101
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Lai CH, Chen AT, Burns AB, Sriram K, Luo Y, Tang X, Branciamore S, O'Meally D, Chang SL, Huang PH, Shyy JYJ, Chien S, Rockne RC, Chen ZB. RAMP2-AS1 Regulates Endothelial Homeostasis and Aging. Front Cell Dev Biol 2021; 9:635307. [PMID: 33644072 PMCID: PMC7907448 DOI: 10.3389/fcell.2021.635307] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/22/2021] [Indexed: 01/23/2023] Open
Abstract
The homeostasis of vascular endothelium is crucial for cardiovascular health and endothelial cell (EC) aging and dysfunction could negatively impact vascular function. Leveraging transcriptome profiles from ECs subjected to various stimuli, including time-series data obtained from ECs under physiological pulsatile flow vs. pathophysiological oscillatory flow, we performed principal component analysis (PCA) to identify key genes contributing to divergent transcriptional states of ECs. Through bioinformatics analysis, we identified that a long non-coding RNA (lncRNA) RAMP2-AS1 encoded on the antisense of RAMP2, a determinant of endothelial homeostasis and vascular integrity, is a novel regulator essential for EC homeostasis and function. Knockdown of RAMP2-AS1 suppressed RAMP2 expression and caused EC functional changes promoting aging, including impaired angiogenesis and increased senescence. Our study demonstrates an integrative approach to quantifying EC aging based on transcriptome changes, which also identified a number of novel regulators, including protein-coding genes and many lncRNAs involved EC functional modulation, exemplified by RAMP2-AS1.
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Affiliation(s)
- Chih-Hung Lai
- Department of Diabetes Complications and Metabolism, City of Hope, Duarte, CA, United States.,Cardiovascular Center, Taichung Veterans General Hospital, Taichung, Taiwan.,Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Aleysha T Chen
- Department of Diabetes Complications and Metabolism, City of Hope, Duarte, CA, United States
| | - Andrew B Burns
- Department of Diabetes Complications and Metabolism, City of Hope, Duarte, CA, United States
| | - Kiran Sriram
- Department of Diabetes Complications and Metabolism, City of Hope, Duarte, CA, United States.,Irell and Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA, United States
| | - Yingjun Luo
- Department of Diabetes Complications and Metabolism, City of Hope, Duarte, CA, United States
| | - Xiaofang Tang
- Department of Diabetes Complications and Metabolism, City of Hope, Duarte, CA, United States
| | - Sergio Branciamore
- Department of Diabetes Complications and Metabolism, City of Hope, Duarte, CA, United States
| | - Denis O'Meally
- Center for Gene Therapy, City of Hope, Duarte, CA, United States
| | - Szu-Ling Chang
- Department of Diabetes Complications and Metabolism, City of Hope, Duarte, CA, United States.,Cardiovascular Center, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Po-Hsun Huang
- Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan
| | - John Y-J Shyy
- Department of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Shu Chien
- Department of Medicine, University of California, San Diego, La Jolla, CA, United States.,Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States
| | - Russell C Rockne
- Irell and Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA, United States.,Division of Mathematical Oncology, Department of Computational and Quantitative Medicine, City of Hope, Duarte, CA, United States
| | - Zhen Bouman Chen
- Department of Diabetes Complications and Metabolism, City of Hope, Duarte, CA, United States.,Irell and Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA, United States
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102
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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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103
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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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104
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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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105
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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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106
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HMGB1 Recruits TET2/AID/TDG to Induce DNA Demethylation in STAT3 Promoter in CD4 + T Cells from aGVHD Patients. J Immunol Res 2020; 2020:7165230. [PMID: 33029541 PMCID: PMC7532413 DOI: 10.1155/2020/7165230] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 08/14/2020] [Accepted: 08/31/2020] [Indexed: 11/20/2022] Open
Abstract
STAT3 is highly expressed in aGVHD CD4+ T cells and plays a critical role in inducing or worsening aGVHD. In our preceding studies, DNA hypomethylation in STAT3 promoter was shown to cause high expression of STAT3 in aGVHD CD4+ T cells, and the process could be modulated by HMGB1, but the underlying mechanism remains unclear. TET2, AID, and TDG are indispensable in DNA demethylation; meanwhile, TET2 and AID also serve extremely important roles in immune response. So, we speculated these enzymes involved in the STAT3 promoter hypomethylation induced by HMGB1 in aGVHD CD4+ T cells. In this study, we found that the binding levels of TET2/AID/TDG to STAT3 promoter were remarkably increased in CD4+T cells from aGVHD patients and were significantly negatively correlated with the STAT3 promoter methylation level. Simultaneously, we revealed that HMGB1 could recruit TET2, AID, and TDG to form a complex in the STAT3 promoter region. Interference with the expression of TET2/AID/TDG inhibited the overexpression of STAT3 caused by HMGB1 downregulation of the STAT3 promoter DNA methylation. These data demonstrated a new molecular mechanism of how HMGB1 promoted the expression of STAT3 in CD4+ T cells from aGVHD patients.
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107
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Spinelli R, Parrillo L, Longo M, Florese P, Desiderio A, Zatterale F, Miele C, Raciti GA, Beguinot F. Molecular basis of ageing in chronic metabolic diseases. J Endocrinol Invest 2020; 43:1373-1389. [PMID: 32358737 PMCID: PMC7481162 DOI: 10.1007/s40618-020-01255-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 04/10/2020] [Indexed: 02/06/2023]
Abstract
AIM Over the last decades, the shift in age distribution towards older ages and the progressive ageing which has occurred in most populations have been paralleled by a global epidemic of obesity and its related metabolic disorders, primarily, type 2 diabetes (T2D). Dysfunction of the adipose tissue (AT) is widely recognized as a significant hallmark of the ageing process that, in turn, results in systemic metabolic alterations. These include insulin resistance, accumulation of ectopic lipids and chronic inflammation, which are responsible for an elevated risk of obesity and T2D onset associated to ageing. On the other hand, obesity and T2D, the paradigms of AT dysfunction, share many physiological characteristics with the ageing process, such as an increased burden of senescent cells and epigenetic alterations. Thus, these chronic metabolic disorders may represent a state of accelerated ageing. MATERIALS AND METHODS A more precise explanation of the fundamental ageing mechanisms that occur in AT and a deeper understanding of their role in the interplay between accelerated ageing and AT dysfunction can be a fundamental leap towards novel therapies that address the causes, not just the symptoms, of obesity and T2D, utilizing strategies that target either senescent cells or DNA methylation. RESULTS In this review, we summarize the current knowledge of the pathways that lead to AT dysfunction in the chronological ageing process as well as the pathophysiology of obesity and T2D, emphasizing the critical role of cellular senescence and DNA methylation. CONCLUSION Finally, we highlight the need for further research focused on targeting these mechanisms.
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Affiliation(s)
- R Spinelli
- Department of Translation Medicine, Federico II University of Naples, 80131, Naples, Italy
- URT Genomic of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, 80131, Naples, Italy
| | - L Parrillo
- Department of Translation Medicine, Federico II University of Naples, 80131, Naples, Italy
- URT Genomic of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, 80131, Naples, Italy
| | - M Longo
- Department of Translation Medicine, Federico II University of Naples, 80131, Naples, Italy
- URT Genomic of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, 80131, Naples, Italy
| | - P Florese
- Department of Translation Medicine, Federico II University of Naples, 80131, Naples, Italy
- URT Genomic of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, 80131, Naples, Italy
| | - A Desiderio
- Department of Translation Medicine, Federico II University of Naples, 80131, Naples, Italy
- URT Genomic of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, 80131, Naples, Italy
| | - F Zatterale
- Department of Translation Medicine, Federico II University of Naples, 80131, Naples, Italy
- URT Genomic of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, 80131, Naples, Italy
| | - C Miele
- Department of Translation Medicine, Federico II University of Naples, 80131, Naples, Italy
- URT Genomic of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, 80131, Naples, Italy
| | - G Alexander Raciti
- Department of Translation Medicine, Federico II University of Naples, 80131, Naples, Italy
- URT Genomic of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, 80131, Naples, Italy
| | - F Beguinot
- Department of Translation Medicine, Federico II University of Naples, 80131, Naples, Italy.
- URT Genomic of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, 80131, Naples, Italy.
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108
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Garali I, Sahbatou M, Daunay A, Baudrin LG, Renault V, Bouyacoub Y, Deleuze JF, How-Kit A. Improvements and inter-laboratory implementation and optimization of blood-based single-locus age prediction models using DNA methylation of the ELOVL2 promoter. Sci Rep 2020; 10:15652. [PMID: 32973211 PMCID: PMC7515898 DOI: 10.1038/s41598-020-72567-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 09/02/2020] [Indexed: 01/21/2023] Open
Abstract
Several blood-based age prediction models have been developed using less than a dozen to more than a hundred DNA methylation biomarkers. Only one model (Z-P1) based on pyrosequencing has been developed using DNA methylation of a single locus located in the ELOVL2 promoter, which is considered as one of the best age-prediction biomarker. Although multi-locus models generally present better performances compared to the single-locus model, they require more DNA and present more inter-laboratory variations impacting the predictions. Here we developed 17,018 single-locus age prediction models based on DNA methylation of the ELOVL2 promoter from pooled data of four different studies (training set of 1,028 individuals aged from 0 and 91 years) using six different statistical approaches and testing every combination of the 7 CpGs, aiming to improve the prediction performances and reduce the effects of inter-laboratory variations. Compared to Z-P1 model, three statistical models with the optimal combinations of CpGs presented improved performances (MAD of 4.41–4.77 in the testing set of 385 individuals) and no age-dependent bias. In an independent testing set of 100 individuals (19–65 years), we showed that the prediction accuracy could be further improved by using different CpG combinations and increasing the number of technical replicates (MAD of 4.17).
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Affiliation(s)
- Imene Garali
- Laboratory for Bioinformatics, Foundation Jean Dausset-CEPH, Paris, France.,Laboratory of Excellence GenMed, Paris, France
| | - Mourad Sahbatou
- Laboratory for Human Genetics, Foundation Jean Dausset-CEPH, Paris, France
| | - Antoine Daunay
- Laboratory for Genomics, Foundation Jean Dausset-CEPH, 75010, Paris, France
| | - Laura G Baudrin
- Laboratory of Excellence GenMed, Paris, France.,Laboratory for Genomics, Foundation Jean Dausset-CEPH, 75010, Paris, France
| | - Victor Renault
- Laboratory for Bioinformatics, Foundation Jean Dausset-CEPH, Paris, France
| | - Yosra Bouyacoub
- Laboratory of Excellence GenMed, Paris, France.,Laboratory for Genomics, Foundation Jean Dausset-CEPH, 75010, Paris, France
| | - Jean-François Deleuze
- Laboratory for Bioinformatics, Foundation Jean Dausset-CEPH, Paris, France.,Laboratory of Excellence GenMed, Paris, France.,Laboratory for Human Genetics, Foundation Jean Dausset-CEPH, Paris, France.,Laboratory for Genomics, Foundation Jean Dausset-CEPH, 75010, 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, 75010, Paris, France.
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109
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Can Bone-Specific Alkaline Phosphatase and Osteocalcine Levels Be Used to Determine the Age in Children? Am J Forensic Med Pathol 2020; 41:182-187. [DOI: 10.1097/paf.0000000000000555] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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110
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Freire-Aradas A, Pośpiech E, Aliferi A, Girón-Santamaría L, Mosquera-Miguel A, Pisarek A, Ambroa-Conde A, Phillips C, Casares de Cal MA, Gómez-Tato A, Spólnicka M, Woźniak A, Álvarez-Dios J, Ballard D, Court DS, Branicki W, Carracedo Á, Lareu MV. A Comparison of Forensic Age Prediction Models Using Data From Four DNA Methylation Technologies. Front Genet 2020; 11:932. [PMID: 32973877 PMCID: PMC7466768 DOI: 10.3389/fgene.2020.00932] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 07/27/2020] [Indexed: 12/20/2022] Open
Abstract
Individual age estimation can be applied to criminal, legal, and anthropological investigations. DNA methylation has been established as the biomarker of choice for age prediction, since it was observed that specific CpG positions in the genome show systematic changes during an individual’s lifetime, with progressive increases or decreases in methylation levels. Subsequently, several forensic age prediction models have been reported, providing average age prediction error ranges of ±3–4 years, using a broad spectrum of technologies and underlying statistical analyses. DNA methylation assessment is not categorical but quantitative. Therefore, the detection platform used plays a pivotal role, since quantitative and semi-quantitative technologies could potentially result in differences in detected DNA methylation levels. In the present study, we analyzed as a shared sample pool, 84 blood-based DNA controls ranging from 18 to 99 years old using four different technologies: EpiTYPER®, pyrosequencing, MiSeq, and SNaPshotTM. The DNA methylation levels detected for CpG sites from ELOVL2, FHL2, and MIR29B2 with each system were compared. A restricted three CpG-site age prediction model was rebuilt for each system, as well as for a combination of technologies, based on previous training datasets, and age predictions were calculated accordingly for all the samples detected with the previous technologies. While the DNA methylation patterns and subsequent age predictions from EpiTYPER®, pyrosequencing, and MiSeq systems are largely comparable for the CpG sites studied, SNaPshotTM gives bigger differences reflected in higher predictive errors. However, these differences can be reduced by applying a z-score data transformation.
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Affiliation(s)
- A Freire-Aradas
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain
| | - E Pośpiech
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - A Aliferi
- King's Forensics, Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - L Girón-Santamaría
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain
| | - A Mosquera-Miguel
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain
| | - A Pisarek
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - A Ambroa-Conde
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain
| | - C Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain
| | - M A Casares de Cal
- Faculty of Mathematics, University of Santiago de Compostela, Galicia, Spain
| | - A Gómez-Tato
- Faculty of Mathematics, University of Santiago de Compostela, Galicia, Spain
| | - M Spólnicka
- Central Forensic Laboratory of the Police, Warsaw, Poland
| | - A Woźniak
- Central Forensic Laboratory of the Police, Warsaw, Poland
| | - J Álvarez-Dios
- Faculty of Mathematics, University of Santiago de Compostela, Galicia, Spain
| | - D Ballard
- King's Forensics, Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - D Syndercombe Court
- King's Forensics, Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - W Branicki
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland.,Central Forensic Laboratory of the Police, Warsaw, Poland
| | - Ángel Carracedo
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain.,Fundación Pública Galega de Medicina Xenómica - CIBERER-IDIS, Santiago de Compostela, Spain
| | - M V Lareu
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain
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111
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Correia Dias H, Corte-Real F, Cunha E, Manco L. DNA methylation age estimation from human bone and teeth. AUST J FORENSIC SCI 2020. [DOI: 10.1080/00450618.2020.1805011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Helena Correia Dias
- Research Centre for Anthropology and Health (CIAS), Department of Life Sciences, University of Coimbra, Coimbra, Portugal
- Centre for Functional Ecology (CEF), Laboratory of Forensic Anthropology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
- National Institute of Legal Medicine and Forensic Sciences, 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
- Centre for Functional Ecology (CEF), Laboratory of Forensic Anthropology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
- National Institute of Legal Medicine and Forensic Sciences, Coimbra, Portugal
| | - Licínio Manco
- Research Centre for Anthropology and Health (CIAS), Department of Life Sciences, University of Coimbra, Coimbra, Portugal
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112
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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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113
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Bergsma T, Rogaeva E. DNA Methylation Clocks and Their Predictive Capacity for Aging Phenotypes and Healthspan. Neurosci Insights 2020; 15:2633105520942221. [PMID: 32743556 PMCID: PMC7376380 DOI: 10.1177/2633105520942221] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/23/2020] [Indexed: 12/12/2022] Open
Abstract
The number of age predictors based on DNA methylation (DNAm) profile is rising
due to their potential in predicting healthspan and application in age-related
illnesses, such as neurodegenerative diseases. The cumulative assessment of DNAm
levels at age-related CpGs (DNAm clock) may reflect biological aging. Such DNAm
clocks have been developed using various training models and could mirror
different aspects of disease/aging mechanisms. Hence, evaluating several DNAm
clocks together may be the most effective strategy in capturing the complexity
of the aging process. However, various confounders may influence the outcome of
these age predictors, including genetic and environmental factors, as well as
technical differences in the selected DNAm arrays. These factors should be taken
into consideration when interpreting DNAm clock predictions. In the current
review, we discuss 15 reported DNAm clocks with consideration for their utility
in investigating neurodegenerative diseases and suggest research directions
towards developing a more optimal measure for biological aging.
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Affiliation(s)
- Tessa Bergsma
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, Canada.,Faculty of Science and Engineering, University of Groningen, Groningen, The Netherlands
| | - Ekaterina Rogaeva
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, Canada.,Division of Neurology, Department of Medicine, University of Toronto, Toronto, ON, Canada
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114
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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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115
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Lau PY, Fung WK. Evaluation of marker selection methods and statistical models for chronological age prediction based on DNA methylation. Leg Med (Tokyo) 2020; 47:101744. [PMID: 32659707 DOI: 10.1016/j.legalmed.2020.101744] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 06/02/2020] [Accepted: 06/26/2020] [Indexed: 12/16/2022]
Abstract
In forensic investigation, retrieving biological information from DNA evidence is a promising field of interest. One of the applications is on the estimation of the age of the donor based on DNA methylation. A large number of studies focused on age prediction using the 450 K Human Methylation Beadchip. Various marker selection methods and prediction models have been considered. However, there is a lack of research evaluating different high-dimensional variable selection methods of CpG sites with various models for age prediction. The aim of this study is to evaluate four variable selection methods (forward selection, LASSO, elastic net and SCAD) combined with a classical statistical model and sophisticated machine learning models based on the mean absolute deviation (MAD) and the root-mean-square error (RMSE). We used publicly available 450 K data set containing 991 whole blood samples (age 19-101 years). We found that the multiple linear regression model with 16 markers selected from the forward selection method performed very well in age prediction (MAD = 3.76 years and RMSE = 5.01 years). On the other hand, the highly advanced ultrahigh dimensional variable selection methods and sophisticated machine learning algorithms appeared unnecessary for age prediction based on DNA methylation.
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Affiliation(s)
- Pui Yin Lau
- Department of Statistics and Actuarial Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Wing Kam Fung
- Department of Statistics and Actuarial Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
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116
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The biological age of the heart is consistently younger than chronological age. Sci Rep 2020; 10:10752. [PMID: 32612244 PMCID: PMC7329913 DOI: 10.1038/s41598-020-67622-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 06/11/2020] [Indexed: 02/06/2023] Open
Abstract
Chronological age represents the main factor in donor selection criteria for organ transplantation, however aging is very heterogeneous. Defining the biological aging of individual organs may contribute to supporting this process. In this study we examined the biological age of the heart [right (RA)/left atrium (LA)] and peripheral blood leucocytes in the same subject, and compared these to assess whether blood mirrors cardiac biological aging. Biological aging was studied in 35 donors (0.4–72 years) by exploring mitotic and non-mitotic pathways, using telomere length (TL) and age-dependent methylation changes in certain CpG loci (DNAmAge). Heart non-mitotic DNAmAge was strongly younger than that of both blood (− 10 years, p < 0.0001) and chronological age (− 12 years, p < 0.0001). Instead, heart and blood mitotic age (TL) were similar, and there was no difference in DNAmAge and TL between RA and LA. DNAmAge negatively correlated with TL in heart and blood (p ≤ 0.01). Finally, blood and heart TL (p < 0.01) and DNAmAge (p < 0.0001) were correlated. Therefore, blood can be a proxy indicator of heart biological age. While future investigation on post-transplant graft performance in relation to biological aging is still needed, our study could contribute to opening up novel basic and clinical research platforms in the field of organ transplantation.
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117
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Han Y, Franzen J, Stiehl T, Gobs M, Kuo CC, Nikolić M, Hapala J, Koop BE, Strathmann K, Ritz-Timme S, Wagner W. New targeted approaches for epigenetic age predictions. BMC Biol 2020; 18:71. [PMID: 32580727 PMCID: PMC7315536 DOI: 10.1186/s12915-020-00807-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 06/08/2020] [Indexed: 12/16/2022] Open
Abstract
Background Age-associated DNA methylation changes provide a promising biomarker for the aging process. While genome-wide DNA methylation profiles enable robust age-predictors by integration of many age-associated CG dinucleotides (CpGs), there are various alternative approaches for targeted measurements at specific CpGs that better support standardized and cost-effective high-throughput analysis. Results In this study, we utilized 4647 Illumina BeadChip profiles of blood to select CpG sites that facilitate reliable age-predictions based on pyrosequencing. We demonstrate that the precision of DNA methylation measurements can be further increased with droplet digital PCR (ddPCR). In comparison, bisulfite barcoded amplicon sequencing (BBA-seq) gave slightly lower correlation between chronological age and DNA methylation at individual CpGs, while the age-predictions were overall relatively accurate. Furthermore, BBA-seq data revealed that the correlation of methylation levels with age at neighboring CpG sites follows a bell-shaped curve, often associated with a CTCF binding site. We demonstrate that within individual BBA-seq reads the DNA methylation at neighboring CpGs is not coherently modified, but reveals a stochastic pattern. Based on this, we have developed a new approach for epigenetic age predictions based on the binary sequel of methylated and non-methylated sites in individual reads, which reflects heterogeneity in epigenetic aging within a sample. Conclusion Targeted DNA methylation analysis at few age-associated CpGs by pyrosequencing, BBA-seq, and particularly ddPCR enables high precision of epigenetic age-predictions. Furthermore, we demonstrate that the stochastic evolution of age-associated DNA methylation patterns in BBA-seq data enables epigenetic clocks for individual DNA strands.
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Affiliation(s)
- Yang Han
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany.,Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Julia Franzen
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany.,Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Thomas Stiehl
- Interdisciplinary Center for Scientific Computing (IWR), Institute of Applied Mathematics, University of Heidelberg, Heidelberg, Germany
| | - Michael Gobs
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany.,Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Chao-Chung Kuo
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany.,Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Miloš Nikolić
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany.,Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Jan Hapala
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany.,Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany
| | | | - Klaus Strathmann
- Institute for Transfusion Medicine, RWTH Aachen University Medical School, Aachen, Germany
| | - Stefanie Ritz-Timme
- Institute for Legal Medicine, Heinrich Heine University, Düsseldorf, Germany
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany. .,Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany.
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118
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Development and optimization of the VISAGE basic prototype tool for forensic age estimation. Forensic Sci Int Genet 2020; 48:102322. [PMID: 32574993 DOI: 10.1016/j.fsigen.2020.102322] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 04/22/2020] [Accepted: 06/03/2020] [Indexed: 01/03/2023]
Abstract
The VISAGE (VISible Attributes through GEnomics) consortium aims to develop, optimize and validate prototype tools to broaden the use of DNA intelligence methods in forensic routine laboratories. This includes age estimation based on the quantification of DNA methylation at specific CpG sites. Here, we present the VISAGE basic prototype tool for age estimation targeting 32 CpGs from five genes ELOVL2, MIR29B2CHG (herein, MIR29B2C), FHL2, TRIM59 and KLF14. The assay interrogates these well described age markers by multiplex PCR for bisulfite converted DNA and massively parallel sequencing on a MiSeq FGx instrument. We describe protocol optimizations including tests on five bisulfite conversion kits and an evaluation of the assay's reproducibility and sensitivity with artificially methylated DNA standards. We observed robust quantification of methylation levels with a mean standard deviation of 1.4 % across ratios. Sensitivity tests showed no increase of variability down to 20 ng DNA input into bisulfite conversion with a median difference below 1.6 % between technical replicates.
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119
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Montesanto A, D'Aquila P, Lagani V, Paparazzo E, Geracitano S, Formentini L, Giacconi R, Cardelli M, Provinciali M, Bellizzi D, Passarino G. A New Robust Epigenetic Model for Forensic Age Prediction. J Forensic Sci 2020; 65:1424-1431. [PMID: 32453457 DOI: 10.1111/1556-4029.14460] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/22/2020] [Accepted: 05/04/2020] [Indexed: 12/12/2022]
Abstract
Forensic DNA phenotyping refers to an emerging field of forensic sciences aimed at the prediction of externally visible characteristics of unknown sample donors directly from biological materials. The aging process significantly affects most of the above characteristics making the development of a reliable method of age prediction very important. Today, the so-called "epigenetic clocks" represent the most accurate models for age prediction. Since they are technically not achievable in a typical forensic laboratory, forensic DNA technology has triggered efforts toward the simplification of these models. The present study aimed to build an epigenetic clock using a set of methylation markers of five different genes in a sample of the Italian population of different ages covering the whole span of adult life. In a sample of 330 subjects, 42 selected markers were analyzed with a machine learning approach for building a prediction model for age prediction. A ridge linear regression model including eight of the proposed markers was identified as the best performing model across a plethora of candidates. This model was tested on an independent sample of 83 subjects providing a median error of 4.5 years. In the present study, an epigenetic model for age prediction was validated in a sample of the Italian population. However, its applicability to advanced ages still represents the main limitation in forensic caseworks.
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Affiliation(s)
- Alberto Montesanto
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, 87036, Italy
| | - Patrizia D'Aquila
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, 87036, Italy
| | - Vincenzo Lagani
- Gnosis Data Analysis PC, Heraklion, GR700-13, Greece.,Institute of Chemical Biology, Ilia State University, Tbilisi, 0162, Georgia
| | - Ersilia Paparazzo
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, 87036, Italy
| | - Silvana Geracitano
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, 87036, Italy
| | - Laura Formentini
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, Ancona, Italy
| | - Robertina Giacconi
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, Ancona, Italy
| | - Maurizio Cardelli
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, Ancona, Italy
| | - Mauro Provinciali
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, Ancona, Italy
| | - Dina Bellizzi
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, 87036, Italy
| | - Giuseppe Passarino
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, 87036, Italy
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120
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The evaluation of seven age-related CpGs for forensic purpose in blood from Chinese Han population. Forensic Sci Int Genet 2020; 46:102251. [DOI: 10.1016/j.fsigen.2020.102251] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 01/14/2020] [Accepted: 01/19/2020] [Indexed: 01/26/2023]
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121
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Lee HY, Hong SR, Lee JE, Hwang IK, Kim NY, Lee JM, Fleckhaus J, Jung SE, Lee YH. Epigenetic age signatures in bones. Forensic Sci Int Genet 2020; 46:102261. [DOI: 10.1016/j.fsigen.2020.102261] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 02/03/2020] [Accepted: 02/04/2020] [Indexed: 01/28/2023]
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122
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Dias HC, Cordeiro C, Pereira J, Pinto C, Real FC, Cunha E, Manco L. DNA methylation age estimation in blood samples of living and deceased individuals using a multiplex SNaPshot assay. Forensic Sci Int 2020; 311:110267. [PMID: 32325350 DOI: 10.1016/j.forsciint.2020.110267] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/20/2020] [Accepted: 03/22/2020] [Indexed: 12/30/2022]
Abstract
Many studies in the forensic field have reported that analysis of DNA methylation is the most reliable method of predicting age. In a previous study, 5 CpG sites located in ELOVL2, FHL2, KLF14, C1orf132 and TRIM59 genes were tested for age prediction purposes in blood, saliva and buccal swab samples from Korean individuals using a multiplex methylation SNaPshot assay. The main goals of the present study were i) to replicate the same multiplex SNaPshot assay in blood samples from Portuguese individuals, ii) to compare DNA methylation status between two different populations and iii) to address putative differences in the methylation status between blood from living and deceased individuals. Blood samples from 59 living individuals (37 females, 22 males; aged 1-94 years-old) and from 62 deceased individuals (13 females, 49 males; aged 28-86 years-old) were evaluated. The specific primers were those previously described. Linear regression models were used to analyse relationships between methylation levels and chronological age using IBM SPSS software v.24. Our results allowed to build a final age prediction model (APM) for blood samples of living individuals with 3 CpG sites, at ELOVL2, FHL2 and C1orf132 genes, explaining 96.3% of age variation, with a mean absolute deviation (MAD) from chronological age of 4.25 years. Some differences were found in the extent of the age association in the targeted loci comparing Portuguese with Korean individuals. The final APM built for deceased individuals included 4 CpG sites, at ELOVL2, FHL2, C1orf132 and TRIM59 genes, explaining 79.3% of age variation, with a MAD of 5.36 years. Combining both sets of samples from living and deceased individuals, the most accurate APM with 4 CpGs, at ELOVL2, FHL2, C1orf132 and TRIM59 genes, explained 92.5% of variation in age, with a MAD of 4.97 years. In conclusion, our study replicated in blood samples of Portuguese living individuals a previous SNaPshot assay for age estimation. The possibility that age markers might be population specific and that postmortem changes can alter the methylation status among specific loci was suggested by our data. Our study showed the usefulness of the multiplex methylation SNaPshot assay for forensic analysis in blood samples of living and deceased individuals.
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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
| | - Cristina Cordeiro
- National Institute of Legal Medicine and Forensic Sciences, Portugal; Faculty of Medicine, University of Coimbra, Portugal
| | - Janet Pereira
- Department of Hematology, Centro Hospitalar e Universitário de Coimbra (CHUC), Coimbra, Portugal
| | - Catarina Pinto
- Department of Hematology, Centro Hospitalar e Universitário de Coimbra (CHUC), Coimbra, Portugal
| | - Francisco Corte Real
- National Institute of Legal Medicine and Forensic Sciences, Portugal; Faculty of Medicine, University of Coimbra, 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
| | - Licínio Manco
- Research Centre for Anthropology and Health (CIAS), Department of Life Sciences, University of Coimbra, Portugal.
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123
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Gensous N, Garagnani P, Santoro A, Giuliani C, Ostan R, Fabbri C, Milazzo M, Gentilini D, di Blasio AM, Pietruszka B, Madej D, Bialecka-Debek A, Brzozowska A, Franceschi C, Bacalini MG. One-year Mediterranean diet promotes epigenetic rejuvenation with country- and sex-specific effects: a pilot study from the NU-AGE project. GeroScience 2020; 42:687-701. [PMID: 31981007 PMCID: PMC7205853 DOI: 10.1007/s11357-019-00149-0] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 12/13/2019] [Indexed: 12/12/2022] Open
Abstract
Mediterranean diet has been proposed to promote healthy aging, but its effects on aging biomarkers have been poorly investigated. We evaluated the impact of a 1-year Mediterranean-like diet in a pilot study including 120 elderly healthy subjects from the NU-AGE study (60 Italians, 60 Poles) by measuring the changes in their epigenetic age, assessed by Horvath's clock. We observed a trend towards epigenetic rejuvenation of participants after nutritional intervention. The effect was statistically significant in the group of Polish females and in subjects who were epigenetically older at baseline. A genome-wide association study of epigenetic age changes after the intervention did not return significant (adjusted p value < 0.05) loci. However, we identified small-effect alleles (nominal p value < 10-4), mapping in genes enriched in pathways related to energy metabolism, regulation of cell cycle, and of immune functions. Together, these findings suggest that Mediterranean diet can promote epigenetic rejuvenation but with country-, sex-, and individual-specific effects, thus highlighting the need for a personalized approach to nutritional interventions.
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Affiliation(s)
- Noémie Gensous
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum - University of Bologna, Via San Giacomo 12, 40126, Bologna, Italy
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum - University of Bologna, Via San Giacomo 12, 40126, Bologna, Italy.
- Center for Applied Biomedical Research (CRBA), St. Orsola-Malpighi University Hospital, Bologna, Italy.
- Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet at Huddinge University Hospital, S-141 86, Stockholm, Sweden.
- CNR Institute of Molecular Genetics "Luigi Luca Cavalli-Sforza", Unit of Bologna, Bologna, Italy.
| | - Aurelia Santoro
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum - University of Bologna, Via San Giacomo 12, 40126, Bologna, Italy
| | - Cristina Giuliani
- Department of Biological, Geological, and Environmental Sciences (BiGeA), Laboratory of Molecular Anthropology and Centre for Genome Biology, University of Bologna, Bologna, Italy
| | - Rita Ostan
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum - University of Bologna, Via San Giacomo 12, 40126, Bologna, Italy
| | - Cristina Fabbri
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum - University of Bologna, Via San Giacomo 12, 40126, Bologna, Italy
| | - Maddalena Milazzo
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum - University of Bologna, Via San Giacomo 12, 40126, Bologna, Italy
| | - Davide Gentilini
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
- Istituto Auxologico Italiano IRCCS, Cusano Milanino, Milan, Italy
| | | | - Barbara Pietruszka
- Department of Human Nutrition, Warsaw University of Life Sciences-SGGW, Warsaw, Poland
| | - Dawid Madej
- Department of Human Nutrition, Warsaw University of Life Sciences-SGGW, Warsaw, Poland
| | - Agata Bialecka-Debek
- Department of Human Nutrition, Warsaw University of Life Sciences-SGGW, Warsaw, Poland
| | - Anna Brzozowska
- Department of Human Nutrition, Warsaw University of Life Sciences-SGGW, Warsaw, Poland
| | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum - University of Bologna, Via San Giacomo 12, 40126, Bologna, Italy
- Laboratory of Systems Medicine of Healthy Aging and Department of Applied Mathematics, Lobachevsky Univeristy, Nizhny Novgorod, Russia
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
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124
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Inter-laboratory adaption of age estimation models by DNA methylation analysis—problems and solutions. Int J Legal Med 2020; 134:953-961. [DOI: 10.1007/s00414-020-02263-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 01/31/2020] [Indexed: 12/24/2022]
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125
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Zolotarenko AD, Chekalin EV, Bruskin SA. Modern Molecular Genetic Methods for Age Estimation in Forensics. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795419120147] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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126
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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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127
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Guarasci F, D'Aquila P, Montesanto A, Corsonello A, Bellizzi D, Passarino G. Individual DNA Methylation Profile is Correlated with Age and can be Targeted to Modulate Healthy Aging and Longevity. Curr Pharm Des 2019; 25:4139-4149. [DOI: 10.2174/1381612825666191112095655] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 11/07/2019] [Indexed: 02/06/2023]
Abstract
:Patterns of DNA methylation, the best characterized epigenetic modification, are modulated by aging. In humans, different studies at both site-specific and genome-wide levels have reported that modifications of DNA methylation are associated with the chronological aging process but also with the quality of aging (or biological aging), providing new perspectives for establishing powerful biomarkers of aging.:In this article, the role of DNA methylation in aging and longevity has been reviewed by analysing literature data about DNA methylation variations occurring during the lifetime in response to environmental factors and genetic background, and their association with the aging process and, in particular, with the quality of aging. Special attention has been devoted to the relationship between nuclear DNA methylation patterns, mitochondrial DNA epigenetic modifications, and longevity. Mitochondrial DNA has recently been reported to modulate global DNA methylation levels of the nuclear genome during the lifetime, and, in spite of the previous belief, it has been found to be the target of methylation modifications.:Analysis of DNA methylation profiles across lifetime shows that a remodeling of the methylome occurs with age and/or with age-related decline. Thus, it can be an excellent biomarker of aging and of the individual decline and frailty status. The knowledge about the mechanisms underlying these modifications is crucial since it might allow the opportunity for targeted treatment to modulate the rate of aging and longevity.
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Affiliation(s)
- Francesco Guarasci
- Department of Biology, Ecology and Earth Science, University of Calabria, 87030 Rende, Italy
| | - Patrizia D'Aquila
- Department of Biology, Ecology and Earth Science, University of Calabria, 87030 Rende, Italy
| | - Alberto Montesanto
- Department of Biology, Ecology and Earth Science, University of Calabria, 87030 Rende, Italy
| | - Andrea Corsonello
- Unit of Geriatric Pharmacoepidemiology, Scientific Research Institute - Italian National Research Center on Aging (IRCCS INRCA), Cosenza, Italy
| | - Dina Bellizzi
- Department of Biology, Ecology and Earth Science, University of Calabria, 87030 Rende, Italy
| | - Giuseppe Passarino
- Department of Biology, Ecology and Earth Science, University of Calabria, 87030 Rende, Italy
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128
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El Khoury LY, Gorrie-Stone T, Smart M, Hughes A, Bao Y, Andrayas A, Burrage J, Hannon E, Kumari M, Mill J, Schalkwyk LC. Systematic underestimation of the epigenetic clock and age acceleration in older subjects. Genome Biol 2019; 20:283. [PMID: 31847916 PMCID: PMC6915902 DOI: 10.1186/s13059-019-1810-4] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 09/03/2019] [Indexed: 11/18/2022] Open
Abstract
Background The Horvath epigenetic clock is widely used. It predicts age quite well from 353 CpG sites in the DNA methylation profile in unknown samples and has been used to calculate “age acceleration” in various tissues and environments. Results The model systematically underestimates age in tissues from older people. This is seen in all examined tissues but most strongly in the cerebellum and is consistently observed in multiple datasets. Age acceleration is thus age-dependent, and this can lead to spurious associations. The current literature includes examples of association tests with age acceleration calculated in a wide variety of ways. Conclusions The concept of an epigenetic clock is compelling, but caution should be taken in interpreting associations with age acceleration. Association tests of age acceleration should include age as a covariate.
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Affiliation(s)
- Louis Y El Khoury
- School of Life Sciences, University of Essex, Colchester, UK.,Present Address: Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | | | - Melissa Smart
- Institute for Social and Economic Research, University of Essex, Colchester, UK
| | - Amanda Hughes
- MRC Integrative Epidemiology Unit - University of Bristol, Bristol, UK
| | - Yanchun Bao
- Institute for Social and Economic Research, University of Essex, Colchester, UK
| | | | - Joe Burrage
- Medical School, University of Exeter, Exeter, UK
| | - Eilis Hannon
- Medical School, University of Exeter, Exeter, UK
| | - Meena Kumari
- Institute for Social and Economic Research, University of Essex, Colchester, UK
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129
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McCord B, Gauthier Q, Alghanim H, Antunes J, Fernandez Tejero N, Duncan G, Balamurugan K. Applications of epigenetic methylation in body fluid identification, age determination and phenotyping. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.10.061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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130
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Gentile F, Castoldi E, Serventi P, Colloca D, Ciccotelli R, Marino A. Early evaluation of five age-correlated DNA methylation markers in an Italian population sample. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.10.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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131
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MapReduce-Based Parallel Genetic Algorithm for CpG-Site Selection in Age Prediction. Genes (Basel) 2019; 10:genes10120969. [PMID: 31775313 PMCID: PMC6947642 DOI: 10.3390/genes10120969] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 11/12/2019] [Accepted: 11/15/2019] [Indexed: 11/23/2022] Open
Abstract
Genomic biomarkers such as DNA methylation (DNAm) are employed for age prediction. In recent years, several studies have suggested the association between changes in DNAm and its effect on human age. The high dimensional nature of this type of data significantly increases the execution time of modeling algorithms. To mitigate this problem, we propose a two-stage parallel algorithm for selection of age related CpG-sites. The algorithm first attempts to cluster the data into similar age ranges. In the next stage, a parallel genetic algorithm (PGA), based on the MapReduce paradigm (MR-based PGA), is used for selecting age-related features of each individual age range. In the proposed method, the execution of the algorithm for each age range (data parallel), the evaluation of chromosomes (task parallel) and the calculation of the fitness function (data parallel) are performed using a novel parallel framework. In this paper, we consider 16 different healthy DNAm datasets that are related to the human blood tissue and that contain the relevant age information. These datasets are combined into a single unioned set, which is in turn randomly divided into two sets of train and test data with a ratio of 7:3, respectively. We build a Gradient Boosting Regressor (GBR) model on the selected CpG-sites from the train set. To evaluate the model accuracy, we compared our results with state-of-the-art approaches that used these datasets, and observed that our method performs better on the unseen test dataset with a Mean Absolute Deviation (MAD) of 3.62 years, and a correlation (R2) of 95.96% between age and DNAm. In the train data, the MAD and R2 are 1.27 years and 99.27%, respectively. Finally, we evaluate our method in terms of the effect of parallelization in computation time. The algorithm without parallelization requires 4123 min to complete, whereas the parallelized execution on 3 computing machines having 32 processing cores each, only takes a total of 58 min. This shows that our proposed algorithm is both efficient and scalable.
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132
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HIrisPlex-S system for eye, hair, and skin color prediction from DNA: Massively parallel sequencing solutions for two common forensically used platforms. Forensic Sci Int Genet 2019; 43:102152. [DOI: 10.1016/j.fsigen.2019.102152] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/26/2019] [Accepted: 08/22/2019] [Indexed: 11/22/2022]
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133
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Novel multiplex strategy for DNA methylation-based age prediction from small amounts of DNA via Pyrosequencing. Forensic Sci Int Genet 2019; 44:102189. [PMID: 31648151 DOI: 10.1016/j.fsigen.2019.102189] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 10/11/2019] [Accepted: 10/12/2019] [Indexed: 11/20/2022]
Abstract
DNA methylation-based age estimation is a promising new tool for forensic molecular biology. There is growing understanding of the best predictive CpG loci and their performance in various sample types. Since forensic samples usually provide only small amounts of DNA, the sensitivity of the method is crucial. Pyrosequencing is one of the most sensitive methods but only capable to analyze different target regions separately. Thus, multiple input DNA samples are required for investigations of different target regions, which is required for all current age estimation models. To overcome this limitation, we developed a novel multiplex strategy for Pyrosequencing, which allows the investigation of different target regions from a single small amount of input DNA. A pre-amplification step was introduced to increase the amount of target-specific template for the subsequent sequencing PCR step. We tested this multiplex strategy for eight target regions including 15 age CpGs associated with the genes of ELOVL2, FHL2, CCDC102B, C1orf132, KLF14, EDARADD, PDE4C and SST. Except for FHL2, all target regions were successfully sequenced with the multiplex strategy and the precision in terms of reproducibility of the measurements was equal to the singleplex strategy. The measured methylation values at the age CpGs displayed borderline significant differences between both analytical strategies for six out of 14 CpG sites whereas both strategies delivered equal methylation values for the remaining eight age CpGs. In total, our results indicate that the multiplex strategy can act as a promising alternative for age estimation studies in cases when only limited amounts of DNA samples are available.
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134
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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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135
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Alsaleh H, Haddrill PR. Identifying blood-specific age-related DNA methylation markers on the Illumina MethylationEPIC® BeadChip. Forensic Sci Int 2019; 303:109944. [PMID: 31546163 DOI: 10.1016/j.forsciint.2019.109944] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 08/14/2019] [Accepted: 09/01/2019] [Indexed: 01/02/2023]
Abstract
The past decade has seen rapid development in DNA methylation (DNAm) microarrays, including the Illumina HumanMethylation27 and HumanMethylation450 (450K) chips, which have played an essential role in identifying and evaluating age-related (AR) DNAm markers in different tissues. Recently, a new array, the Illumina MethylationEPIC (EPIC) was introduced, with nearly double the number of probes as the 450K (∼850,000 probes). In this study, we test these newly added probes for age association using a large cohort of 754 DNAm profiles from blood samples assayed on the EPIC BeadChip, for individuals aged 0-88 years old. 52 AR CpG sites (Spearman's abs(rho) >0.6 and P-value <10-83) were identified, 21 of which were novel sites and mapped to 18 genes, nine of which (LHFPL4, SLC12A8, EGFEM1P, GPR158, TAL1, KIAA1755, LOC730668, DUSP16, and FAM65C) have never previously been reported to be associated with age. The data were subsequently split into a 527-sample training set and a 227-sample testing set to build and validate two age prediction models using elastic net regression and multivariate regression. Elastic net regression selected 425 CpG markers with a mean absolute deviation (MAD) of 2.6 years based on the testing set. To build a multivariate linear regression model, AR CpG sites with R2 > 0.5 at FDR < 0.05 were input into stepwise regression to select the best subset for age prediction. The resulting six CpG markers were linearly modelled with age and explained 81% of age-correlated variation in DNAm levels. Age estimation accuracy using bootstrap analysis was 4.5 years, with 95% confidence intervals of 4.56 to 4.57 years based on the testing set. These results suggest that EPIC BeadChip probes for age estimation fall within the range of probes found on the previous Illumina HumanMethylation platforms in terms of their age-prediction ability.
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Affiliation(s)
- Hussain Alsaleh
- Centre for Forensic Science, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, Scotland, UK; General Department for Forensic Evidence, State of Kuwait Ministry of Interior, Kuwait.
| | - Penelope R Haddrill
- Centre for Forensic Science, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, Scotland, UK
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136
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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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137
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Kukla-Bartoszek M, Pośpiech E, Woźniak A, Boroń M, Karłowska-Pik J, Teisseyre P, Zubańska M, Bronikowska A, Grzybowski T, Płoski R, Spólnicka M, Branicki W. DNA-based predictive models for the presence of freckles. Forensic Sci Int Genet 2019; 42:252-259. [DOI: 10.1016/j.fsigen.2019.07.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 06/12/2019] [Accepted: 07/21/2019] [Indexed: 01/05/2023]
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138
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Exploring Epigenetic Age in Response to Intensive Relaxing Training: A Pilot Study to Slow Down Biological Age. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16173074. [PMID: 31450859 PMCID: PMC6747190 DOI: 10.3390/ijerph16173074] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 08/14/2019] [Accepted: 08/20/2019] [Indexed: 12/15/2022]
Abstract
DNA methylation (DNAm) is an emerging estimator of biological aging, i.e., the often-defined "epigenetic clock", with a unique accuracy for chronological age estimation (DNAmAge). In this pilot longitudinal study, we examine the hypothesis that intensive relaxing training of 60 days in patients after myocardial infarction and in healthy subjects may influence leucocyte DNAmAge by turning back the epigenetic clock. Moreover, we compare DNAmAge with another mechanism of biological age, leucocyte telomere length (LTL) and telomerase. DNAmAge is reduced after training in healthy subjects (p = 0.053), but not in patients. LTL is preserved after intervention in healthy subjects, while it continues to decrease in patients (p = 0.051). The conventional negative correlation between LTL and chronological age becomes positive after training in both patients (p < 0.01) and healthy subjects (p < 0.05). In our subjects, DNAmAge is not associated with LTL. Our findings would suggest that intensive relaxing practices influence different aging molecular mechanisms, i.e., DNAmAge and LTL, with a rejuvenating effect. Our study reveals that DNAmAge may represent an accurate tool to measure the effectiveness of lifestyle-based interventions in the prevention of age-related diseases.
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139
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Mansour H, Sperhake JP, Bekaert B, Krebs O, Friedrich P, Fuhrmann A, Püschel K. New aspects of dental implants and DNA technology in human identification. Forensic Sci Int 2019; 302:109926. [PMID: 31444040 DOI: 10.1016/j.forsciint.2019.109926] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 07/11/2019] [Accepted: 08/05/2019] [Indexed: 01/29/2023]
Abstract
Missing, ineligible or delayed reference data to establish conventional dental or DNA identification are common scenarios in forensic practice. Therefore, it is worthwhile to explore new avenues that facilitate human identification. Due to the recent remarkable evolution in the prosthetic dental restorations based on dental implants and the emergence of novel DNA technologies utilized to infer the biological profile, the identification process has become easier than ever before. We report on a characteristic case, which highlights the particular importance of dental implants and DNA approaches in the prospective investigations for human identification. The aim of this publication is to focus on the possibility of identifying the batch numbers, even if they were not engraved in dental implants, making antemortem dental records of dental implants more easily accessible to establish a comparative dental identification. In addition, the reported case presents the supplementary data yielded through estimating the epigenetic age using DNA methylation as well as the biogeographical origin using Y-Haplotype and mitochondrial DNA analyses. Our results demonstrate that expanded oral implant investigations that also include implants extraction and comprehensive microscopic measurements can lead to identifying their batch numbers despite the numerous number of implants systems manufactured and distributed worldwide. Data saved by dental implant manufacturers can be very supportive and represent additional reference data for dental identification, when antemortem dental records are still missing. Furthermore, DNA methylation and mitochondrial DNA analyses can support the progress of investigation.
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Affiliation(s)
- Hussam Mansour
- University Medical Center Hamburg-Eppendorf, Institute of Legal Medicine, Butenfeld34, 22529 Hamburg, Germany.
| | - Jan Peter Sperhake
- University Medical Center Hamburg-Eppendorf, Institute of Legal Medicine, Butenfeld34, 22529 Hamburg, Germany.
| | - Bram Bekaert
- KU Leuven - University of Leuven, Department of Imaging & Pathology, Campus St-Rafaël, Kapucijnenvoer 33, Leuven, Belgium; KU-Leuven - University of Leuven, University Hospitals Leuven, Department of Forensic Medicine, Laboratory of Forensic Genetics and Molecular Archeology, Campus St-Rafaël, Kapucijnenvoer 33, Leuven, Belgium.
| | - Oliver Krebs
- University Medical Center Hamburg-Eppendorf, Institute of Legal Medicine, Butenfeld34, 22529 Hamburg, Germany.
| | - Peter Friedrich
- State Criminal Investigation Department of the City of Hamburg (LKA 41), Bruno-Georges-Platz 1, 22297 Hamburg, Germany.
| | - Andreas Fuhrmann
- University Medical Center Hamburg-Eppendorf, Institute of Legal Medicine, Butenfeld34, 22529 Hamburg, Germany.
| | - Klaus Püschel
- University Medical Center Hamburg-Eppendorf, Institute of Legal Medicine, Butenfeld34, 22529 Hamburg, Germany.
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140
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Abstract
Identifying and validating molecular targets of interventions that extend the human health span and lifespan has been difficult, as most clinical biomarkers are not sufficiently representative of the fundamental mechanisms of ageing to serve as their indicators. In a recent breakthrough, biomarkers of ageing based on DNA methylation data have enabled accurate age estimates for any tissue across the entire life course. These 'epigenetic clocks' link developmental and maintenance processes to biological ageing, giving rise to a unified theory of life course. Epigenetic biomarkers may help to address long-standing questions in many fields, including the central question: why do we age?
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141
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Evaluation of six blood-based age prediction models using DNA methylation analysis by pyrosequencing. Sci Rep 2019; 9:8862. [PMID: 31222117 PMCID: PMC6586942 DOI: 10.1038/s41598-019-45197-w] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 05/22/2019] [Indexed: 01/08/2023] Open
Abstract
DNA methylation has been identified as the most promising molecular biomarker for the prediction of age. Several DNA methylation-based models have been proposed for age prediction based on blood samples, using mainly pyrosequencing. These methods present different performances for age prediction and have rarely, if ever, been evaluated and intercompared in an independent validation study. Here, for the first time, we evaluate and compare six blood-based age prediction models (Bekaert1, Park2, Thong3, Weidner4, and the Zbiec-Piekarska 15 and Zbiec-Piekarska 26), using DNA methylation analysis by pyrosequencing on 100 blood samples from French individuals aged between 19–65 years. For each model, we perform correlation analysis and evaluate age-prediction performance (mean absolute deviation (MAD) and standard error of the estimate (SEE)). The best age-prediction performances were found with the Bekaert and Thong models (MAD of 4.5–5.2, SEE of 6.8–7.2), followed by the Zbiec-Piekarska 1 model (MAD of 6.8 and SEE of 9.2), while the Park, Weidner and Zbiec-Piekarska 2 models presented lower performances (MAD of 7.2–8.7 and SEE of 9.2–10.3). Given these results, we recommend performing systematic, independent evaluation of all age prediction models on a same cohort to validate the different models and compare their performance.
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142
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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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143
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Xu Y, Li X, Yang Y, Li C, Shao X. Human age prediction based on DNA methylation of non-blood tissues. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2019; 171:11-18. [PMID: 30902246 DOI: 10.1016/j.cmpb.2019.02.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 02/12/2019] [Accepted: 02/18/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND AND OBJECTIVE The study of human aging contributes to disease prevention, treatment and life extension. Recently, epigenetics studies have evidenced that there is a close association between DNA methylation and human ages. A quantitatively statistical modeling between DNA methylation and ages could predict the person's age more accurately. METHODS We propose a regression model to predict human age based on gradient boosting regressor (GBR). We collect a total of 1280 publicly available non-blood tissues samples with ages ranged from 0 to 90 years old. We calculate the Pearson correlation between CpG's DNA methylation level and age to select age-related CpGs. RESULTS Thirteen age-related CpG sites are selected. GBR has the smallest mean absolute deviation to the actual age comparing with other three different models including Bayesian ridge, multiple linear regression, and support vector regression. In the training datasets, the cross-validation results show that the correlation R2 between predicted age and DNA methylation is 0.89, and the mean absolute deviation is 4.66 years. In an independent testing set with 262 samples, the GBR achieves the mean absolute deviation of 6.08 years. Meanwhile we also briefly describe the function of the selected thirteen CpG sites. CONCLUSIONS We build an age predictor to study the association between ages and the DNA methylation of human non-blood tissues. Our new model provides a more accurate estimation of human ages which will be instrumental for understanding the regulation of DNA methylation on human aging and will accurately monitor the individual aging process.
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Affiliation(s)
- Yan Xu
- School of Mathematics and Physics, University of Science and Technology Beijing, Beijing 100083, China; Beijing Key Laboratory for Magneto-photoelectrical Composite and Interface Science, University of Science and Technology Beijing, Beijing 100083, China.
| | - Xingyan Li
- School of Mathematics and Physics, University of Science and Technology Beijing, Beijing 100083, China.
| | - Yingxi Yang
- School of Mathematics and Physics, University of Science and Technology Beijing, Beijing 100083, China.
| | - Chunhui Li
- School of Mathematics and Statistics, Beijing Institute of Technology, Beijing 100081, China.
| | - Xiaojian Shao
- Digital Technologies Research Centre, National Research Council Canada, Ottawa, Ontario K1A 0R6, Canada.
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144
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Peng F, Feng L, Chen J, Wang L, Li P, Ji A, Zeng C, Liu F, Li C. Validation of methylation-based forensic age estimation in time-series bloodstains on FTA cards and gauze at room temperature conditions. Forensic Sci Int Genet 2019; 40:168-174. [PMID: 30878720 DOI: 10.1016/j.fsigen.2019.03.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 02/18/2019] [Accepted: 03/05/2019] [Indexed: 01/17/2023]
Abstract
We previously proposed a prediction model consisting of 9 CpG sites for forensic age estimation with high practical potentials in Chinese males. Here, we further evaluated the performance of this prediction model in two independent batches of time-series bloodstain samples naturally exposed to room temperature conditions. The first batch consists of 30 Han Chinese males (18-59 years of age) whose peripheral blood was converted into bloodstains on Flinders Technology Association (FTA) cards and naturally exposed to room temperature conditions for different time points up to 3 months. The second batch consists of 99 Han Chinese males (21-66 years of age) whose peripheral blood was divided into 3 replicates, converted into bloodstains on gauze, and naturally exposed to room temperature conditions for 3 months. For each time point and each replicate, the methylation levels at the 9 CpG sites were detected using the EpiTYPER system. Applying the 9-CpG age prediction model to these bloodstain samples resulted in highly accurate age predictions for all time points and replicates (0.81 <R2 < 0.91, 2.94 < MAD < 3.55 years). The updated model combining our previous and current data achieved similarly high prediction results. Therefore, our 9-CpG age prediction model was successfully validated in time-series bloodstain samples converted on both FTA card and gauze under natural room temperature conditions, demonstrating high potentials in future forensic applications to Han Chinese males.
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Affiliation(s)
- Fuduan Peng
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Lei Feng
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, Ministry of Public Security, Beijing, China.
| | - Jing Chen
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, Ministry of Public Security, Beijing, China
| | - Ling Wang
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, Ministry of Public Security, Beijing, China
| | - Pei Li
- Xingtai Public Security Bureau, Hebei, China
| | - Anquan Ji
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, Ministry of Public Security, Beijing, China
| | - Changqing Zeng
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Fan Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China; Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands.
| | - Caixia Li
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, Ministry of Public Security, Beijing, China.
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145
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Li G, Liu KY, Qiu ZP. An integrative module analysis of DNA methylation landscape in aging. Exp Ther Med 2019; 17:3411-3416. [PMID: 30988719 PMCID: PMC6447821 DOI: 10.3892/etm.2019.7334] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 02/06/2019] [Indexed: 02/02/2023] Open
Abstract
To investigate the molecular mechanism of aging, the combination of module analysis and DNA methylation data was used to detect dynamically controlled modules for aging. Multiple differential expression networks (DENs) were constructed based on the microarray profiles across different aging groups (<70 years, 70–80 years, and >80 years). Next, a module-based approach was utilized to extract the common candidate modules across all age groups. We used Module Connectivity Dynamic Score (MCDS) to quantify the connectivity change of the common modules among the different age groups. Functional analyses were implemented for the genes in the common modules to further identify the significant biological processes. A total of two DENs were constructed. Overall 657 informative genes were screened out. When false discovery rate (FDR) was set as 0.05, we found that 148 modules were significant. Only 1 significant 2-differential modules (DMs) (module 493) with dynamic changes was discovered. Significantly, the genes in the module 493 participated in 7 significant pathways, including pentose phosphate pathway, carbon metabolism, and citrate cycle (TCA cycle). In conclusion, pathway functions [pentose phosphate pathway, carbon metabolism, citrate cycle (TCA cycle), chromosomal instability, ateroid biosynthesis, PPAR signaling pathway, and immune response] may serve as potential therapeutic targets in aging.
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Affiliation(s)
- Gang Li
- Department of Orthopedics, School of Medicine, Shihezi University, Shihezi, Xinjiang 832000, P.R. China
| | - Ke-Yu Liu
- Department of Orthopedics, School of Medicine, Shihezi University, Shihezi, Xinjiang 832000, P.R. China
| | - Zhong-Peng Qiu
- Department of Orthopedics, School of Medicine, Shihezi University, Shihezi, Xinjiang 832000, P.R. China
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146
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Richards R, Patel J, Stevenson K, Harbison S. Assessment of DNA methylation markers for forensic applications. AUST J FORENSIC SCI 2019. [DOI: 10.1080/00450618.2019.1574898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- R. Richards
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | - J. Patel
- The Institute of Environmental Science & Research Ltd. (ESR), Auckland, New Zealand
| | - K. Stevenson
- The Institute of Environmental Science & Research Ltd. (ESR), Auckland, New Zealand
| | - S. Harbison
- The Institute of Environmental Science & Research Ltd. (ESR), Auckland, New Zealand
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147
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Ashapkin VV, Kutueva LI, Vanyushin BF. Epigenetic Clock: Just a Convenient Marker or an Active Driver of Aging? ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1178:175-206. [PMID: 31493228 DOI: 10.1007/978-3-030-25650-0_10] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A global DNA hypomethylation and local changes in the methylation levels of specific DNA loci occur during aging in mammals. Global hypomethylation mainly affects highly methylated repeat sequences, such as transposable elements; it is an essentially stochastic process usually referred to as "epigenetic drift." Specific changes in DNA methylation affect various genome sequences and could be either hypomethylation or hypermethylation, but the prevailing tendencies are hypermethylation of promoter sequences associated with CpG islands and hypomethylation of CpG poor genes. Methylation levels of multiple CpG sites display a strong correlation to age common between individuals of the same species. Collectively, methylation of such CpG sites could be used as "epigenetic clocks" to predict biological age. Furthermore, the discrepancy between epigenetic and chronological ages could be predictive of all-cause mortality and multiple age-associated diseases. Random changes in DNA methylation (epigenetic drift) could also affect the aging phenotype, causing accidental changes in gene expression and increasing the transcriptional noise between cells of the same tissue. Both effects could become detrimental to tissue functioning and cause a gradual decline in organ function during aging. Strong evidence shows that epigenetic systems contribute to lifespan control in various organisms. Similar to other cell systems, the epigenome is prone to gradual degradation due to the genome damage, stressful agents and other aging factors. However, unlike mutations and many other hallmarks of aging, age-related epigenetic changes could be fully or partially reversed to a "young" state.
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Affiliation(s)
- Vasily V Ashapkin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.
| | - Lyudmila I Kutueva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Boris F Vanyushin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
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148
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Hong SR, Shin KJ, Jung SE, Lee EH, Lee HY. Platform-independent models for age prediction using DNA methylation data. Forensic Sci Int Genet 2019; 38:39-47. [DOI: 10.1016/j.fsigen.2018.10.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 09/07/2018] [Accepted: 10/08/2018] [Indexed: 10/28/2022]
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149
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DNA methylation-based age prediction using massively parallel sequencing data and multiple machine learning models. Forensic Sci Int Genet 2018; 37:215-226. [DOI: 10.1016/j.fsigen.2018.09.003] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 08/23/2018] [Accepted: 09/06/2018] [Indexed: 01/09/2023]
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150
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Kowalczyk M, Zawadzka E, Szewczuk D, Gryzińska M, Jakubczak A. Molecular markers used in forensic genetics. MEDICINE, SCIENCE, AND THE LAW 2018; 58:201-209. [PMID: 30269675 DOI: 10.1177/0025802418803852] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Forensic genetics is a field that has become subject to increasing interest in recent years. Both the technology and the markers used for forensic purposes have changed since the 1980s. The minisatellite sequences used in the famous Pitchfork case introduced genetics to the forensic sciences. Minisatellite sequences have now been replaced by more sensitive microsatellite markers, which have become the basis for the creation of genetic profile databases. Modern molecular methods also exploit single nucleotide polymorphisms, which are often the only way to identify degraded DNA samples. The same type of variation is taken into consideration in attempting to establish the ethnicity of a perpetrator and to determine phenotypic traits such as the eye or hair colour of the individual who is the source of the genetic material. This paper contains a review of the techniques and molecular markers used in human and animal forensic genetics, and also presents the potential trends in forensic genetics such as phenotyping.
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Affiliation(s)
- Marek Kowalczyk
- 1 Department of Biological Basis of Animal Production, Faculty of Biology, Animal Sciences and Bioeconomy, University of Life Sciences in Lublin, Poland
| | - Ewelina Zawadzka
- 1 Department of Biological Basis of Animal Production, Faculty of Biology, Animal Sciences and Bioeconomy, University of Life Sciences in Lublin, Poland
| | | | - Magdalena Gryzińska
- 1 Department of Biological Basis of Animal Production, Faculty of Biology, Animal Sciences and Bioeconomy, University of Life Sciences in Lublin, Poland
| | - Andrzej Jakubczak
- 1 Department of Biological Basis of Animal Production, Faculty of Biology, Animal Sciences and Bioeconomy, University of Life Sciences in Lublin, Poland
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