germany
| | - Christa Augustin
- Institute of Legal Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany.
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11
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Yang F, Qian J, Qu H, Ji Z, Li J, Hu W, Cheng F, Fang X, Yan J. DNA methylation-based age prediction with bloodstains using pyrosequencing and random forest regression. Electrophoresis 2023; 44:835-844. [PMID: 36739525 DOI: 10.1002/elps.202200250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 12/08/2022] [Accepted: 01/24/2023] [Indexed: 02/06/2023]
Abstract
The use of DNA methylation to predict chronological age has shown promising potential for obtaining additional information in forensic investigations. To date, several studies have reported age prediction models based on DNA methylation in body fluids with high DNA content. However, it is often difficult to apply these existing methods in practice due to the low amount of DNA present in stains of body fluids that are part of a trace material. In this study, we present a sensitive and rapid test for age prediction with bloodstains based on pyrosequencing and random forest regression. This assay requires only 0.1 ng of genomic DNA and the entire procedure can be completed within 10 h, making it practical for forensic investigations that require a short turnaround time. We examined the methylation levels of 46 CpG sites from six genes using bloodstain samples from 128 males and 113 females aged 10-79 years. A random forest regression model was then used to construct an age prediction model for males and females separately. The final age prediction models were developed with seven CpG sites (three for males and four for females) based on the performance of the random forest regression. The mean absolute deviation was less than 3 years for each model. Our results demonstrate that DNA methylation-based age prediction using pyrosequencing and random forest regression has potential applications in forensics to accurately predict the biological age of a bloodstain donor.
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Affiliation(s)
- Fenglong Yang
- School of Forensic Medicine, Shanxi Medical University, Shanxi, P. R. China
| | - Jialin Qian
- Beijing Center for Physical and Chemical Analysis, Beijing, P. R. China
| | - Hongzhu Qu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, P. R. China
| | - Zhimin Ji
- School of Forensic Medicine, Shanxi Medical University, Shanxi, P. R. China
| | - Junli Li
- School of Forensic Medicine, Shanxi Medical University, Shanxi, P. R. China
| | - Wenjing Hu
- School of Forensic Medicine, Shanxi Medical University, Shanxi, P. R. China
| | - Feng Cheng
- School of Forensic Medicine, Shanxi Medical University, Shanxi, P. R. China
| | - Xiangdong Fang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, P. R. China
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Shanxi, P. R. China
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12
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Jiang L, Zhang K, Wei X, Li J, Wang S, Wang Z, Zhou Y, Zha L, Luo H, Song F. Developing a male-specific age predictive model based on Y-CpGs for forensic analysis. Forensic Sci Int 2023; 343:111566. [PMID: 36640536 DOI: 10.1016/j.forsciint.2023.111566] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/22/2022] [Accepted: 01/09/2023] [Indexed: 01/13/2023]
Abstract
In forensic work, predicting the age of the criminal suspect or victim could provide beneficial clues for investigation. Epigenetic age estimation based on age-correlated DNA methylation has been one of the most widely studied methods of age estimation. However, almost all available epigenetic age prediction models are based on autosomal CpGs, which are only applicable to single-source DNA samples. In this study, we screened the available methylation data sets to identify loci with potential to meet the objectives of this study and then established a male-specific age prediction model based on 2 SNaPshot systems that contain 13 Y-CpGs and the mean absolute deviation (MAD) values were 4-6 years. The multiplex methylation SNaPshot systems and age-predictive model have been validated for sensitivity (the DNA input could be as low as 0.5 ng) and male specificity. They are supposed to have feasibility in forensic practice. In addition, it demonstrated that the method was also applicable to bloodstains, which were commonly found at crime scenes. The results showed good performance (the training set: R2 = 0.9341, MAD = 4.65 years; the test set: R2 = 0.8952, MAD = 5.73 years) in case investigation for predicting male age. For mixtures, when the male to female DNA ratio is 1:1, 1:10, the deviation between the actual age and the predicted age obtained by the model was less than 8 years, which offers great hope for future prediction of the age of males in mixtures and will be a powerful tool for special cases, such as sexual assault. Furthermore, the work provides a basis for the application of Y-CpGs in forensic science.
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Affiliation(s)
- Lanrui Jiang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan Province 610041, China
| | - Ke Zhang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan Province 610041, China; Public Security Bureau of Zhengzhou City, Zhengzhou, Henan Province 450003, China
| | - Xiaowen Wei
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan Province 610041, China
| | - Jiahang Li
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan Province 610041, China
| | - Shuangshuang Wang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan Province 610041, China
| | - Zefei Wang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan Province 610041, China
| | - Yuxiang Zhou
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan Province 610041, China
| | - Lagabaiyila Zha
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, Hunan Province 410013, China
| | - Haibo Luo
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan Province 610041, China.
| | - Feng Song
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan Province 610041, China.
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13
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Gensous N, Sala C, Pirazzini C, Ravaioli F, Milazzo M, Kwiatkowska KM, Marasco E, De Fanti S, Giuliani C, Pellegrini C, Santoro A, Capri M, Salvioli S, Monti D, Castellani G, Franceschi C, Bacalini MG, Garagnani P. A Targeted Epigenetic Clock for the Prediction of Biological Age. Cells 2022; 11:cells11244044. [PMID: 36552808 PMCID: PMC9777448 DOI: 10.3390/cells11244044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 11/28/2022] [Accepted: 12/06/2022] [Indexed: 12/15/2022] Open
Abstract
Epigenetic clocks were initially developed to track chronological age, but accumulating evidence indicates that they can also predict biological age. They are usually based on the analysis of DNA methylation by genome-wide methods, but targeted approaches, based on the assessment of a small number of CpG sites, are advisable in several settings. In this study, we developed a targeted epigenetic clock purposely optimized for the measurement of biological age. The clock includes six genomic regions mapping in ELOVL2, NHLRC1, AIM2, EDARADD, SIRT7 and TFAP2E genes, selected from a re-analysis of existing microarray data, whose DNA methylation is measured by EpiTYPER assay. In healthy subjects (n = 278), epigenetic age calculated using the targeted clock was highly correlated with chronological age (Spearman correlation = 0.89). Most importantly, and in agreement with previous results from genome-wide clocks, epigenetic age was significantly higher and lower than expected in models of increased (persons with Down syndrome, n = 62) and decreased (centenarians, n = 106; centenarians' offspring, n = 143; nutritional intervention in elderly, n = 233) biological age, respectively. These results support the potential of our targeted epigenetic clock as a new marker of biological age and open its evaluation in large cohorts to further promote the assessment of biological age in healthcare practice.
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Affiliation(s)
- Noémie Gensous
- Department of Internal Medicine and Clinical Immunology, CHU Bordeaux (Groupe Hospitalier Saint-André), 33077 Bordeaux, France
- UMR/CNRS 5164, ImmunoConcEpT, CNRS, University of Bordeaux, 33076 Bordeaux, France
| | - Claudia Sala
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138 Bologna, Italy
| | - Chiara Pirazzini
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, Via Altura 3, 40139 Bologna, Italy
| | - Francesco Ravaioli
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138 Bologna, Italy
| | - Maddalena Milazzo
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138 Bologna, Italy
| | | | - Elena Marasco
- Personal Genomics S.R.L., Via Roveggia, 43/B, 37134 Verona, Italy
| | - Sara De Fanti
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, Via Altura 3, 40139 Bologna, Italy
| | - Cristina Giuliani
- Laboratory of Molecular Anthropology, Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy
| | - Camilla Pellegrini
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, Via Altura 3, 40139 Bologna, Italy
| | - Aurelia Santoro
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138 Bologna, Italy
- Interdepartmental Center, “Alma Mater Research Institute on Global Challenges and Climate Change (Alma Climate)”, University of Bologna, 40126 Bologna, Italy
| | - Miriam Capri
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138 Bologna, Italy
- Interdepartmental Center, “Alma Mater Research Institute on Global Challenges and Climate Change (Alma Climate)”, University of Bologna, 40126 Bologna, Italy
| | - Stefano Salvioli
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138 Bologna, Italy
- Interdepartmental Center, “Alma Mater Research Institute on Global Challenges and Climate Change (Alma Climate)”, University of Bologna, 40126 Bologna, Italy
| | - Daniela Monti
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Florence, 50139 Florence, Italy
| | - Gastone Castellani
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138 Bologna, Italy
| | - Claudio Franceschi
- Laboratory of Systems Medicine of Healthy Aging, Department of Applied Mathematics, Lobachevsky University, 603105 Nizhny Novgorod, Russia
| | - Maria Giulia Bacalini
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, Via Altura 3, 40139 Bologna, Italy
- Correspondence: ; Tel.: +39-051-6225977
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138 Bologna, Italy
- Interdepartmental Center, “Alma Mater Research Institute on Global Challenges and Climate Change (Alma Climate)”, University of Bologna, 40126 Bologna, Italy
- Applied Biomedical Research Center (CRBA), S. Orsola-Malpighi Polyclinic, 40138 Bologna, Italy
- Department of Laboratory Medicine, Clinical Chemistry, Karolinska Institutet, Karolinska University Hospital, 14152 Huddinge, Sweden
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14
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Exploiting Signal Joint T Cell Receptor Excision Circle to Investigate the Impact of COVID-19 and Autoimmune Diseases on Age Prediction and Immunosenescence. Biomedicines 2022; 10:biomedicines10123193. [PMID: 36551949 PMCID: PMC9775389 DOI: 10.3390/biomedicines10123193] [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: 11/12/2022] [Revised: 11/27/2022] [Accepted: 12/03/2022] [Indexed: 12/14/2022] Open
Abstract
Signal joint T cell receptor excision circles (sjTRECs) are a promising marker for age estimation and immunosenescence in different ethnic groups. Several limitations are expected to overshadow their use as accurate markers for age prediction. The current study was conducted to determine the influence of immunologic disorders, such as autoimmune diseases and COVID-19, on the accuracy of sjTRECs as molecular markers for age estimation and immunosenescence among living Egyptians. Peripheral blood sjTRECs level was measured by qPCR in 90 autoimmune patients, 58 COVID-19 patients, and 85 healthy controls. The mean dCt values were significantly (p = 0.0002) different between the three groups, with the highest values in healthy subjects, followed by autoimmune and COVID-19 patients. A significant negative correlation was identified between the sjTRECs levels and ages in all studied cases. There were significant positive correlations between chronological age and predicted age for healthy individuals, autoimmune, and COVID-19 patients with mean absolute deviations (MAD) of 9.40, 11.04, and 9.71, respectively. The two patients' groups exhibited early immunosenescence, which was more noticeable among the young adults with COVID-19 and autoimmune patients of age range (18-49 years). Autoimmunity may represent a critical factor impacting the accuracy of sjTRECs quantitation for age prediction.
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15
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Li A, Koch Z, Ideker T. Epigenetic aging: Biological age prediction and informing a mechanistic theory of aging. J Intern Med 2022; 292:733-744. [PMID: 35726002 DOI: 10.1111/joim.13533] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Numerous studies have shown that epigenetic age-an individual's degree of aging based on patterns of DNA methylation-can be computed and is associated with an array of factors including diet, lifestyle, genetics, and disease. One can expect that still further associations will emerge with additional aging research, but to what end? Prediction of age was an important first step, but-in our view-the focus must shift from chasing increasingly accurate age computations to understanding the links between the epigenome and the mechanisms and physiological changes of aging. Here, we outline emerging areas of epigenetic aging research that prioritize biological understanding and clinical application. First, we survey recent progress in epigenetic clocks, which are beginning to predict not only chronological age but aging outcomes such as all-cause mortality and onset of disease, or which integrate aging signals across multiple biological processes. Second, we discuss research that exemplifies how investigation of the epigenome is building a mechanistic theory of aging and informing clinical practice. Such examples include identifying methylation sites and the genes most strongly predictive of aging-a subset of which have shown strong potential as biomarkers of neurodegenerative disease and cancer; relating epigenetic clock predictions to hallmarks of aging; and using longitudinal studies of DNA methylation to characterize human disease, resulting in the discovery of epigenetic indications of type 1 diabetes and the propensity for psychotic experiences.
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Affiliation(s)
- Adam Li
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Zane Koch
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Trey Ideker
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, California, USA
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16
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Daunay A, Hardy LM, Bouyacoub Y, Sahbatou M, Touvier M, Blanché H, Deleuze JF, How-Kit A. Centenarians consistently present a younger epigenetic age than their chronological age with four epigenetic clocks based on a small number of CpG sites. Aging (Albany NY) 2022; 14:7718-7733. [PMID: 36202132 PMCID: PMC9596211 DOI: 10.18632/aging.204316] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/23/2022] [Indexed: 11/25/2022]
Abstract
Aging is a progressive time-dependent biological process affecting differentially individuals, who can sometimes present exceptional longevity. Epigenetic alterations are one of the hallmarks of aging, which comprise the epigenetic drift and clock at DNA methylation level. In the present study, we estimated the DNA methylation-based age (DNAmage) using four epigenetic clocks based on a small number of CpGs in French centenarians and semi-supercentenarians (CSSC, n=214) as well as nonagenarians' and centenarians' offspring (NCO, n=143) compared to individuals from the French general population (CG, n=149). DNA methylation analysis of the nine CpGs included in the epigenetic clocks showed high correlation with chronological age (-0.66>R>0.54) and also the presence of an epigenetic drift for four CpGs that was only visible in CSSC. DNAmage analysis showed that CSSC and to a lesser extend NCO present a younger DNAmage than their chronological age (15-28.5 years for CSSC, 4.4-11.5 years for NCO and 4.2-8.2 years for CG), which were strongly significant in CSSC compared to CG (p-values<2.2e-16). These differences suggest that epigenetic aging and potentially biological aging are slowed in exceptionally long-lived individuals and that epigenetic clocks based on a small number of CpGs are sufficient to reveal alterations of the global epigenetic clock.
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Affiliation(s)
- Antoine Daunay
- Laboratory for Genomics, Foundation Jean Dausset - CEPH, Paris, France
| | - Lise M Hardy
- Laboratory for Genomics, Foundation Jean Dausset - CEPH, Paris, France.,Laboratory of Excellence GenMed, Paris, France
| | - Yosra Bouyacoub
- Laboratory for Genomics, Foundation Jean Dausset - CEPH, Paris, France.,Laboratory of Excellence GenMed, Paris, France
| | - Mourad Sahbatou
- Laboratory for Genomics, Foundation Jean Dausset - CEPH, Paris, France
| | - Mathilde Touvier
- Sorbonne Paris Nord University, Nutritional Epidemiology Research Team (EREN), Epidemiology and Statistics Research Center Inserm U1153, Inrae U1125, Cnam, University of Paris (CRESS), Bobigny, France
| | - Hélène Blanché
- Laboratory of Excellence GenMed, Paris, France.,Centre de Ressources Biologiques, CEPH Biobank, Foundation Jean Dausset - CEPH, Paris, France
| | - Jean-François Deleuze
- Laboratory for Genomics, Foundation Jean Dausset - CEPH, Paris, France.,Laboratory of Excellence GenMed, Paris, France.,Centre de Ressources Biologiques, CEPH Biobank, Foundation Jean Dausset - CEPH, Paris, France.,Centre National de Recherche en Génomique Humaine, CEA, Institut François Jacob, Evry, France
| | - Alexandre How-Kit
- Laboratory for Genomics, Foundation Jean Dausset - CEPH, Paris, France
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17
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Freire-Aradas A, Girón-Santamaría L, Mosquera-Miguel A, Ambroa-Conde A, Phillips C, Casares de Cal M, Gómez-Tato A, Álvarez-Dios J, Pospiech E, Aliferi A, Syndercombe Court D, Branicki W, Lareu M. A common epigenetic clock from childhood to old age. Forensic Sci Int Genet 2022; 60:102743. [DOI: 10.1016/j.fsigen.2022.102743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 06/22/2022] [Accepted: 06/23/2022] [Indexed: 11/04/2022]
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18
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Novel feature selection methods for construction of accurate epigenetic clocks. PLoS Comput Biol 2022; 18:e1009938. [PMID: 35984867 PMCID: PMC9432708 DOI: 10.1371/journal.pcbi.1009938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 08/31/2022] [Accepted: 07/11/2022] [Indexed: 11/22/2022] Open
Abstract
Epigenetic clocks allow us to accurately predict the age and future health of individuals based on the methylation status of specific CpG sites in the genome and are a powerful tool to measure the effectiveness of longevity interventions. There is a growing need for methods to efficiently construct epigenetic clocks. The most common approach is to create clocks using elastic net regression modelling of all measured CpG sites, without first identifying specific features or CpGs of interest. The addition of feature selection approaches provides the opportunity to optimise the identification of predictive CpG sites. Here, we apply novel feature selection methods and combinatorial approaches including newly adapted neural networks, genetic algorithms, and ‘chained’ combinations. Human whole blood methylation data of ~470,000 CpGs was used to develop clocks that predict age with R2 correlation scores of greater than 0.73, the most predictive of which uses 35 CpG sites for a R2 correlation score of 0.87. The five most frequent sites across all clocks were modelled to build a clock with a R2 correlation score of 0.83. These two clocks are validated on two external datasets where they maintain excellent predictive accuracy. When compared with three published epigenetic clocks (Hannum, Horvath, Weidner) also applied to these validation datasets, our clocks outperformed all three models. We identified gene regulatory regions associated with selected CpGs as possible targets for future aging studies. Thus, our feature selection algorithms build accurate, generalizable clocks with a low number of CpG sites, providing important tools for the field. Epigenetic clocks accurately predict a person’s age by measuring the levels of a chemical mark (methylation) at specific sites of the DNA. More of these clocks are being built all the time, and there is a need for tools to best construct these clocks, and particularly to pick the specific DNA sites to include. We propose several novel machine-learning tools for the optimised selection of these DNA sites, known as feature selection approaches. We applied our approaches to a large human blood dataset to develop several clocks that accurately predict age using 35 or less DNA sites with more accuracy than previously published clocks when applied to other datasets for validation. Some of the DNA sites identified may be associated with interesting genes to explore further for their role in aging. These approaches should enable the building of more accurate, generalizable age prediction clocks from a low number of DNA sites.
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19
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Perez GA, Villarraso JC. An Entropy Approach to Multiple Sclerosis Identification. J Pers Med 2022; 12:jpm12030398. [PMID: 35330398 PMCID: PMC8948909 DOI: 10.3390/jpm12030398] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/01/2022] [Accepted: 03/03/2022] [Indexed: 11/16/2022] Open
Abstract
Multiple sclerosis (MS) is a relatively common neurodegenerative illness that frequently causes a large level of disability in patients. While its cause is not fully understood, it is likely due to a combination of genetic and environmental factors. Diagnosis of multiple sclerosis through a simple clinical examination might be challenging as the evolution of the illness varies significantly from patient to patient, with some patients experiencing long periods of remission. In this regard, having a quick and inexpensive tool to help identify the illness, such as DNA CpG (cytosine-phosphate-guanine) methylation, might be useful. In this paper, a technique is presented, based on the concept of Shannon Entropy, to select CpGs as inputs for non-linear classification algorithms. It will be shown that this approach generates accurate classifications that are a statistically significant improvement over using all the data available or randomly selecting the same number of CpGs. The analysis controlled for factors such as age, gender and smoking status of the patient. This approach managed to reduce the number of CpGs used while at the same time significantly increasing the accuracy.
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Affiliation(s)
- Gerardo Alfonso Perez
- Department of Biochemistry and Molecular Biology, University of Cordoba, 14071 Cordoba, Spain;
- Correspondence:
| | - Javier Caballero Villarraso
- Department of Biochemistry and Molecular Biology, University of Cordoba, 14071 Cordoba, Spain;
- Biochemical Laboratory, Reina Sofia University Hospital, 14004 Cordoba, Spain
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20
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Lucknuch T, Praihirunkit P. Evaluation of Age-associated DNA Methylation Markers in Colorectal Cancer of Thai Population. FORENSIC SCIENCE INTERNATIONAL: REPORTS 2022. [DOI: 10.1016/j.fsir.2022.100265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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21
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Becker J, Böhme P, Reckert A, Eickhoff SB, Koop BE, Blum J, Gündüz T, Takayama M, Wagner W, Ritz-Timme S. Evidence for differences in DNA methylation between Germans and Japanese. Int J Legal Med 2021; 136:405-413. [PMID: 34739581 PMCID: PMC8847189 DOI: 10.1007/s00414-021-02736-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 10/22/2021] [Indexed: 12/16/2022]
Abstract
As a contribution to the discussion about the possible effects of ethnicity/ancestry on age estimation based on DNA methylation (DNAm) patterns, we directly compared age-associated DNAm in German and Japanese donors in one laboratory under identical conditions. DNAm was analyzed by pyrosequencing for 22 CpG sites (CpGs) in the genes PDE4C, RPA2, ELOVL2, DDO, and EDARADD in buccal mucosa samples from German and Japanese donors (N = 368 and N = 89, respectively). Twenty of these CpGs revealed a very high correlation with age and were subsequently tested for differences between German and Japanese donors aged between 10 and 65 years (N = 287 and N = 83, respectively). ANCOVA was performed by testing the Japanese samples against age- and sex-matched German subsamples (N = 83 each; extracted 500 times from the German total sample). The median p values suggest a strong evidence for significant differences (p < 0.05) at least for two CpGs (EDARADD, CpG 2, and PDE4C, CpG 2) and no differences for 11 CpGs (p > 0.3). Age prediction models based on DNAm data from all 20 CpGs from German training data did not reveal relevant differences between the Japanese test samples and German subsamples. Obviously, the high number of included “robust CpGs” prevented relevant effects of differences in DNAm at two CpGs. Nevertheless, the presented data demonstrates the need for further research regarding the impact of confounding factors on DNAm in the context of ethnicity/ancestry to ensure a high quality of age estimation. One approach may be the search for “robust” CpG markers—which requires the targeted investigation of different populations, at best by collaborative research with coordinated research strategies.
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Affiliation(s)
- J Becker
- Institute of Legal Medicine, University Hospital Düsseldorf, 40225, Düsseldorf, Germany.
| | - P Böhme
- Institute of Legal Medicine, University Hospital Düsseldorf, 40225, Düsseldorf, Germany
| | - A Reckert
- Institute of Legal Medicine, University Hospital Düsseldorf, 40225, Düsseldorf, Germany
| | - S B Eickhoff
- Institute for Systems Neuroscience, University Hospital Düsseldorf, 40225, Düsseldorf, Germany.,Institute of Neuroscience and Medicine, Brain and Behaviour, (INM-7), Research Centre Jülich, 52428, Jülich, Germany
| | - B E Koop
- Institute of Legal Medicine, University Hospital Düsseldorf, 40225, Düsseldorf, Germany
| | - J Blum
- Institute of Legal Medicine, University Hospital Düsseldorf, 40225, Düsseldorf, Germany
| | - T Gündüz
- Institute of Legal Medicine, University Hospital Düsseldorf, 40225, Düsseldorf, Germany
| | - M Takayama
- Department of Forensic Medicine, Faculty of Medicine, Fukuoka University, Fukuoka, Japan.,Tokyo Medical Examiner's Office, Tokyo, Japan
| | - W Wagner
- Helmholtz Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, 52074, Aachen, Germany
| | - S Ritz-Timme
- Institute of Legal Medicine, University Hospital Düsseldorf, 40225, Düsseldorf, Germany
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22
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Habibe JJ, Clemente-Olivo MP, de Vries CJ. How (Epi)Genetic Regulation of the LIM-Domain Protein FHL2 Impacts Multifactorial Disease. Cells 2021; 10:cells10102611. [PMID: 34685595 PMCID: PMC8534169 DOI: 10.3390/cells10102611] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/23/2021] [Accepted: 09/24/2021] [Indexed: 01/13/2023] Open
Abstract
Susceptibility to complex pathological conditions such as obesity, type 2 diabetes and cardiovascular disease is highly variable among individuals and arises from specific changes in gene expression in combination with external factors. The regulation of gene expression is determined by genetic variation (SNPs) and epigenetic marks that are influenced by environmental factors. Aging is a major risk factor for many multifactorial diseases and is increasingly associated with changes in DNA methylation, leading to differences in gene expression. Four and a half LIM domains 2 (FHL2) is a key regulator of intracellular signal transduction pathways and the FHL2 gene is consistently found as one of the top hyper-methylated genes upon aging. Remarkably, FHL2 expression increases with methylation. This was demonstrated in relevant metabolic tissues: white adipose tissue, pancreatic β-cells, and skeletal muscle. In this review, we provide an overview of the current knowledge on regulation of FHL2 by genetic variation and epigenetic DNA modification, and the potential consequences for age-related complex multifactorial diseases.
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Affiliation(s)
- Jayron J. Habibe
- Department of Medical Biochemistry, Amsterdam University Medical Centers, Amsterdam Cardiovascular Sciences, and Amsterdam Gastroenterology, Endocrinology and Metabolism, 1105 AZ Amsterdam, The Netherlands; (J.J.H.); (M.P.C.-O.)
- Department of Physiology, Amsterdam University Medical Centers, Amsterdam Cardiovascular Sciences, 1081 HV Amsterdam, The Netherlands
| | - Maria P. Clemente-Olivo
- Department of Medical Biochemistry, Amsterdam University Medical Centers, Amsterdam Cardiovascular Sciences, and Amsterdam Gastroenterology, Endocrinology and Metabolism, 1105 AZ Amsterdam, The Netherlands; (J.J.H.); (M.P.C.-O.)
| | - Carlie J. de Vries
- Department of Medical Biochemistry, Amsterdam University Medical Centers, Amsterdam Cardiovascular Sciences, and Amsterdam Gastroenterology, Endocrinology and Metabolism, 1105 AZ Amsterdam, The Netherlands; (J.J.H.); (M.P.C.-O.)
- Correspondence:
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23
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Jin Z, Liu L, Yu Y, Li D, Zhu X, Yan D, Zhu Z. TRIM59: A potential diagnostic and prognostic biomarker in human tumors. PLoS One 2021; 16:e0257445. [PMID: 34534244 PMCID: PMC8448305 DOI: 10.1371/journal.pone.0257445] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 09/01/2021] [Indexed: 12/24/2022] Open
Abstract
TRIM59 is a protein that is highly expressed in a variety of tumors and promotes tumor development. However, the use of TRIM59 as tumor diagnosis and prognosis biomarker has not been fully explored. We collected datasets from the cancer genome atlas (TCGA) and gene expression omnibus (GEO) to investigate its potential as a biomarker for diagnosis and prognosis. A total of 46 studies, including 11,558 patients were included in this study. Here, we showed that TRIM59 was significantly upregulated in 15 type of human solid tumors in comparison to their adjacent tissues. Receiver operating characteristic curve (ROC) results provided further evidence for the use of TRIM59 as a potential tumor diagnosis biomarker. Overall survival (OS) was compared between TRIM59 high expression and low expression groups. High expression of TRIM59 indicated a poor prognosis in multiple solid tumors. Taken together, these analyses showed that TRIM59 was upregulated in various types of tumors and had the potential to be used as a diagnostic and prognostic biomarker in human solid tumors.
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Affiliation(s)
- Zheng Jin
- Department of Immunology, College of Basic Medical Sciences, Jilin University, Changchun City, Jilin Province, China
| | - Liping Liu
- Department of Immunology, College of Basic Medical Sciences, Jilin University, Changchun City, Jilin Province, China
| | - Youran Yu
- College of Pharmacy, Shanghai University of Medicine & Health Sciences, Shanghai, China
| | - Dong Li
- Department of Immunology, College of Basic Medical Sciences, Jilin University, Changchun City, Jilin Province, China
| | - Xun Zhu
- Department of Immunology, College of Basic Medical Sciences, Jilin University, Changchun City, Jilin Province, China
| | - Dongmei Yan
- Department of Immunology, College of Basic Medical Sciences, Jilin University, Changchun City, Jilin Province, China
- * E-mail: (DY); (ZZ)
| | - Zhenhua Zhu
- Department of Orthopaedic Trauma, Center for Orthopaedic Surgery, The Third Affiliated Hospital of Southern Medical University, Guangzhou, Guangdong Province, China
- * E-mail: (DY); (ZZ)
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24
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Piniewska-Róg D, Heidegger A, Pośpiech E, Xavier C, Pisarek A, Jarosz A, Woźniak A, Wojtas M, Phillips C, Kayser M, Parson W, Branicki W. Impact of excessive alcohol abuse on age prediction using the VISAGE enhanced tool for epigenetic age estimation in blood. Int J Legal Med 2021; 135:2209-2219. [PMID: 34405265 PMCID: PMC8523459 DOI: 10.1007/s00414-021-02665-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 07/06/2021] [Indexed: 12/13/2022]
Abstract
DNA methylation-based clocks provide the most accurate age estimates with practical implications for clinical and forensic genetics. However, the effects of external factors that may influence the estimates are poorly studied. Here, we evaluated the effect of alcohol consumption on epigenetic age prediction in a cohort of extreme alcohol abusers. Blood samples from deceased alcohol abusers and age- and sex-matched controls were analyzed using the VISAGE enhanced tool for age prediction from somatic tissues that enables examination of 44 CpGs within eight age markers. Significantly altered DNA methylation was recorded for alcohol abusers in MIR29B2CHG. This resulted in a mean predicted age of 1.4 years higher compared to the controls and this trend increased in older individuals. The association of alcohol abuse with epigenetic age acceleration, as determined by the prediction analysis performed based on MIR29B2CHG, was small but significant (β = 0.190; P-value = 0.007). However, the observed alteration in DNA methylation of MIR29B2CHG had a non-significant effect on age estimation with the VISAGE age prediction model. The mean absolute error in the alcohol-abusing cohort was 3.1 years, compared to 3.3 years in the control group. At the same time, upregulation of MIR29B2CHG expression may have a biological function, which merits further studies.
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Affiliation(s)
- Danuta Piniewska-Róg
- Jagiellonian University Medical College, Faculty of Medicine, Department of Forensic Medicine, Grzegórzecka 16, 31-531, Krakow, Poland
| | - Antonia Heidegger
- Institute of Legal Medicine, Medical University of Innsbruck, Muellerstrasse 44, 6020, Innsbruck, Austria
| | - Ewelina Pośpiech
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-348, Krakow, Poland
| | - Catarina Xavier
- Institute of Legal Medicine, Medical University of Innsbruck, Muellerstrasse 44, 6020, Innsbruck, Austria
| | - Aleksandra Pisarek
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-348, Krakow, Poland
| | - Agata Jarosz
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-348, Krakow, Poland
| | - Anna Woźniak
- Central Forensic Laboratory of the Police, Aleje Ujazdowskie 7, 00-583, Warsaw, Poland
| | - Marta Wojtas
- Jagiellonian University Medical College, Faculty of Medicine, Department of Forensic Medicine, Grzegórzecka 16, 31-531, Krakow, Poland
| | - Christopher Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, R/ San Francisco s/n, 15782, Santiago de Compostela, Spain
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Muellerstrasse 44, 6020, Innsbruck, Austria
- Forensic Science Program, The Pennsylvania State University, 13 Thomas Building, University Park, PA, 16802, USA
| | - Wojciech Branicki
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-348, Krakow, Poland.
- Central Forensic Laboratory of the Police, Aleje Ujazdowskie 7, 00-583, Warsaw, Poland.
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25
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Kukla-Bartoszek M, Teisseyre P, Pośpiech E, Karłowska-Pik J, Zieliński P, Woźniak A, Boroń M, Dąbrowski M, Zubańska M, Jarosz A, Płoski R, Grzybowski T, Spólnicka M, Mielniczuk J, Branicki W. Searching for improvements in predicting human eye colour from DNA. Int J Legal Med 2021; 135:2175-2187. [PMID: 34259936 PMCID: PMC8523394 DOI: 10.1007/s00414-021-02645-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/17/2021] [Indexed: 01/29/2023]
Abstract
Increasing understanding of human genome variability allows for better use of the predictive potential of DNA. An obvious direct application is the prediction of the physical phenotypes. Significant success has been achieved, especially in predicting pigmentation characteristics, but the inference of some phenotypes is still challenging. In search of further improvements in predicting human eye colour, we conducted whole-exome (enriched in regulome) sequencing of 150 Polish samples to discover new markers. For this, we adopted quantitative characterization of eye colour phenotypes using high-resolution photographic images of the iris in combination with DIAT software analysis. An independent set of 849 samples was used for subsequent predictive modelling. Newly identified candidates and 114 additional literature-based selected SNPs, previously associated with pigmentation, and advanced machine learning algorithms were used. Whole-exome sequencing analysis found 27 previously unreported candidate SNP markers for eye colour. The highest overall prediction accuracies were achieved with LASSO-regularized and BIC-based selected regression models. A new candidate variant, rs2253104, located in the ARFIP2 gene and identified with the HyperLasso method, revealed predictive potential and was included in the best-performing regression models. Advanced machine learning approaches showed a significant increase in sensitivity of intermediate eye colour prediction (up to 39%) compared to 0% obtained for the original IrisPlex model. We identified a new potential predictor of eye colour and evaluated several widely used advanced machine learning algorithms in predictive analysis of this trait. Our results provide useful hints for developing future predictive models for eye colour in forensic and anthropological studies.
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Affiliation(s)
- Magdalena Kukla-Bartoszek
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland. .,Malopolska Centre of Biotechnology of the Jagiellonian University, Kraków, Poland.
| | - Paweł Teisseyre
- Institute of Computer Science, Polish Academy of Sciences, Warsaw, Poland.,Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Ewelina Pośpiech
- Malopolska Centre of Biotechnology of the Jagiellonian University, Kraków, Poland
| | - Joanna Karłowska-Pik
- Faculty of Mathematics and Computer Science, Nicolaus Copernicus University in Toruń, Toruń, Poland
| | - Piotr Zieliński
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Anna Woźniak
- Central Forensic Laboratory of the Police, Warsaw, Poland
| | - Michał Boroń
- Central Forensic Laboratory of the Police, Warsaw, Poland
| | - Michał Dąbrowski
- Laboratory of Bioinformatics, Neurobiology Centre, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Magdalena Zubańska
- Faculty of Law and Administration, Department of Criminology and Forensic Sciences, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland.,Unit of Forensic Sciences, Faculty of Internal Security, Police Academy, Szczytno, Poland
| | - Agata Jarosz
- Malopolska Centre of Biotechnology of the Jagiellonian University, Kraków, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Warsaw Medical University, Warsaw, Poland
| | - Tomasz Grzybowski
- Division of Molecular and Forensic Genetics, Department of Forensic Medicine, Nicolaus Copernicus University in Toruń, Collegium Medicum in Bydgoszcz, Bydgoszcz, Poland
| | | | - Jan Mielniczuk
- Institute of Computer Science, Polish Academy of Sciences, Warsaw, Poland.,Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Wojciech Branicki
- Malopolska Centre of Biotechnology of the Jagiellonian University, Kraków, Poland. .,Central Forensic Laboratory of the Police, Warsaw, Poland.
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26
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DNA methylation of decedent blood samples to estimate the chronological age of human remains. Int J Legal Med 2021; 135:2163-2173. [PMID: 34245337 DOI: 10.1007/s00414-021-02650-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 06/24/2021] [Indexed: 01/21/2023]
Abstract
Chronological age estimation may offer valuable investigative leads in human identification cases. Bisulfite pyrosequencing analysis of single CpG sites on five genes (KLF14, ELOVL2, C1orf132, TRIM59, and FHL2) was performed on 264 postmortem blood samples from individuals aged 3 months to 93 years. The goals were to develop age prediction models based on the correlation between the methylation profile and chronological age and to assess the accuracy of the prediction. Linear regression between methylation levels and age at each CpG site revealed that the five markers show a statistically significant correlation with age. The methylation data from a training set of 160 postmortem blood samples were used to develop an age prediction model with a correlation coefficient of 0.65, explaining 73.1% of age variation, with a mean absolute deviation from the chronological age of 7.60 years. The accuracy of the model was evaluated with a test set of 72 samples producing a mean absolute deviation of 7.42 years. The training and test sets were also categorized by specific age groups to assess accuracy and deviation from chronological age. The data for both sets revealed a lower prediction potential as an individual increases in age, particularly for the age categories above 50 years.
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27
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Noroozi R, Ghafouri-Fard S, Pisarek A, Rudnicka J, Spólnicka M, Branicki W, Taheri M, Pośpiech E. DNA methylation-based age clocks: From age prediction to age reversion. Ageing Res Rev 2021; 68:101314. [PMID: 33684551 DOI: 10.1016/j.arr.2021.101314] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 02/25/2021] [Accepted: 03/01/2021] [Indexed: 12/12/2022]
Abstract
Aging as an irretrievable occurrence throughout the entire life is characterized by a progressive decline in physiological functionality and enhanced disease vulnerability. Numerous studies have demonstrated that epigenetic modifications, particularly DNA methylation (DNAm), correlate with aging and age-related diseases. Several investigations have attempted to predict chronological age using the age-related alterations in the DNAm of certain CpG sites. Here we categorize different studies that tracked the aging process in the DNAm landscape to show how epigenetic age clocks evolved from a chronological age estimator to an indicator of lifespan and healthspan. We also describe the health and disease predictive potential of estimated epigenetic age acceleration regarding different clinical conditions and lifestyle factors. Considering the revealed age-related epigenetic changes, the recent age-reprogramming strategies are discussed which are promising methods for resetting the aging clocks.
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Affiliation(s)
- Rezvan Noroozi
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Aleksandra Pisarek
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Joanna Rudnicka
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Wojciech Branicki
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
| | - Mohammad Taheri
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Ewelina Pośpiech
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
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28
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Zhang J, Fu H, Xu Y. Age Prediction of Human Based on DNA Methylation by Blood Tissues. Genes (Basel) 2021; 12:genes12060870. [PMID: 34204075 PMCID: PMC8228382 DOI: 10.3390/genes12060870] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/27/2021] [Accepted: 06/05/2021] [Indexed: 12/14/2022] Open
Abstract
In recent years, scientists have found a close correlation between DNA methylation and aging in epigenetics. With the in-depth research in the field of DNA methylation, researchers have established a quantitative statistical relationship to predict the individual ages. This work used human blood tissue samples to study the association between age and DNA methylation. We built two predictors based on healthy and disease data, respectively. For the health data, we retrieved a total of 1191 samples from four previous reports. By calculating the Pearson correlation coefficient between age and DNA methylation values, 111 age-related CpG sites were selected. Gradient boosting regression was utilized to build the predictive model and obtained the R2 value of 0.86 and MAD of 3.90 years on testing dataset, which were better than other four regression methods as well as Horvath’s results. For the disease data, 354 rheumatoid arthritis samples were retrieved from a previous study. Then, 45 CpG sites were selected to build the predictor and the corresponded MAD and R2 were 3.11 years and 0.89 on the testing dataset respectively, which showed the robustness of our predictor. Our results were better than the ones from other four regression methods. Finally, we also analyzed the twenty-four common CpG sites in both healthy and disease datasets which illustrated the functional relevance of the selected CpG sites.
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29
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Pellegrini C, Pirazzini C, Sala C, Sambati L, Yusipov I, Kalyakulina A, Ravaioli F, Kwiatkowska KM, Durso DF, Ivanchenko M, Monti D, Lodi R, Franceschi C, Cortelli P, Garagnani P, Bacalini MG. A Meta-Analysis of Brain DNA Methylation Across Sex, Age, and Alzheimer's Disease Points for Accelerated Epigenetic Aging in Neurodegeneration. Front Aging Neurosci 2021; 13:639428. [PMID: 33790779 PMCID: PMC8006465 DOI: 10.3389/fnagi.2021.639428] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/05/2021] [Indexed: 12/14/2022] Open
Abstract
Alzheimer's disease (AD) is characterized by specific alterations of brain DNA methylation (DNAm) patterns. Age and sex, two major risk factors for AD, are also known to largely affect the epigenetic profiles in brain, but their contribution to AD-associated DNAm changes has been poorly investigated. In this study we considered publicly available DNAm datasets of four brain regions (temporal, frontal, entorhinal cortex, and cerebellum) from healthy adult subjects and AD patients, and performed a meta-analysis to identify sex-, age-, and AD-associated epigenetic profiles. In one of these datasets it was also possible to distinguish 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) profiles. We showed that DNAm differences between males and females tend to be shared between the four brain regions, while aging differently affects cortical regions compared to cerebellum. We found that the proportion of sex-dependent probes whose methylation is modified also during aging is higher than expected, but that differences between males and females tend to be maintained, with only a few probes showing age-by-sex interaction. We did not find significant overlaps between AD- and sex-associated probes, nor disease-by-sex interaction effects. On the contrary, we found that AD-related epigenetic modifications are significantly enriched in probes whose DNAm varies with age and that there is a high concordance between the direction of changes (hyper or hypo-methylation) in aging and AD, supporting accelerated epigenetic aging in the disease. In summary, our results suggest that age-associated DNAm patterns concur to the epigenetic deregulation observed in AD, providing new insights on how advanced age enables neurodegeneration.
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Affiliation(s)
- Camilla Pellegrini
- Istituto di Ricovero e Cura a Carattere Scientifico Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Chiara Pirazzini
- Istituto di Ricovero e Cura a Carattere Scientifico Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Claudia Sala
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy
| | - Luisa Sambati
- Istituto di Ricovero e Cura a Carattere Scientifico Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Igor Yusipov
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky University, Nizhny Novgorod, Russia
| | - Alena Kalyakulina
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky University, Nizhny Novgorod, Russia
| | - Francesco Ravaioli
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Katarzyna M. Kwiatkowska
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Danielle F. Durso
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, United States
| | - Mikhail Ivanchenko
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky University, Nizhny Novgorod, Russia
| | - Daniela Monti
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio,” University of Florence, Florence, Italy
| | - Raffaele Lodi
- Istituto di Ricovero e Cura a Carattere Scientifico Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Claudio Franceschi
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky University, Nizhny Novgorod, Russia
| | - Pietro Cortelli
- Istituto di Ricovero e Cura a Carattere Scientifico Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
- Department of Laboratory Medicine, Clinical Chemistry, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Applied Biomedical Research Center, Policlinico S.Orsola-Malpighi Polyclinic, Bologna, Italy
- National Research Council of Italy Institute of Molecular Genetics “Luigi Luca Cavalli-Sforza,” Unit of Bologna, Bologna, Italy
| | - Maria Giulia Bacalini
- Istituto di Ricovero e Cura a Carattere Scientifico Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
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30
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Woźniak A, Heidegger A, Piniewska-Róg D, Pośpiech E, Xavier C, Pisarek A, Kartasińska E, Boroń M, Freire-Aradas A, Wojtas M, de la Puente M, Niederstätter H, Płoski R, Spólnicka M, Kayser M, Phillips C, Parson W, Branicki W. Development of the VISAGE enhanced tool and statistical models for epigenetic age estimation in blood, buccal cells and bones. Aging (Albany NY) 2021; 13:6459-6484. [PMID: 33707346 PMCID: PMC7993733 DOI: 10.18632/aging.202783] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 02/16/2021] [Indexed: 01/07/2023]
Abstract
DNA methylation is known as a biomarker for age with applications in forensics. Here we describe the VISAGE (VISible Attributes through GEnomics) Consortium's enhanced tool for epigenetic age estimation in somatic tissues. The tool is based on eight DNA methylation markers (44 CpGs), bisulfite multiplex PCR followed by sequencing on the MiSeq FGx platform, and three statistical prediction models for blood, buccal cells and bones. The model for blood is based on six CpGs from ELOVL2, MIR29B2CHG, KLF14, FHL2, TRIM59 and PDE4C, and predicts age with a mean absolute error (MAE) of 3.2 years, while the model for buccal cells includes five CpGs from PDE4C, MIR29B2CHG, ELOVL2, KLF14 and EDARADD and predicts age with MAE of 3.7 years, and the model for bones has six CpGs from ELOVL2, KLF14, PDE4C and ASPA and predicts age with MAE of 3.4 years. The VISAGE enhanced tool for age estimation in somatic tissues enables reliable collection of DNA methylation data from small amounts of DNA using a sensitive multiplex MPS assay that provides accurate estimation of age in blood, buccal swabs, and bones using the statistical model tailored to each tissue.
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Affiliation(s)
- Anna Woźniak
- Central Forensic Laboratory of the Police, Warsaw, Poland
| | - Antonia Heidegger
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Danuta Piniewska-Róg
- Department of Forensic Medicine, Jagiellonian University Medical College, Krakow, Poland
| | - Ewelina Pośpiech
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Catarina Xavier
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Aleksandra Pisarek
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Michał Boroń
- Central Forensic Laboratory of the Police, Warsaw, Poland
| | - Ana Freire-Aradas
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Marta Wojtas
- Department of Forensic Medicine, Jagiellonian University Medical College, Krakow, Poland
| | - Maria de la Puente
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria.,Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Harald Niederstätter
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Rafał Płoski
- Department Medical Genetics, Warsaw Medical University, Warsaw, Poland
| | | | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Christopher Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria.,Forensic Science Program, The Pennsylvania State University, University Park, PA 16802, USA
| | - Wojciech Branicki
- Central Forensic Laboratory of the Police, Warsaw, Poland.,Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
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31
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Characterization of the effects of age and childhood maltreatment on ELOVL2 DNA methylation. Dev Psychopathol 2021; 34:864-874. [PMID: 33461631 DOI: 10.1017/s0954579420001972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
DNA methylation of the elongation of very long chain fatty acids protein 2 (ELOVL2) was suggested as a biomarker of biological aging, while childhood maltreatment (CM) has been associated with accelerated biological aging. We investigated the association of age and CM experiences with ELOVL2 methylation in peripheral blood mononuclear cells (PBMC). Furthermore, we investigated ELOVL2 methylation in the umbilical cord blood mononuclear cells (UBMC) of newborns of mothers with and without CM. PBMC and UBMC were isolated from 113 mother-newborn dyads and genomic DNA was extracted. Mothers with and without CM experiences were recruited directly postpartum. Mass array spectrometry and pyrosequencing were used for methylation analyses of ELOVL2 intron 1, and exon 1 and 5' end, respectively. ELOVL2 5' end and intron 1 methylation increased with higher age but were not associated with CM experiences. On the contrary, overall ELOVL2 exon 1 methylation increased with higher CM, but these changes were minimal and did not increase with age. Maternal CM experiences and neonatal methylation of ELOVL2 intron 1 or exon 1 were not significantly correlated. Our study suggests region-specific effects of chronological age and experienced CM on ELOVL2 methylation and shows that the epigenetic biomarker for age within the ELOVL2 gene does not show accelerated biological aging years after CM exposure.
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32
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Thong Z, Tan JYY, Loo ES, Phua YW, Chan XLS, Syn CKC. Artificial neural network, predictor variables and sensitivity threshold for DNA methylation-based age prediction using blood samples. Sci Rep 2021; 11:1744. [PMID: 33462351 PMCID: PMC7814006 DOI: 10.1038/s41598-021-81556-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 12/29/2020] [Indexed: 12/21/2022] Open
Abstract
Regression models are often used to predict age of an individual based on methylation patterns. Artificial neural network (ANN) however was recently shown to be more accurate for age prediction. Additionally, the impact of ethnicity and sex on our previous regression model have not been studied. Furthermore, there is currently no age prediction study investigating the lower limit of input DNA at the bisulfite treatment stage prior to pyrosequencing. Herein, we evaluated both regression and ANN models, and the impact of ethnicity and sex on age prediction for 333 local blood samples using three loci on the pyrosequencing platform. Subsequently, we trained a one locus-based ANN model to reduce the amount of DNA used. We demonstrated that the ANN model has a higher accuracy of age prediction than the regression model. Additionally, we showed that ethnicity did not affect age prediction among local Chinese, Malays and Indians. Although the predicted age of males were marginally overestimated, sex did not impact the accuracy of age prediction. Lastly, we present a one locus, dual CpG model using 25 ng of input DNA that is sufficient for forensic age prediction. In conclusion, the two ANN models validated would be useful for age prediction to provide forensic intelligence leads.
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Affiliation(s)
- Zhonghui Thong
- DNA Profiling Laboratory, Biology Division, Health Sciences Authority, 11 Outram Road, Singapore, 169078, Singapore.
| | - Jolena Ying Ying Tan
- DNA Profiling Laboratory, Biology Division, Health Sciences Authority, 11 Outram Road, Singapore, 169078, Singapore
| | - Eileen Shuzhen Loo
- DNA Profiling Laboratory, Biology Division, Health Sciences Authority, 11 Outram Road, Singapore, 169078, Singapore
| | - Yu Wei Phua
- DNA Profiling Laboratory, Biology Division, Health Sciences Authority, 11 Outram Road, Singapore, 169078, Singapore
| | - Xavier Liang Shun Chan
- DNA Profiling Laboratory, Biology Division, Health Sciences Authority, 11 Outram Road, Singapore, 169078, Singapore
| | - Christopher Kiu-Choong Syn
- DNA Profiling Laboratory, Biology Division, Health Sciences Authority, 11 Outram Road, Singapore, 169078, Singapore
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33
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Soedarsono N, Hanafi MS, Auerkari E. Biological age estimation using DNA methylation analysis: A systematic review. SCIENTIFIC DENTAL JOURNAL 2021. [DOI: 10.4103/sdj.sdj_27_20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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34
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Maulani C, Auerkari EI. Age estimation using DNA methylation technique in forensics: a systematic review. EGYPTIAN JOURNAL OF FORENSIC SCIENCES 2020. [DOI: 10.1186/s41935-020-00214-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
AbstractBackgroundIn addition to the DNA sequence, epigenetic markers have become substantial forensic tools during the last decade. Estimating the age of an individual from human biological remains may provide information for a forensic investigation. Age estimation in molecular strategies can be obtained by telomere length, mRNa mutation, or by sjTRECs but the accuracy is not sufficient in forensic practice because of high margin error.Main bodyOne solution to this problem is to use DNA methylation methods. DNA methylation markers for tissue identification at age-associated CpG sites have been suggested as the most informative biomarkers for estimating the age of an unknown donor. This review aims to give an overview of DNA methylation profiling for estimating the age in cases of forensic relevance and the important aspects in determining the mean absolute deviation (MAD) or mean absolute error (MAE) of the estimated age. Online database searching was performed through PubMed, Scopus, and Google Scholar with keywords selected for forensic age estimation. Thirty-two studies were included in the review, with variable DNA samples but blood commonly as a source. Pyrosequencing and EpiTYPER were methods mostly used in DNA analysis. The MAD in the estimates from DNA methylation was about 3 to 5 years, which was better than other methods such as those based on telomere length or signal-joint T-cell receptor excision circles. The ELOVL2 gene was a commonly used DNA methylation marker in age estimation.ConclusionDNA methylation is a favorable candidate for estimating the age at the time of death in forensic profiling, with an uncertainty mean absolute deviation of about 3 to 5 years in the predicted age. The sample type, platform techniques used, and methods to construct age predictive models were important in determining the accuracy in mean absolute deviation or mean absolute error. The DNA methylation outcome suggests good potential to support conventional STR profiling in forensic cases.
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Sukawutthiya P, Sathirapatya T, Vongpaisarnsin K. A minimal number CpGs of ELOVL2 gene for a chronological age estimation using pyrosequencing. Forensic Sci Int 2020; 318:110631. [PMID: 33279766 DOI: 10.1016/j.forsciint.2020.110631] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 11/17/2020] [Accepted: 11/25/2020] [Indexed: 10/22/2022]
Abstract
Chronological age estimation is an important piece of human identification used in forensic practice. Epigenetic modifications, especially DNA methylation, have been proposed to predict age. The methylation of the ELOVL2 gene is one of the age-related markers that could be tested in fresh or postmortem blood sample. We study the use of DNA methylation markers on the ELOVL2 gene and develop a prediction model to estimate the age from a postmortem blood sample using pyrosequencing. From 100 anonymous blood samples, a correlation study of DNA methylation and age was investigated. The regression analysis revealed 2 CpG sites for model prediction with an adjusted R2 value of 0.7 (p < 0.01). The model explained 74% of the variation in postmortem blood samples (n = 36) with a prediction error (RMSE) of 10.2 years and a mean absolute deviation (MAD) of 7.1 years, whereas the model (excluding a younger age group) had improved with a RMSE of 5.6 years and a MAD of 4.2 years. The performance parameters were analyzed in several simulated models and indicated that these markers are advantageous for age estimation in forensic scenarios. Finally, a robustness and reproducibility of the pyrosequencing technique would enable this approach to be the part of an age prediction in forensic investigation.
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Affiliation(s)
- Poonyapat Sukawutthiya
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Forensic Genetics Research Unit, Ratchadapiseksompotch Fund, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Tikumphorn Sathirapatya
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Forensic Genetics Research Unit, Ratchadapiseksompotch Fund, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Kornkiat Vongpaisarnsin
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Forensic Serology and DNA, King Chulalongkorn Memorial Hospital and Thai Red Cross Society, Bangkok, Thailand; Forensic Genetics Research Unit, Ratchadapiseksompotch Fund, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
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Kothapalli KSD, Park HG, Brenna JT. Polyunsaturated fatty acid biosynthesis pathway and genetics. implications for interindividual variability in prothrombotic, inflammatory conditions such as COVID-19 ✰,✰✰,★,★★. Prostaglandins Leukot Essent Fatty Acids 2020; 162:102183. [PMID: 33038834 PMCID: PMC7527828 DOI: 10.1016/j.plefa.2020.102183] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/29/2020] [Accepted: 09/29/2020] [Indexed: 12/15/2022]
Abstract
COVID-19 symptoms vary from silence to rapid death, the latter mediated by both a cytokine storm and a thrombotic storm. SARS-CoV (2003) induces Cox-2, catalyzing the synthesis, from highly unsaturated fatty acids (HUFA), of eicosanoids and docosanoids that mediate both inflammation and thrombosis. HUFA balance between arachidonic acid (AA) and other HUFA is a likely determinant of net signaling to induce a healthy or runaway physiological response. AA levels are determined by a non-protein coding regulatory polymorphisms that mostly affect the expression of FADS1, located in the FADS gene cluster on chromosome 11. Major and minor haplotypes in Europeans, and a specific functional insertion-deletion (Indel), rs66698963, consistently show major differences in circulating AA (>50%) and in the balance between AA and other HUFA (47-84%) in free living humans; the indel is evolutionarily selective, probably based on diet. The pattern of fatty acid responses is fully consistent with specific genetic modulation of desaturation at the FADS1-mediated 20:3→20:4 step. Well established principles of net tissue HUFA levels indicate that the high linoleic acid and low alpha-linoleic acid in populations drive the net balance of HUFA for any individual. We predict that fast desaturators (insertion allele at rs66698963; major haplotype in Europeans) are predisposed to higher risk and pathological responses to SARS-CoV-2 could be reduced with high dose omega-3 HUFA.
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Affiliation(s)
- Kumar S D Kothapalli
- Dell Pediatric Research Institute, Depts of Pediatrics, of Chemistry, and of Nutrition, University of Texas at Austin, 1400 Barbara Jordan Blvd, Austin, TX, United States.
| | - Hui Gyu Park
- Dell Pediatric Research Institute, Depts of Pediatrics, of Chemistry, and of Nutrition, University of Texas at Austin, 1400 Barbara Jordan Blvd, Austin, TX, United States.
| | - J Thomas Brenna
- Dell Pediatric Research Institute, Depts of Pediatrics, of Chemistry, and of Nutrition, University of Texas at Austin, 1400 Barbara Jordan Blvd, Austin, TX, United States; Division of Nutritional Sciences, Cornell University, Ithaca, NY, United States.
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Daca-Roszak P, Jaksik R, Paczkowska J, Witt M, Ziętkiewicz E. Discrimination between human populations using a small number of differentially methylated CpG sites: a preliminary study using lymphoblastoid cell lines and peripheral blood samples of European and Chinese origin. BMC Genomics 2020; 21:706. [PMID: 33045984 PMCID: PMC7549247 DOI: 10.1186/s12864-020-07092-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 09/22/2020] [Indexed: 02/08/2023] Open
Abstract
Background Epigenetics is one of the factors shaping natural variability observed among human populations. A small proportion of heritable inter-population differences are observed in the context of both the genome-wide methylation level and the methylation status of individual CpG sites. It has been demonstrated that a limited number of carefully selected differentially methylated sites may allow discrimination between main human populations. However, most of the few published results have been performed exclusively on B-lymphocyte cell lines. Results The goal of our study was to identify a set of CpG sites sufficient to discriminate between populations of European and Chinese ancestry based on the difference in the DNA methylation profile not only in cell lines but also in primary cell samples. The preliminary selection of CpG sites differentially methylated in these two populations (pop-CpGs) was based on the analysis of two groups of commercially available ethnically-specific B-lymphocyte cell lines, performed using Illumina Infinium Human Methylation 450 BeadChip Array. A subset of 10 pop-CpGs characterized by the best differentiating criteria (|Mdiff| > 1, q < 0.05; lack of the confounding genomic features), and 10 additional CpGs in their immediate vicinity, were further tested using pyrosequencing technology in both B-lymphocyte cell lines and in the primary samples of the peripheral blood representing two analyzed populations. To assess the population-discriminating potential of the selected set of CpGs (further referred to as “composite pop (CEU-CHB)-CpG marker”), three classification methods were applied. The predictive ability of the composite 8-site pop (CEU-CHB)-CpG marker was assessed using 10-fold cross-validation method on two independent sets of samples. Conclusions Our results showed that less than 10 pop-CpG sites may distinguish populations of European and Chinese ancestry; importantly, this small composite pop-CpG marker performs well in both lymphoblastoid cell lines and in non-homogenous blood samples regardless of a gender.
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Affiliation(s)
- Patrycja Daca-Roszak
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479, Poznan, Poland.
| | - Roman Jaksik
- Silesian University of Technology, Akademicka 16, 44-100, Gliwice, Poland
| | - Julia Paczkowska
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479, Poznan, Poland
| | - Michał Witt
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479, Poznan, Poland
| | - Ewa Ziętkiewicz
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479, Poznan, Poland
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Correia Dias H, Cunha E, Corte Real F, Manco L. Age prediction in living: Forensic epigenetic age estimation based on blood samples. Leg Med (Tokyo) 2020; 47:101763. [PMID: 32721866 DOI: 10.1016/j.legalmed.2020.101763] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/26/2020] [Accepted: 07/16/2020] [Indexed: 10/23/2022]
Abstract
DNA methylation analysis in a variety of genes has brought promising results in age estimation. The main aim of this study was to evaluate DNA methylation levels from four age-correlated genes, ELOVL2, FHL2, EDARADD and PDE4C, in blood samples of healthy Portuguese individuals. Fifty-three samples were analyzed through the bisulfite polymerase chain reaction (PCR) sequencing method for CpG dinucleotide methylation status. Linear regression models were used to analyze relationships between methylation levels and chronological age. The highest age-associated CpG in each locus was chosen to build a multi-locus age prediction model (APM), allowing to obtain a Mean Absolute Deviation (MAD) between chronological and predicted ages of 5.35 years, explaining 94.1% of age variation. Validation approaches demonstrated the accuracy and reproducibility of the proposed multi-locus APM. Testing the APM in 51 blood samples from deceased individuals a MAD of 9.72 years was obtained. Potential differences in methylation status between samples from living and deceased individuals could exist since the highest age-correlated CpGs were different in some genes between both groups. In conclusion, our study using the bisulfite PCR sequencing method is in accordance with the high age prediction accuracy of DNA methylation levels in four previously reported age-associated genes. DNA methylation pattern differences between blood samples from living and deceased individuals should be taken into account in forensic contexts.
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Affiliation(s)
- Helena Correia Dias
- Research Centre for Anthropology and Health (CIAS), Department of Life Sciences, University of Coimbra, Portugal; Centre for Functional Ecology (CEF), Laboratory of Forensic Anthropology, Department of Life Sciences, University of Coimbra, Portugal; National Institute of Legal Medicine and Forensic Sciences, Portugal
| | - Eugénia Cunha
- Centre for Functional Ecology (CEF), Laboratory of Forensic Anthropology, Department of Life Sciences, University of Coimbra, Portugal; National Institute of Legal Medicine and Forensic Sciences, Portugal
| | - Francisco Corte Real
- National Institute of Legal Medicine and Forensic Sciences, Portugal; Faculty of Medicine, University of Coimbra, Portugal
| | - Licínio Manco
- Research Centre for Anthropology and Health (CIAS), Department of Life Sciences, University of Coimbra, Portugal.
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Koop BE, Reckert A, Becker J, Han Y, Wagner W, Ritz-Timme S. Epigenetic clocks may come out of rhythm-implications for the estimation of chronological age in forensic casework. Int J Legal Med 2020; 134:2215-2228. [PMID: 32661599 PMCID: PMC7578121 DOI: 10.1007/s00414-020-02375-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 07/08/2020] [Indexed: 01/01/2023]
Abstract
There is a growing perception that DNA methylation may be influenced by exogenous and endogenous parameters. Knowledge of these factors is of great relevance for the interpretation of DNA-methylation data for the estimation of chronological age in forensic casework. We performed a literature review to identify parameters, which might be of relevance for the prediction of chronological age based on DNA methylation. The quality of age predictions might particularly be influenced by lifetime adversities (chronic stress, trauma/post-traumatic stress disorder (PTSD), violence, low socioeconomic status/education), cancer, obesity and related diseases, infectious diseases (especially HIV and Cytomegalovirus (CMV) infections), sex, ethnicity and exposure to toxins (alcohol, smoking, air pollution, pesticides). Such factors may alter the DNA methylation pattern and may explain the partly high deviations between epigenetic age and chronological age in single cases (despite of low mean absolute deviations) that can also be observed with “epigenetic clocks” comprising a high number of CpG sites. So far, only few publications dealing with forensic age estimation address these confounding factors. Future research should focus on the identification of further relevant confounding factors and the development of models that are “robust” against the influence of such biological factors by systematic investigations under targeted inclusion of diverse and defined cohorts.
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Affiliation(s)
- Barbara Elisabeth Koop
- Institute of Legal Medicine, University Hospital Düsseldorf, 40225, Düsseldorf, Germany.
| | - Alexandra Reckert
- Institute of Legal Medicine, University Hospital Düsseldorf, 40225, Düsseldorf, Germany
| | - Julia Becker
- Institute of Legal Medicine, University Hospital Düsseldorf, 40225, Düsseldorf, Germany
| | - Yang Han
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen Faculty of Medicine, Aachen, Germany
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen Faculty of Medicine, Aachen, Germany
| | - Stefanie Ritz-Timme
- Institute of Legal Medicine, University Hospital Düsseldorf, 40225, Düsseldorf, Germany
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Chen X, Shi W, Zhang H. The role of KLF14 in multiple disease processes. Biofactors 2020; 46:276-282. [PMID: 31925990 DOI: 10.1002/biof.1612] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 10/31/2019] [Indexed: 12/13/2022]
Abstract
Kruppel-like factor 14 (KLF14) is a newly identified member of the KLF family. Expression of KLF14 is induced by TGF-β in intrauterine and ectodermal tissue. Initial researches on KLF14 focused on its role in lipid and glucose metabolism. In recent years, however, the role of KLF14 in regulating cell signaling pathways, cell proliferation and differentiation has been explored. Moreover, the research has gradually extended into the field of tumorigenesis and immune regulation. This paper aims to briefly review the functions of KLF14 in physiologyical and pathological process.
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Affiliation(s)
- Xiaoyan Chen
- Department of Gastroenterology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wenjie Shi
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Heng Zhang
- Department of Gastroenterology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Xie T, Shen C, Liu C, Fang Y, Guo Y, Lan Q, Wang L, Ge J, Zhou Y, Wen S, Yang Q, Zhu B. Ancestry inference and admixture component estimations of Chinese Kazak group based on 165 AIM-SNPs via NGS platform. J Hum Genet 2020; 65:461-468. [DOI: 10.1038/s10038-020-0725-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 11/04/2019] [Accepted: 11/04/2019] [Indexed: 11/09/2022]
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Gatev E, Gladish N, Mostafavi S, Kobor MS. CoMeBack: DNA methylation array data analysis for co-methylated regions. Bioinformatics 2020; 36:2675-2683. [DOI: 10.1093/bioinformatics/btaa049] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 12/23/2019] [Accepted: 01/20/2020] [Indexed: 01/06/2023] Open
Abstract
Abstract
Motivation
High-dimensional DNA methylation (DNAm) array coverage, while sparse in the context of the entire DNA methylome, still constitutes a very large number of CpG probes. The ensuing multiple-test corrections affect the statistical power to detect associations, likely contributing to prevalent limited reproducibility. Array probes measuring proximal CpG sites often have correlated levels of DNAm that may not only be biologically meaningful but also imply statistical dependence and redundancy. New methods that account for such correlations between adjacent probes may enable improved specificity, discovery and interpretation of statistical associations in DNAm array data.
Results
We developed a method named Co-Methylation with genomic CpG Background (CoMeBack) that estimates DNA co-methylation, defined as proximal CpG probes with correlated DNAm across individuals. CoMeBack outputs co-methylated regions (CMRs), spanning sets of array probes constructed based on all genomic CpG sites, including those not measured on the array, and without any phenotypic variable inputs. This approach can reduce the multiple-test correction burden, while enhancing the discovery and specificity of statistical associations. We constructed and validated CMRs in whole blood, using publicly available Illumina Infinium 450 K array data from over 5000 individuals. These CMRs were enriched for enhancer chromatin states, and binding site motifs for several transcription factors involved in blood physiology. We illustrated how CMR-based epigenome-wide association studies can improve discovery and reduce false positives for associations with chronological age.
Availability and implementation
https://bitbucket.org/flopflip/comeback.
Supplementary information
Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Evan Gatev
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC V5T 4S6, Canada
- Department of Finance, Beedie School of Business, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
- BC Children’s Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada
- Centre for Molecular Medicine and Therapeutics, Vancouver, BC V5Z 4H4, Canada
| | - Nicole Gladish
- BC Children’s Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada
- Centre for Molecular Medicine and Therapeutics, Vancouver, BC V5Z 4H4, Canada
- Department of Medical Genetics
| | - Sara Mostafavi
- BC Children’s Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada
- Centre for Molecular Medicine and Therapeutics, Vancouver, BC V5Z 4H4, Canada
- Department of Medical Genetics
- Department of Statistics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Michael S Kobor
- BC Children’s Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada
- Centre for Molecular Medicine and Therapeutics, Vancouver, BC V5Z 4H4, Canada
- Department of Medical Genetics
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Márquez-Ruiz AB, González-Herrera L, Luna JDD, Valenzuela A. DNA methylation levels and telomere length in human teeth: usefulness for age estimation. Int J Legal Med 2020; 134:451-459. [PMID: 31897670 DOI: 10.1007/s00414-019-02242-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 12/19/2019] [Indexed: 01/26/2023]
Abstract
In the last decade, increasing knowledge of epigenetics has led to the development of DNA methylation-based models to predict age, which have shown high predictive accuracy. However, despite the value of teeth as forensic samples, few studies have focused on this source of DNA. This study used bisulfite pyrosequencing to measure the methylation levels of specific CpG sites located in the ELOVL2, ASPA, and PDE4C genes, with the aim of selecting the most age-informative genes and determining their associations with age, in 65 tooth samples from individuals 15 to 85 years old. As a second aim, methylation data and measurements of relative telomere length in the same set of samples were used to develop preliminary age prediction models to evaluate the accuracy of both biomarkers together and separately in estimating age from teeth for forensic purposes. In our sample, several CpG sites from ELOVL2 and PDE4C genes, as well as telomere length, were significantly associated with chronological age. We developed age prediction quantile regression models based on DNA methylation levels, with and without telomere length as an additional variable, and adjusted for type of tooth and sex. Our results suggest that telomere length may have limited usefulness as a supplementary marker for DNA methylation-based age estimation in tooth samples, given that it contributed little improvement in the prediction errors of the models. In addition, even at older ages, DNA methylation appeared to be more informative in predicting age than telomere length when both biomarkers were evaluated separately.
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Affiliation(s)
- Ana Belén Márquez-Ruiz
- Department of Forensic Medicine, Faculty of Medicine, University of Granada, Avda. de la Investigación, 11, 18016, Granada, Spain.
| | - Lucas González-Herrera
- Department of Forensic Medicine, Faculty of Medicine, University of Granada, Avda. de la Investigación, 11, 18016, Granada, Spain
| | - Juan de Dios Luna
- Department of Statistics, Faculty of Medicine, University of Granada, Avda. de la Investigación, 11, 18016, Granada, Spain
| | - Aurora Valenzuela
- Department of Forensic Medicine, Faculty of Medicine, University of Granada, Avda. de la Investigación, 11, 18016, Granada, Spain
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Zhu T, Gao Y, Wang J, Li X, Shang S, Wang Y, Guo S, Zhou H, Liu H, Sun D, Chen H, Wang L, Ning S. CancerClock: A DNA Methylation Age Predictor to Identify and Characterize Aging Clock in Pan-Cancer. Front Bioeng Biotechnol 2019; 7:388. [PMID: 31867319 PMCID: PMC6905170 DOI: 10.3389/fbioe.2019.00388] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 11/18/2019] [Indexed: 01/12/2023] Open
Abstract
Many biological indicators related to chronological age have been proposed. Recent studies found that epigenetic clock or DNA methylation age is highly correlated with chronological age. In particular, a significant difference between DNA methylation age (m-age) and chronological age was observed in cancers. However, the prediction and characterization of m-age in pan-cancer remains an explored area. In this study, 1,631 age-related methylation sites in normal tissues were discovered and analyzed. A comprehensive computational model named CancerClock was constructed to predict the m-age for normal samples based on methylation levels of the extracted methylation sites. LASSO linear regression model was used to screen and train the CancerClock model in normal tissues. The accuracy of CancerClock has proved to be 81%, and the correlation value between chronological age and m-age was 0.939 (P < 0.01). Next, CancerClock was used to evaluate the difference between m-age and chronological age for 33 cancer types from TCGA. There were significant differences between predicted m-age and chronological age in large number of cancer samples. These cancer samples were defined as “age-related cancer samples” and they have some differential methylation sites. The differences between predicted m-age and chronological age may contribute to cancer development. Some of these differential methylation sites were associated with cancer survival. CancerClock provided assistance in estimating the m-age in normal and cancer samples. The changes between m-age and chronological age may improve the diagnosis and prognosis of cancers.
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Affiliation(s)
- Tongtong Zhu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yue Gao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Junwei Wang
- Department of Respiratory Medicine, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xin Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Shipeng Shang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yanxia Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Shuang Guo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Hanxiao Zhou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Hongjia Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Dailin Sun
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Hong Chen
- Department of Respiratory Medicine, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Li Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Shangwei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
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Deák F, Anderson RE, Fessler JL, Sherry DM. Novel Cellular Functions of Very Long Chain-Fatty Acids: Insight From ELOVL4 Mutations. Front Cell Neurosci 2019; 13:428. [PMID: 31616255 PMCID: PMC6763723 DOI: 10.3389/fncel.2019.00428] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 09/06/2019] [Indexed: 12/22/2022] Open
Abstract
Elongation of Very Long chain fatty acids-4 (ELOVL4) protein is a member of the ELOVL family of fatty acid elongases that is collectively responsible for catalyzing formation of long chain fatty acids. ELOVL4 is the only family member that catalyzes production of Very Long Chain Saturated Fatty Acids (VLC-SFA) and Very Long Chain Polyunsaturated Fatty Acids (VLC-PUFA) with chain lengths ≥28 carbons. ELOVL4 and its VLC-SFA and VLC-PUFA products are emerging as important regulators of synaptic signaling and neuronal survival in the central nervous system (CNS). Distinct sets of mutations in ELOVL4 cause three different neurological diseases in humans. Heterozygous inheritance of one set of autosomal dominant ELOVL4 mutations that leads to truncation of the ELOVL4 protein causes Stargardt-like macular dystrophy (STGD3), an aggressive juvenile-onset retinal degeneration. Heterozygous inheritance of a different set of autosomal dominant ELOVL4 mutations that leads to a full-length protein with single amino acid substitutions causes spinocerebellar ataxia 34 (SCA34), a late-onset neurodegenerative disease characterized by gait ataxia and cerebellar atrophy. Homozygous inheritance of a different set of ELOVL4 mutations causes a more severe disease with infantile onset characterized by seizures, spasticity, intellectual disability, ichthyosis, and premature death. ELOVL4 is expressed widely in the CNS and is found primarily in neurons. ELOVL4 is expressed in cell-specific patterns within different regions of the CNS that are likely to be related to disease symptoms. In the retina, ELOVL4 is expressed exclusively in photoreceptors and produces VLC-PUFA that are incorporated into phosphatidylcholine and enriched in the light sensitive membrane disks of the photoreceptor outer segments. VLC-PUFA are enzymatically converted into "elovanoid" compounds that appear to provide paracrine signals that promote photoreceptor and neuronal survival. In the brain, the main ELOVL4 products are VLC-SFA that are incorporated into sphingolipids and enriched in synaptic vesicles, where they regulate kinetics of presynaptic neurotransmitter release. Understanding the function of ELOVL4 and its VLC-SFA and VLC-PUFA products will advance our understanding of basic mechanisms in neural signaling and has potential for developing novel therapies for seizure and neurodegenerative diseases.
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Affiliation(s)
- Ferenc Deák
- Department of Geriatric Medicine, Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States.,Oklahoma Center for Neurosciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States.,Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Robert E Anderson
- Department of Geriatric Medicine, Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States.,Oklahoma Center for Neurosciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States.,Dean McGee Eye Institute, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States.,Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States.,Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Jennifer L Fessler
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - David M Sherry
- Oklahoma Center for Neurosciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States.,Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States.,Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
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46
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Spólnicka M, Pośpiech E, Adamczyk JG, Freire-Aradas A, Pepłońska B, Zbieć-Piekarska R, Makowska Ż, Pięta A, Lareu MV, Phillips C, Płoski R, Żekanowski C, Branicki W. Modified aging of elite athletes revealed by analysis of epigenetic age markers. Aging (Albany NY) 2019; 10:241-252. [PMID: 29466246 PMCID: PMC5842850 DOI: 10.18632/aging.101385] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 02/09/2018] [Indexed: 11/25/2022]
Abstract
Recent progress in epigenomics has led to the development of prediction systems that enable accurate age estimation from DNA methylation data. Our objective was to track responses to intense physical exercise of individual age-correlated DNA methylation markers and to infer their potential impact on the aging processes. The study showed accelerated DNA hypermethylation for two CpG sites in TRIM59 and KLF14. Both markers predicted the investigated elite athletes to be several years older than controls and this effect was more substantial in subjects involved in power sports. Accordingly, the complete 5-CpG model revealed age acceleration of elite athletes (P=1.503x10-7) and the result was more significant amongst power athletes (P=1.051x10-9). The modified methylation of TRIM59 and KLF14 in top athletes may be accounted for by the biological roles played by these genes. Their known anti-tumour and anti-inflammatory activities suggests that intense physical training has a complex influence on aging and potentially launches signalling networks that contribute to the observed lower risk of elite athletes to develop cardiovascular disease and cancer.
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Affiliation(s)
| | - Ewelina Pośpiech
- Malopolska Centre of Biotechnology of the Jagiellonian University, Krakow, Poland
| | - Jakub Grzegorz Adamczyk
- Department of Theory of Sport, Józef Pilsudski University of Physical Education in Warsaw, Warsaw, Poland.,Department of Rehabilitation, Physiotherapy Division, Medical University of Warsaw, Warsaw, Poland
| | - Ana Freire-Aradas
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Beata Pepłońska
- Laboratory of Neurogenetics, Department of Neurodegenerative Disorders, Mossakowski Medical Research Centre, Polish Academy of Sciences, Warsaw, Poland
| | | | | | - Anna Pięta
- Central Forensic Laboratory of the Police, Warsaw, Poland
| | - Maria Victoria Lareu
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Christopher Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Rafał Płoski
- Department of Medical Genetics, Centre for Biostructure, Medical University of Warsaw, Warsaw, Poland
| | - Cezary Żekanowski
- Department of Theory of Sport, Józef Pilsudski University of Physical Education in Warsaw, Warsaw, Poland
| | - Wojciech Branicki
- Central Forensic Laboratory of the Police, Warsaw, Poland.,Malopolska Centre of Biotechnology of the Jagiellonian University, Krakow, Poland
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47
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Correia Dias H, Cordeiro C, Corte Real F, Cunha E, Manco L. Age Estimation Based on DNA Methylation Using Blood Samples From Deceased Individuals. J Forensic Sci 2019; 65:465-470. [PMID: 31490551 DOI: 10.1111/1556-4029.14185] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 08/09/2019] [Accepted: 08/14/2019] [Indexed: 12/13/2022]
Abstract
Age estimation using DNA methylation levels has been widely investigated in recent years because of its potential application in forensic genetics. The main aim of this study was to develop an age predictor model (APM) for blood samples of deceased individuals based in five age-correlated genes. Fifty-one samples were analyzed through the bisulfite polymerase chain reaction (PCR) sequencing method for DNA methylation evaluation in genes ELOVL2, FHL2, EDARADD, PDE4C, and C1orf132. Linear regression was used to analyze relationships between methylation levels and age. The model using the highest age-correlated CpG from each locus revealed a correlation coefficient of 0.888, explaining 76.3% of age variation, with a mean absolute deviation from the chronological age (MAD) of 6.08 years. The model was validated in an independent test set of 19 samples producing a MAD of 8.84 years. The developed APM seems to be informative and could have potential application in forensic analysis.
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Affiliation(s)
- Helena Correia Dias
- Department of Life Sciences, Research Centre for Anthropology and Health (CIAS), University of Coimbra, Coimbra, Portugal.,Department of Life Sciences, Laboratory of Forensic Anthropology, Centre for Functional Ecology (CEF), University of Coimbra, Coimbra, Portugal.,National Institute of Legal Medicine and Forensic Sciences, Coimbra, Portugal
| | - Cristina Cordeiro
- National Institute of Legal Medicine and Forensic Sciences, Coimbra, Portugal.,Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Francisco Corte Real
- National Institute of Legal Medicine and Forensic Sciences, Coimbra, Portugal.,Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Eugénia Cunha
- Department of Life Sciences, Laboratory of Forensic Anthropology, Centre for Functional Ecology (CEF), University of Coimbra, Coimbra, Portugal.,National Institute of Legal Medicine and Forensic Sciences, Coimbra, Portugal
| | - Licínio Manco
- Department of Life Sciences, Research Centre for Anthropology and Health (CIAS), University of Coimbra, Coimbra, Portugal
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48
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Gensous N, Bacalini MG, Franceschi C, Meskers CGM, Maier AB, Garagnani P. Age-Related DNA Methylation Changes: Potential Impact on Skeletal Muscle Aging in Humans. Front Physiol 2019; 10:996. [PMID: 31427991 PMCID: PMC6688482 DOI: 10.3389/fphys.2019.00996] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 07/18/2019] [Indexed: 12/27/2022] Open
Abstract
Human aging is accompanied by a decline in muscle mass and muscle function, which is commonly referred to as sarcopenia. Sarcopenia is associated with detrimental clinical outcomes, such as a reduced quality of life, frailty, an increased risk of falls, fractures, hospitalization, and mortality. The exact underlying mechanisms of sarcopenia are poorly delineated and the molecular mechanisms driving the development and progression of this disorder remain to be uncovered. Previous studies have described age-related differences in gene expression, with one study identifying an age-specific expression signature of sarcopenia, but little is known about the influence of epigenetics, and specially of DNA methylation, in its pathogenesis. In this review, we will focus on the available knowledge in literature on the characterization of DNA methylation profiles during skeletal muscle aging and the possible impact of physical activity and nutrition. We will consider the possible use of the recently developed DNA methylation-based biomarkers of aging called epigenetic clocks in the assessment of physical performance in older individuals. Finally, we will discuss limitations and future directions of this field.
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Affiliation(s)
- Noémie Gensous
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | | | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy.,Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Carel G M Meskers
- Amsterdam UMC, Department of Rehabilitation Medicine, Amsterdam Movement Sciences, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Andrea B Maier
- Department of Human Movement Sciences, @AgeAmsterdam, Faculty of Behavioural and Movement Sciences, Amsterdam Movement Sciences, Vrije Universiteit Amsterdam, Amsterdam, Netherlands.,Department of Medicine and Aged Care, @AgeMelbourne, The Royal Melbourne Hospital, The University of Melbourne, Melbourne, VIC, Australia
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy.,Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.,Applied Biomedical Research Center (CRBA), Policlinico S.Orsola-Malpighi Polyclinic, Bologna, Italy.,CNR Institute of Molecular Genetics, Unit of Bologna, Bologna, Italy
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49
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Xin Y, Dong K, Cao F, Tian Y, Sun J, Peng M, Liu W, Shi P. Studies of hTERT DNA methylation assays on the human age prediction. Int J Legal Med 2019; 133:1333-1339. [PMID: 31165262 DOI: 10.1007/s00414-019-02076-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 05/17/2019] [Indexed: 11/25/2022]
Abstract
As an important aspect of epigenetics, DNA methylation has been proven to be suitable for forensic DNA analysis. By detecting changes in DNA methylation, it is desirable to construct a model of age patterns associated with it to infer the age of the individual. The hTERT gene methylation is closely related to tumors, but there are few reports on the relationship between hTERT gene promoter methylation and age. In this study, we utilized the methylation-specific polymerase chain reaction and real-time PCR (relative quantification and absolute quantification) approach to explore the connection between hTERT DNA methylation and age prediction. We fit three models for age prediction based on methylation assay for 90 blood samples from donors aged 1-79 years old. Among them, the model of absolute quantification of real-time enabled the age prediction with R2 = 0.9634. We verified the linear regression model with a validation set of 30 blood samples where prediction average error was 4.29 years. Generally, this reliable method improves the DNA methylation analysis of forensic samples.
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Affiliation(s)
- Ye Xin
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Kaikai Dong
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Fangqi Cao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
- Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Zhongshan North No 1 Road, Shanghai, 200083, China
| | - Yuxiang Tian
- Department of Clinical Laboratory, Shanghai Xuhui District Dahua Hospital, Shanghai, 200237, China
| | - Jing Sun
- Qinghai Provincial Key Laboratory of Qinghai-Tibet Plateau Biological Resources, Northwest Institute of Plateau Biology, The Chinese Academy of Sciences, Xiguan Avenue 59, Xining, 11 Qinghai Province, 810001, China
| | - Min Peng
- Qinghai Provincial Key Laboratory of Qinghai-Tibet Plateau Biological Resources, Northwest Institute of Plateau Biology, The Chinese Academy of Sciences, Xiguan Avenue 59, Xining, 11 Qinghai Province, 810001, China
| | - Wenbin Liu
- Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Zhongshan North No 1 Road, Shanghai, 200083, China.
| | - Ping Shi
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.
- Qinghai Provincial Key Laboratory of Qinghai-Tibet Plateau Biological Resources, Northwest Institute of Plateau Biology, The Chinese Academy of Sciences, Xiguan Avenue 59, Xining, 11 Qinghai Province, 810001, China.
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50
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Steiger H, Booij L, Kahan `E, McGregor K, Thaler L, Fletcher E, Labbe A, Joober R, Israël M, Szyf M, Agellon LB, Gauvin L, St-Hilaire A, Rossi E. A longitudinal, epigenome-wide study of DNA methylation in anorexia nervosa: results in actively ill, partially weight-restored, long-term remitted and non-eating-disordered women. J Psychiatry Neurosci 2019; 44:205-213. [PMID: 30693739 PMCID: PMC6488489 DOI: 10.1503/jpn.170242] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 05/30/2018] [Accepted: 09/04/2018] [Indexed: 12/12/2022] Open
Abstract
Background This study explored state-related tendencies in DNA methylation in people with anorexia nervosa. Methods We measured genome-wide DNA methylation in 75 women with active anorexia nervosa (active), 31 women showing stable remission of anorexia nervosa (remitted) and 41 women with no eating disorder (NED). We also obtained post-intervention methylation data from 52 of the women from the active group. Results Comparisons between members of the active and NED groups showed 58 differentially methylated sites (Q < 0.01) that corresponded to genes relevant to metabolic and nutritional status (lipid and glucose metabolism), psychiatric status (serotonin receptor activity) and immune function. Methylation levels in members of the remitted group differed from those in the active group on 265 probes that also involved sites associated with genes for serotonin and insulin activity, glucose metabolism and immunity. Intriguingly, the direction of methylation effects in remitted participants tended to be opposite to those seen in active participants. The chronicity of Illness correlated (usually inversely, at Q < 0.01) with methylation levels at 64 sites that mapped onto genes regulating glutamate and serotonin activity, insulin function and epigenetic age. In contrast, body mass index increases coincided (at Q < 0.05) with generally increased methylation-level changes at 73 probes associated with lipid and glucose metabolism, immune and inflammatory processes, and olfaction. Limitations Sample sizes were modest for this type of inquiry, and findings may have been subject to uncontrolled effects of medication and substance use. Conclusion Findings point to the possibility of reversible epigenetic alterations in anorexia nervosa, and suggest that an adequate pathophysiological model would likely need to include psychiatric, metabolic and immune components.
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Affiliation(s)
- Howard Steiger
- From the Eating Disorders Program, Douglas University Institute (Steiger, Kahan, Thaler, Fletcher, Israël, St-Hilaire, Rossi); the Research Centre, Douglas University Institute (Steiger, Kahan, Thaler, Fletcher, Joober, Israël, St-Hilaire, Rossi); the Department of Psychiatry, McGill University (Steiger, Booij, Thaler, Joober, Israël, St-Hilaire); the Department of Psychology, Concordia University (Booij); the Sainte-Justine Hospital Research Centre, University of Montreal (Booij); the Department of Epidemiology, Biostatistics, and Occupational Health, McGill University (McGregor); the Department of Decision Sciences, HEC Montreal (Labbe); the Department of Pharmacology and Therapeutics, McGill University (Szyf); the School of Human Nutrition, McGill University (Agellon); and the Centre de recherche du Centre Hospitalier, de l’Université de Montréal (CRCHUM) (Gauvin), Montreal, Que., Canada
| | - Linda Booij
- From the Eating Disorders Program, Douglas University Institute (Steiger, Kahan, Thaler, Fletcher, Israël, St-Hilaire, Rossi); the Research Centre, Douglas University Institute (Steiger, Kahan, Thaler, Fletcher, Joober, Israël, St-Hilaire, Rossi); the Department of Psychiatry, McGill University (Steiger, Booij, Thaler, Joober, Israël, St-Hilaire); the Department of Psychology, Concordia University (Booij); the Sainte-Justine Hospital Research Centre, University of Montreal (Booij); the Department of Epidemiology, Biostatistics, and Occupational Health, McGill University (McGregor); the Department of Decision Sciences, HEC Montreal (Labbe); the Department of Pharmacology and Therapeutics, McGill University (Szyf); the School of Human Nutrition, McGill University (Agellon); and the Centre de recherche du Centre Hospitalier, de l’Université de Montréal (CRCHUM) (Gauvin), Montreal, Que., Canada
| | - `Esther Kahan
- From the Eating Disorders Program, Douglas University Institute (Steiger, Kahan, Thaler, Fletcher, Israël, St-Hilaire, Rossi); the Research Centre, Douglas University Institute (Steiger, Kahan, Thaler, Fletcher, Joober, Israël, St-Hilaire, Rossi); the Department of Psychiatry, McGill University (Steiger, Booij, Thaler, Joober, Israël, St-Hilaire); the Department of Psychology, Concordia University (Booij); the Sainte-Justine Hospital Research Centre, University of Montreal (Booij); the Department of Epidemiology, Biostatistics, and Occupational Health, McGill University (McGregor); the Department of Decision Sciences, HEC Montreal (Labbe); the Department of Pharmacology and Therapeutics, McGill University (Szyf); the School of Human Nutrition, McGill University (Agellon); and the Centre de recherche du Centre Hospitalier, de l’Université de Montréal (CRCHUM) (Gauvin), Montreal, Que., Canada
| | - Kevin McGregor
- From the Eating Disorders Program, Douglas University Institute (Steiger, Kahan, Thaler, Fletcher, Israël, St-Hilaire, Rossi); the Research Centre, Douglas University Institute (Steiger, Kahan, Thaler, Fletcher, Joober, Israël, St-Hilaire, Rossi); the Department of Psychiatry, McGill University (Steiger, Booij, Thaler, Joober, Israël, St-Hilaire); the Department of Psychology, Concordia University (Booij); the Sainte-Justine Hospital Research Centre, University of Montreal (Booij); the Department of Epidemiology, Biostatistics, and Occupational Health, McGill University (McGregor); the Department of Decision Sciences, HEC Montreal (Labbe); the Department of Pharmacology and Therapeutics, McGill University (Szyf); the School of Human Nutrition, McGill University (Agellon); and the Centre de recherche du Centre Hospitalier, de l’Université de Montréal (CRCHUM) (Gauvin), Montreal, Que., Canada
| | - Lea Thaler
- From the Eating Disorders Program, Douglas University Institute (Steiger, Kahan, Thaler, Fletcher, Israël, St-Hilaire, Rossi); the Research Centre, Douglas University Institute (Steiger, Kahan, Thaler, Fletcher, Joober, Israël, St-Hilaire, Rossi); the Department of Psychiatry, McGill University (Steiger, Booij, Thaler, Joober, Israël, St-Hilaire); the Department of Psychology, Concordia University (Booij); the Sainte-Justine Hospital Research Centre, University of Montreal (Booij); the Department of Epidemiology, Biostatistics, and Occupational Health, McGill University (McGregor); the Department of Decision Sciences, HEC Montreal (Labbe); the Department of Pharmacology and Therapeutics, McGill University (Szyf); the School of Human Nutrition, McGill University (Agellon); and the Centre de recherche du Centre Hospitalier, de l’Université de Montréal (CRCHUM) (Gauvin), Montreal, Que., Canada
| | - Emilie Fletcher
- From the Eating Disorders Program, Douglas University Institute (Steiger, Kahan, Thaler, Fletcher, Israël, St-Hilaire, Rossi); the Research Centre, Douglas University Institute (Steiger, Kahan, Thaler, Fletcher, Joober, Israël, St-Hilaire, Rossi); the Department of Psychiatry, McGill University (Steiger, Booij, Thaler, Joober, Israël, St-Hilaire); the Department of Psychology, Concordia University (Booij); the Sainte-Justine Hospital Research Centre, University of Montreal (Booij); the Department of Epidemiology, Biostatistics, and Occupational Health, McGill University (McGregor); the Department of Decision Sciences, HEC Montreal (Labbe); the Department of Pharmacology and Therapeutics, McGill University (Szyf); the School of Human Nutrition, McGill University (Agellon); and the Centre de recherche du Centre Hospitalier, de l’Université de Montréal (CRCHUM) (Gauvin), Montreal, Que., Canada
| | - Aurelie Labbe
- From the Eating Disorders Program, Douglas University Institute (Steiger, Kahan, Thaler, Fletcher, Israël, St-Hilaire, Rossi); the Research Centre, Douglas University Institute (Steiger, Kahan, Thaler, Fletcher, Joober, Israël, St-Hilaire, Rossi); the Department of Psychiatry, McGill University (Steiger, Booij, Thaler, Joober, Israël, St-Hilaire); the Department of Psychology, Concordia University (Booij); the Sainte-Justine Hospital Research Centre, University of Montreal (Booij); the Department of Epidemiology, Biostatistics, and Occupational Health, McGill University (McGregor); the Department of Decision Sciences, HEC Montreal (Labbe); the Department of Pharmacology and Therapeutics, McGill University (Szyf); the School of Human Nutrition, McGill University (Agellon); and the Centre de recherche du Centre Hospitalier, de l’Université de Montréal (CRCHUM) (Gauvin), Montreal, Que., Canada
| | - Ridha Joober
- From the Eating Disorders Program, Douglas University Institute (Steiger, Kahan, Thaler, Fletcher, Israël, St-Hilaire, Rossi); the Research Centre, Douglas University Institute (Steiger, Kahan, Thaler, Fletcher, Joober, Israël, St-Hilaire, Rossi); the Department of Psychiatry, McGill University (Steiger, Booij, Thaler, Joober, Israël, St-Hilaire); the Department of Psychology, Concordia University (Booij); the Sainte-Justine Hospital Research Centre, University of Montreal (Booij); the Department of Epidemiology, Biostatistics, and Occupational Health, McGill University (McGregor); the Department of Decision Sciences, HEC Montreal (Labbe); the Department of Pharmacology and Therapeutics, McGill University (Szyf); the School of Human Nutrition, McGill University (Agellon); and the Centre de recherche du Centre Hospitalier, de l’Université de Montréal (CRCHUM) (Gauvin), Montreal, Que., Canada
| | - Mimi Israël
- From the Eating Disorders Program, Douglas University Institute (Steiger, Kahan, Thaler, Fletcher, Israël, St-Hilaire, Rossi); the Research Centre, Douglas University Institute (Steiger, Kahan, Thaler, Fletcher, Joober, Israël, St-Hilaire, Rossi); the Department of Psychiatry, McGill University (Steiger, Booij, Thaler, Joober, Israël, St-Hilaire); the Department of Psychology, Concordia University (Booij); the Sainte-Justine Hospital Research Centre, University of Montreal (Booij); the Department of Epidemiology, Biostatistics, and Occupational Health, McGill University (McGregor); the Department of Decision Sciences, HEC Montreal (Labbe); the Department of Pharmacology and Therapeutics, McGill University (Szyf); the School of Human Nutrition, McGill University (Agellon); and the Centre de recherche du Centre Hospitalier, de l’Université de Montréal (CRCHUM) (Gauvin), Montreal, Que., Canada
| | - Moshe Szyf
- From the Eating Disorders Program, Douglas University Institute (Steiger, Kahan, Thaler, Fletcher, Israël, St-Hilaire, Rossi); the Research Centre, Douglas University Institute (Steiger, Kahan, Thaler, Fletcher, Joober, Israël, St-Hilaire, Rossi); the Department of Psychiatry, McGill University (Steiger, Booij, Thaler, Joober, Israël, St-Hilaire); the Department of Psychology, Concordia University (Booij); the Sainte-Justine Hospital Research Centre, University of Montreal (Booij); the Department of Epidemiology, Biostatistics, and Occupational Health, McGill University (McGregor); the Department of Decision Sciences, HEC Montreal (Labbe); the Department of Pharmacology and Therapeutics, McGill University (Szyf); the School of Human Nutrition, McGill University (Agellon); and the Centre de recherche du Centre Hospitalier, de l’Université de Montréal (CRCHUM) (Gauvin), Montreal, Que., Canada
| | - Luis B. Agellon
- From the Eating Disorders Program, Douglas University Institute (Steiger, Kahan, Thaler, Fletcher, Israël, St-Hilaire, Rossi); the Research Centre, Douglas University Institute (Steiger, Kahan, Thaler, Fletcher, Joober, Israël, St-Hilaire, Rossi); the Department of Psychiatry, McGill University (Steiger, Booij, Thaler, Joober, Israël, St-Hilaire); the Department of Psychology, Concordia University (Booij); the Sainte-Justine Hospital Research Centre, University of Montreal (Booij); the Department of Epidemiology, Biostatistics, and Occupational Health, McGill University (McGregor); the Department of Decision Sciences, HEC Montreal (Labbe); the Department of Pharmacology and Therapeutics, McGill University (Szyf); the School of Human Nutrition, McGill University (Agellon); and the Centre de recherche du Centre Hospitalier, de l’Université de Montréal (CRCHUM) (Gauvin), Montreal, Que., Canada
| | - Lise Gauvin
- From the Eating Disorders Program, Douglas University Institute (Steiger, Kahan, Thaler, Fletcher, Israël, St-Hilaire, Rossi); the Research Centre, Douglas University Institute (Steiger, Kahan, Thaler, Fletcher, Joober, Israël, St-Hilaire, Rossi); the Department of Psychiatry, McGill University (Steiger, Booij, Thaler, Joober, Israël, St-Hilaire); the Department of Psychology, Concordia University (Booij); the Sainte-Justine Hospital Research Centre, University of Montreal (Booij); the Department of Epidemiology, Biostatistics, and Occupational Health, McGill University (McGregor); the Department of Decision Sciences, HEC Montreal (Labbe); the Department of Pharmacology and Therapeutics, McGill University (Szyf); the School of Human Nutrition, McGill University (Agellon); and the Centre de recherche du Centre Hospitalier, de l’Université de Montréal (CRCHUM) (Gauvin), Montreal, Que., Canada
| | - Annie St-Hilaire
- From the Eating Disorders Program, Douglas University Institute (Steiger, Kahan, Thaler, Fletcher, Israël, St-Hilaire, Rossi); the Research Centre, Douglas University Institute (Steiger, Kahan, Thaler, Fletcher, Joober, Israël, St-Hilaire, Rossi); the Department of Psychiatry, McGill University (Steiger, Booij, Thaler, Joober, Israël, St-Hilaire); the Department of Psychology, Concordia University (Booij); the Sainte-Justine Hospital Research Centre, University of Montreal (Booij); the Department of Epidemiology, Biostatistics, and Occupational Health, McGill University (McGregor); the Department of Decision Sciences, HEC Montreal (Labbe); the Department of Pharmacology and Therapeutics, McGill University (Szyf); the School of Human Nutrition, McGill University (Agellon); and the Centre de recherche du Centre Hospitalier, de l’Université de Montréal (CRCHUM) (Gauvin), Montreal, Que., Canada
| | - Erika Rossi
- From the Eating Disorders Program, Douglas University Institute (Steiger, Kahan, Thaler, Fletcher, Israël, St-Hilaire, Rossi); the Research Centre, Douglas University Institute (Steiger, Kahan, Thaler, Fletcher, Joober, Israël, St-Hilaire, Rossi); the Department of Psychiatry, McGill University (Steiger, Booij, Thaler, Joober, Israël, St-Hilaire); the Department of Psychology, Concordia University (Booij); the Sainte-Justine Hospital Research Centre, University of Montreal (Booij); the Department of Epidemiology, Biostatistics, and Occupational Health, McGill University (McGregor); the Department of Decision Sciences, HEC Montreal (Labbe); the Department of Pharmacology and Therapeutics, McGill University (Szyf); the School of Human Nutrition, McGill University (Agellon); and the Centre de recherche du Centre Hospitalier, de l’Université de Montréal (CRCHUM) (Gauvin), Montreal, Que., Canada
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