Isolation and identification of age-related DNA methylation markers for forensic age-prediction

2014 ◽  
Vol 11 ◽  
pp. 117-125 ◽  
Author(s):  
Shao Hua Yi ◽  
Long Chang Xu ◽  
Kun Mei ◽  
Rong Zhi Yang ◽  
Dai Xin Huang
Keyword(s):  
Dna Methylation ◽  
Isolation And Identification ◽  
Age Related ◽  
Age Prediction

scholarly journals Human Age Prediction Based on DNA Methylation Using a Gradient Boosting Regressor

Genes ◽  
2018 ◽  
Vol 9 (9) ◽  
pp. 424 ◽  
Author(s):  
Xingyan Li ◽  
Weidong Li ◽  
Yan Xu
Keyword(s):  
Dna Methylation ◽  
Pearson Correlation ◽  
Training Data ◽  
Training Dataset ◽  
Gradient Boosting ◽  
Independent Dataset ◽  
Blood Samples ◽  
Cpg Sites ◽  
Age Related ◽  
Age Prediction

All tissues of organisms will become old as time goes on. In recent years, epigenetic investigations have found that there is a close correlation between DNA methylation and aging. With the development of DNA methylation research, a quantitative statistical relationship between DNA methylation and different ages was established based on the change rule of methylation with age, it is then possible to predict the age of individuals. All the data in this work were retrieved from the Illumina HumanMethylation BeadChip platform (27K or 450K). We analyzed 16 sets of healthy samples and 9 sets of diseased samples. The healthy samples included a total of 1899 publicly available blood samples (0–103 years old) and the diseased samples included 2395 blood samples. Six age-related CpG sites were selected through calculating Pearson correlation coefficients between age and DNA methylation values. We built a gradient boosting regressor model for these age-related CpG sites. 70% of the data was randomly selected as training data and the other 30% as independent data in each dataset for 25 runs in total. In the training dataset, the healthy samples showed that the correlation between predicted age and DNA methylation was 0.97, and the mean absolute deviation (MAD) was 2.72 years. In the independent dataset, the MAD was 4.06 years. The proposed model was further tested using the diseased samples. The MAD was 5.44 years for the training dataset and 7.08 years for the independent dataset. Furthermore, our model worked well when it was applied to saliva samples. These results illustrated that the age prediction based on six DNA methylation markers is very effective using the gradient boosting regressor.

Age-related DNA methylation changes for forensic age-prediction

2014 ◽  
Vol 129 (2) ◽  
pp. 237-244 ◽  
Author(s):  
Shao Hua Yi ◽  
Yun Shu Jia ◽  
Kun Mei ◽  
Rong Zhi Yang ◽  
Dai Xin Huang
Keyword(s):  
Dna Methylation ◽  
Age Related ◽  
Age Prediction

scholarly journals DNA methylation differs extensively between strains of the same geographical origin and changes with age in Daphnia magna

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Jack Hearn ◽  
Fiona Plenderleith ◽  
Tom J. Little
Keyword(s):  
Dna Methylation ◽  
Caloric Restriction ◽  
Daphnia Magna ◽  
Single Gene ◽  
Methylation Status ◽  
Strain Differences ◽  
Life History Trait ◽  
Food Level ◽  
Epigenetic Clock ◽  
Age Related

Abstract Background Patterns of methylation influence lifespan, but methylation and lifespan may also depend on diet, or differ between genotypes. Prior to this study, interactions between diet and genotype have not been explored together to determine their influence on methylation. The invertebrate Daphnia magna is an excellent choice for testing the epigenetic response to the environment: parthenogenetic offspring are identical to their siblings (making for powerful genetic comparisons), they are relatively short lived and have well-characterised inter-strain life-history trait differences. We performed a survival analysis in response to caloric restriction and then undertook a 47-replicate experiment testing the DNA methylation response to ageing and caloric restriction of two strains of D. magna. Results Methylated cytosines (CpGs) were most prevalent in exons two to five of gene bodies. One strain exhibited a significantly increased lifespan in response to caloric restriction, but there was no effect of food-level CpG methylation status. Inter-strain differences dominated the methylation experiment with over 15,000 differently methylated CpGs. One gene, Me31b, was hypermethylated extensively in one strain and is a key regulator of embryonic expression. Sixty-one CpGs were differentially methylated between young and old individuals, including multiple CpGs within the histone H3 gene, which were hypermethylated in old individuals. Across all age-related CpGs, we identified a set that are highly correlated with chronological age. Conclusions Methylated cytosines are concentrated in early exons of gene sequences indicative of a directed, non-random, process despite the low overall DNA methylation percentage in this species. We identify no effect of caloric restriction on DNA methylation, contrary to our previous results, and established impacts of caloric restriction on phenotype and gene expression. We propose our approach here is more robust in invertebrates given genome-wide CpG distributions. For both strain and ageing, a single gene emerges as differentially methylated that for each factor could have widespread phenotypic effects. Our data showed the potential for an epigenetic clock at a subset of age positions, which is exciting but requires confirmation.

scholarly journals Age-related differences in monocyte DNA methylation and immune function in healthy Kenyan adults and children

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Katherine R. Dobbs ◽  
Paula Embury ◽  
Emmily Koech ◽  
Sidney Ogolla ◽  
Stephen Munga ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Young Adults ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Innate Immune ◽  
Inflammatory Gene Expression ◽  
Cpg Sites ◽  
Age Related ◽  
Adults And Children

Abstract Background Age-related changes in adaptive and innate immune cells have been associated with a decline in effective immunity and chronic, low-grade inflammation. Epigenetic, transcriptional, and functional changes in monocytes occur with aging, though most studies to date have focused on differences between young adults and the elderly in populations with European ancestry; few data exist regarding changes that occur in circulating monocytes during the first few decades of life or in African populations. We analyzed DNA methylation profiles, cytokine production, and inflammatory gene expression profiles in monocytes from young adults and children from western Kenya. Results We identified several hypo- and hyper-methylated CpG sites in monocytes from Kenyan young adults vs. children that replicated findings in the current literature of differential DNA methylation in monocytes from elderly persons vs. young adults across diverse populations. Differentially methylated CpG sites were also noted in gene regions important to inflammation and innate immune responses. Monocytes from Kenyan young adults vs. children displayed increased production of IL-8, IL-10, and IL-12p70 in response to TLR4 and TLR2/1 stimulation as well as distinct inflammatory gene expression profiles. Conclusions These findings complement previous reports of age-related methylation changes in isolated monocytes and provide novel insights into the role of age-associated changes in innate immune functions.

DNA methylation-based age clocks: From age prediction to age reversion

2021 ◽  
Vol 68 ◽  
pp. 101314
Author(s):  
Rezvan Noroozi ◽  
Soudeh Ghafouri-Fard ◽  
Aleksandra Pisarek ◽  
Joanna Rudnicka ◽  
Magdalena Spólnicka ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Age Prediction

scholarly journals The mediating effect of lifestyles on the association between social factors and DNA methylation

2020 ◽  
Vol 30 (Supplement_5) ◽  
Author(s):  
A Maugeri ◽  
M Barchitta ◽  
G Favara ◽  
C La Mastra ◽  
MC La Rosa ◽  
...  
Keyword(s):  
Physical Activity ◽  
Dna Methylation ◽  
Socioeconomic Status ◽  
Mediterranean Diet ◽  
Educational Level ◽  
Methylation Level ◽  
Mediating Effect ◽  
High Educational Level ◽  
Age Related ◽  
High Educational

Abstract Background Social disadvantage and unhealthy lifestyles may induce molecular changes associated with aging and age-related diseases. For instance, previous studies reported socioeconomic difference in DNA methylation, which in turn led to aberrant gene expression and genome instability. Socioeconomic status (SES) alone, however, does not completely explain this difference, and further studies are needed to unveil what factors contribute to it. Methods We conducted a cross-sectional study on 349 Italian women, aged 25-64 years, to assess SES differences in LINE-1 methylation level - a surrogate marker of global DNA methylation - and to examine the mediating effect of lifestyles (i.e. diet, smoking habits, physical activity, and weight status). Educational level was used as SES indicator. The adherence to Mediterranean diet (MD) was assessed by the Mediterranean Diet Score (MDS). Leukocyte LINE-1 methylation was assessed by pyrosequencing. Mediation analysis was conducted using the PROCESS macro for the SPSS software. Results We first observed that women with high educational level were more likely to be normal weight (p < 0.001) and to adhere to MD (p = 0.018), and less likely to perform physical activity (p = 0.012) than their less educated counterpart. Moreover, age-adjusted linear regression demonstrated that LINE-1 methylation level increased with increasing educational level (β = 0.016; SE = 0.003; p < 0.001). In line, mediation analysis demonstrated an indirect effect of high educational level on LINE-1 methylation through the adherence to MD (β = 0.003; 95%CI=0.001-0.006). Specifically, the mediator could account for 9.5% of the total effect. None of the other lifestyles, instead, exhibited a significant mediating effect. Conclusions To our knowledge, this is the first study demonstrating the mediation of diet in the relationship between SES and DNA methylation. Thus, our findings add even more value to the promotion of healthy dietary habits among social disadvantaged people. Key messages Social disadvantage is associated with epigenetic changes related to aging and age-related diseases. Adherence to the Mediterranean diet might mediate the association between socioeconomic status and DNA methylation.

scholarly journals Age Prediction of Human Based on DNA Methylation by Blood Tissues

Genes ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 870
Author(s):  
Jiansheng Zhang ◽  
Hongli Fu ◽  
Yan Xu
Keyword(s):  
Dna Methylation ◽  
Pearson Correlation ◽  
Close Correlation ◽  
Gradient Boosting ◽  
Tissue Samples ◽  
Regression Methods ◽  
Cpg Sites ◽  
Testing Dataset ◽  
Age Related ◽  
Better Than

In recent years, scientists have found a close correlation between DNA methylation and aging in epigenetics. With the in-depth research in the field of DNA methylation, researchers have established a quantitative statistical relationship to predict the individual ages. This work used human blood tissue samples to study the association between age and DNA methylation. We built two predictors based on healthy and disease data, respectively. For the health data, we retrieved a total of 1191 samples from four previous reports. By calculating the Pearson correlation coefficient between age and DNA methylation values, 111 age-related CpG sites were selected. Gradient boosting regression was utilized to build the predictive model and obtained the R2 value of 0.86 and MAD of 3.90 years on testing dataset, which were better than other four regression methods as well as Horvath’s results. For the disease data, 354 rheumatoid arthritis samples were retrieved from a previous study. Then, 45 CpG sites were selected to build the predictor and the corresponded MAD and R2 were 3.11 years and 0.89 on the testing dataset respectively, which showed the robustness of our predictor. Our results were better than the ones from other four regression methods. Finally, we also analyzed the twenty-four common CpG sites in both healthy and disease datasets which illustrated the functional relevance of the selected CpG sites.

scholarly journals Author Correction: Artificial neural network, predictor variables and sensitivity threshold for DNA methylation-based age prediction using blood samples

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Zhonghui Thong ◽  
Jolena Ying Ying Tan ◽  
Eileen Shuzhen Loo ◽  
Yu Wei Phua ◽  
Xavier Liang Shun Chan ◽  
...  
Keyword(s):  
Neural Network ◽  
Dna Methylation ◽  
Artificial Neural Network ◽  
Predictor Variables ◽  
Sensitivity Threshold ◽  
Blood Samples ◽  
Artificial Neural ◽  
Age Prediction

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

scholarly journals DNA methylation is associated with airflow obstruction in patients living with HIV

Thorax ◽  
2020 ◽  
pp. thoraxjnl-2020-215866
Author(s):  
Ana I Hernandez Cordero ◽  
Chen Xi Yang ◽  
Maen Obeidat ◽  
Julia Yang ◽  
Julie MacIsaac ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Lung Function ◽  
Viral Infections ◽  
Airflow Obstruction ◽  
Normal Lung ◽  
People Living With Hiv ◽  
Global Methylation ◽  
Age Related ◽  
Impaired Lung Function ◽  
Living With Hiv

IntroductionPeople living with HIV (PLWH) suffer from age-related comorbidities such as COPD. The processes responsible for reduced lung function in PLWH are largely unknown. We performed an epigenome-wide association study to investigate whether blood DNA methylation is associated with impaired lung function in PLWH.MethodsUsing blood DNA methylation profiles from 161 PLWH, we tested the effect of methylation on FEV1, FEV1/FVC ratio and FEV1 decline over a median of 5 years. We evaluated the global methylation of PLWH with airflow obstruction by testing the differential methylation of transposable elements Alu and LINE-1, a well-described marker of epigenetic ageing.ResultsAirflow obstruction as defined by a FEV1/FVC<0.70 was associated with 1393 differentially methylated positions (DMPs), while 4676 were associated with airflow obstruction based on the FEV1/FVC<lower limit of normal. These DMPs were enriched for biological pathways associated with chronic viral infections. The airflow obstruction group was globally hypomethylated compared with those without airflow obstruction. 103 and 7112 DMPs were associated with FEV1 and FEV1/FVC, respectively. No positions were associated with FEV1 decline.ConclusionA large number of DMPs were associated with airflow obstruction and lung function in a unique cohort of PLWH. Airflow obstruction in even relatively young PLWH is associated with global hypomethylation, suggesting advanced epigenetic ageing compared with those with normal lung function. The disturbance of the epigenetic regulation of key genes not previously identified in non-HIV COPD cohorts could explain the unique risk of COPD in PLWH.

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