DNA methylation and chromatin accessibility predict age in the domestic dog

Across mammals, the epigenome is highly predictive of chronological age. These “epigenetic clocks,” most of which have been built using DNA methylation (DNAm) profiles, have gained traction as biomarkers of aging and organismal health. While the ability of DNAm to predict chronological age has been repeatedly demonstrated, the ability of other epigenetic features to predict age remains unclear. Here, we use two types of epigenetic information—DNAm, and chromatin accessibility as measured by ATAC-seq—to develop age predictors in peripheral blood mononuclear cells sampled from a population of domesticated dogs. We measured DNAm and ATAC-seq profiles for 71 dogs, building separate predictive clocks from each, as well as the combined dataset. We also use fluorescence-assisted cell sorting to quantify major lymphoid populations for each sample. We found that chromatin accessibility can accurately predict chronological age (R²_ATAC = 26%), though less accurately than the DNAm clock (R²_DNAm = 33%), and the clock built from the combined datasets was comparable to both (R²_combined = 29%). We also observed various populations of CD62L+ T cells significantly correlated with dog age. Finally, we found that all three clocks selected features that were in or near at least two protein-coding genes: BAIAP2 and SCARF2, both previously implicated in processes related to cognitive or neurological impairment. Taken together, these results highlight the potential of chromatin accessibility as a complementary epigenetic resource for modeling and investigating biologic age.     

Prediction of Cardiorespiratory Fitness by the Six-Minute Step Test and Its Association with Muscle Strength and Power in Sedentary Obese and Lean Young Women: A Cross-Sectional Study

Impaired cardiorespiratory fitness (CRF) is a hallmark characteristic in obese and lean sedentary young women. Peak oxygen consumption (VO_2peak) prediction from the six-minute step test (6MST) has not been established for sedentary females. It is recognized that lower-limb muscle strength and power play a key role during functional activities. The aim of this study was to investigate cardiorespiratory responses during the 6MST and CPX and to develop a predictive equation to estimate VO_2peak in both lean and obese subjects. Additionally we aim to investigate how muscle function impacts functional performance. Lean (LN = 13) and obese (OB = 18) women, aged 20–45, underwent a CPX, two 6MSTs, and isokinetic and isometric knee extensor strength and power evaluations. Regression analysis assessed the ability to predict VO_2peak from the 6MST, age and body mass index (BMI). CPX and 6MST main outcomes were compared between LN and OB and correlated with strength and power variables. CRF, functional capacity, and muscle strength and power were lower in the OB compared to LN (<0.05). During the 6MST, LN and OB reached ~90% of predicted maximal heart rate and ~80% of the VO_2peak obtained during CPX. BMI, age and number of step cycles (NSC) explained 83% of the total variance in VO_2peak. Moderate to strong correlations between VO_2peak at CPX and VO_2peak at 6MST (r = 0.86), VO_2peak at CPX and NSC (r = 0.80), as well as between VO_2peak, NSC and muscle strength and power variables were found (p<0.05). These findings indicate the 6MST, BMI and age accurately predict VO_2peak in both lean and obese young sedentary women. Muscle strength and power were related to measures of aerobic and functional performance.     

DNA methylation age is associated with mortality in a longitudinal Danish twin study

An epigenetic profile defining the DNA methylation age (DNAm age) of an individual has been suggested to be a biomarker of aging, and thus possibly providing a tool for assessment of health and mortality. In this study, we estimated the DNAm age of 378 Danish twins, age 30–82 years, and furthermore included a 10‐year longitudinal study of the 86 oldest‐old twins (mean age of 86.1 at follow‐up), which subsequently were followed for mortality for 8 years. We found that the DNAm age is highly correlated with chronological age across all age groups (r = 0.97), but that the rate of change of DNAm age decreases with age. The results may in part be explained by selective mortality of those with a high DNAm age. This hypothesis was supported by a classical survival analysis showing a 35% (4–77%) increased mortality risk for each 5‐year increase in the DNAm age vs. chronological age. Furthermore, the intrapair twin analysis revealed a more‐than‐double mortality risk for the DNAm oldest twin compared to the co‐twin and a ‘dose–response pattern’ with the odds of dying first increasing 3.2 (1.05–10.1) times per 5‐year DNAm age difference within twin pairs, thus showing a stronger association of DNAm age with mortality in the oldest‐old when controlling for familial factors. In conclusion, our results support that DNAm age qualifies as a biomarker of aging.     

Developmental origins of physical fitness: the Helsinki Birth Cohort Study

Background

Cardiorespiratory fitness (CRF) is a major factor influencing health and disease outcomes including all-cause mortality and cardiovascular disease. Importantly CRF is also modifiable and could therefore have a major public health impact. Early life exposures play a major role in chronic disease development. Our aim was to explore the potential prenatal and childhood origins of CRF in later life.

Methods/Principal Findings

This sub-study of the HBCS (Helsinki Birth Cohort Study) includes 606 men and women who underwent a thorough clinical examination and participated in the UKK 2-km walk test, which has been validated against a maximal exercise stress test as a measure of CRF in population studies. Data on body size at birth and growth during infancy and childhood were obtained from hospital, child welfare and school health records. Body size at birth was not associated with adult CRF. A 1 cm increase in height at 2 and 7 years was associated with 0.21 ml/kg/min (95% CI 0.02 to 0.40) and 0.16 ml/kg/min (95% CI 0.03 to 0.28) higher VO_2max, respectively. Adjustment for adult lean body mass strengthened these findings. Weight at 2 and 7 years and height at 11 years became positively associated with CRF after adult lean body mass adjustment. However, a 1 kg/m² higher BMI at 11 years was associated with −0.57 ml/kg/min (95% CI −0.91 to −0.24) lower adult VO_2max, and remained so after adjustment for adult lean body mass.

Conclusion/Significance

We did not observe any significant associations between body size at birth and CRF in later life. However, childhood growth was associated with CRF in adulthood. These findings suggest, importantly from a public point of view, that early growth may play a role in predicting adult CRF.     

The association between adverse childhood experiences and epigenetic age acceleration in the Canadian longitudinal study on aging (CLSA)

Research examining the association between exposure to a wide range of adverse childhood experiences (ACEs) and accelerated biological aging in older adults is limited. The purpose of this study was to examine the association of ACEs, both as a cumulative score and individual forms of adversity, with epigenetic age acceleration assessed using the DNA methylation (DNAm) GrimAge and DNAm PhenoAge epigenetic clocks in middle and older-aged adults. This cross-sectional study analyzed baseline and first follow-up data on 1445 participants aged 45–85 years from the Canadian Longitudinal Study on Aging (CLSA) who provided blood samples for DNAm analysis. ACEs were assessed using a validated self-reported questionnaire. Epigenetic age acceleration was estimated by regressing each epigenetic clock estimate on chronological age. Cumulative ACEs score was associated with higher DNAm GrimAge acceleration (β: 0.07; 95% CI: 0.02, 0.11) after adjusting for covariates. Childhood exposure to parental separation or divorce (β: 0.06; 95% CI: 0.00, 0.11) and emotional abuse (β: 0.06; 95% CI: 0.00, 0.12) were associated with higher DNAm GrimAge acceleration after adjusting for other adversities and covariates. There was no statistical association between ACEs and DNAm PhenoAge acceleration. Early life adversity may become biologically embedded and lead to premature biological aging, in relation to DNAm GrimAge, which estimates risk of mortality. Strategies that increase awareness of ACEs and promote healthy child development are needed to prevent ACEs.     

Development of DNA methylation-based epigenetic age predictors in loblolly pine (Pinus taeda)

Biological ageing is connected to life history variation across ecological scales and informs a basic understanding of age-related declines in organismal function. Altered DNA methylation dynamics are a conserved aspect of biological ageing and have recently been modelled to predict chronological age among vertebrate species. In addition to their utility in estimating individual age, differences between chronological and predicted ages arise due to acceleration or deceleration of epigenetic ageing, and these discrepancies are linked to disease risk and multiple life history traits. Although evidence suggests that patterns of DNA methylation can describe ageing in plants, predictions with epigenetic clocks have yet to be performed. Here, we resolve the DNA methylome across CpG, CHG, and CHH-methylation contexts in the loblolly pine tree (Pinus taeda) and construct epigenetic clocks capable of predicting ages in this species within 6% of its maximum lifespan. Although patterns of CHH-methylation showed little association with age, both CpG and CHG-methylation contexts were strongly associated with ageing, largely becoming hypomethylated with age. Among age-associated loci were those in close proximity to malate dehydrogenase, NADH dehydrogenase, and 18S and 26S ribosomal RNA genes. This study reports one of the first epigenetic clocks in plants and demonstrates the universality of age-associated DNA methylation dynamics which can inform conservation and management practices, as well as our ecological and evolutionary understanding of biological ageing in plants.     

Obesity Is Associated With Altered Lung Function Independently of Physical Activity and Fitness

Measures of obesity, especially central adiposity, have been associated with reduced lung function. However, previous studies may have been affected by confounding by physical activity and fitness. This study aimed to examine the relationship among body fatness, fat distribution, and lung function, adjusted for physical activity energy expenditure (PAEE) and aerobic fitness (VO₂max), in a cohort of British white adults with a family history of type 2 diabetes. A total of 320 adults (mean age 40.4 ± 6.0 years) attended for anthropometric and VO₂max testing, and had ambulatory heart rate monitoring for 4 days to determine PAEE. Spirometry was used to measure forced expiratory volume in 1 s (FEV₁) and forced vital capacity (FVC). The tests were repeated 12 months later, and a cross‐sectional analysis using linear regression with repeated measures was performed. Measures of obesity (BMI, waist circumference (WC), fat mass (FM), body fat percentage (BF%)) were associated with lower lung function in men and women (P < 0.01), while waist‐to‐hip ratio (WHR) was associated with lower lung function in men only (P < 0.001). Associations remained after adjusting for age, smoking status, height, PAEE, and VO₂max. The estimated difference in mean FEV₁ and FVC per unit increase in the exposure measures were consistently stronger in men compared to women (P for interaction <0.001). Obesity is inversely associated with lung function in adults, but central fat distribution appears to have a stronger relationship with respiratory mechanics in men than in women. These associations were independent of the degree of physical activity and aerobic fitness in this cohort.     

Epigenetic age is a cell‐intrinsic property in transplanted human hematopoietic cells

The age of tissues and cells can be accurately estimated by DNA methylation analysis. The multitissue DNA methylation (DNAm) age predictor combines the DNAm levels of 353 CpG dinucleotides to arrive at an age estimate referred to as DNAm age. Recent studies based on short‐term observations showed that the DNAm age of reconstituted blood following allogeneic hematopoietic stem cell transplantation (HSCT) reflects the age of the donor. However, it is not known whether the DNAm age of donor blood remains independent of the recipient's age over the long term. Importantly, long‐term studies including child recipients have the potential to clearly reveal whether DNAm age is cell‐intrinsic or whether it is modulated by extracellular cues in vivo. Here, we address this question by analyzing blood methylation data from HSCT donor and recipient pairs who greatly differed in chronological age (age differences between 1 and 49 years). We found that the DNAm age of the reconstituted blood was not influenced by the recipient's age, even 17 years after HSCT, in individuals without relapse of their hematologic disorder. However, the DNAm age of recipients with relapse of leukemia was unstable. These data are consistent with our previous findings concerning the abnormal DNAm age of cancer cells, and it can potentially be exploited to monitor the health of HSCT recipients. Our data demonstrate that transplanted human hematopoietic stem cells have an intrinsic DNAm age that is unaffected by the environment in a recipient of a different age.     

Epigenetic Aging Signatures Are Coherently Modified in Cancer

Aging is associated with highly reproducible DNA methylation (DNAm) changes, which may contribute to higher prevalence of malignant diseases in the elderly. In this study, we analyzed epigenetic aging signatures in 5,621 DNAm profiles of 25 cancer types from The Cancer Genome Atlas (TCGA). Overall, age-associated DNAm patterns hardly reflect chronological age of cancer patients, but they are coherently modified in a non-stochastic manner, particularly at CpGs that become hypermethylated upon aging in non-malignant tissues. This coordinated regulation in epigenetic aging signatures can therefore be used for aberrant epigenetic age-predictions, which facilitate disease stratification. For example, in acute myeloid leukemia (AML) higher epigenetic age-predictions are associated with increased incidence of mutations in RUNX1, WT1, and IDH2, whereas mutations in TET2, TP53, and PML-PARA translocation are more frequent in younger age-predictions. Furthermore, epigenetic aging signatures correlate with overall survival in several types of cancer (such as lower grade glioma, glioblastoma multiforme, esophageal carcinoma, chromophobe renal cell carcinoma, cutaneous melanoma, lung squamous cell carcinoma, and neuroendocrine neoplasms). In conclusion, age-associated DNAm patterns in cancer are not related to chronological age of the patient, but they are coordinately regulated, particularly at CpGs that become hypermethylated in normal aging. Furthermore, the apparent epigenetic age-predictions correlate with clinical parameters and overall survival in several types of cancer, indicating that regulation of DNAm patterns in age-associated CpGs is relevant for cancer development.     

FTO Genotype and the Weight Loss Benefits of Moderate Intensity Exercise

The fat mass and obesity‐associated (FTO) gene was genotyped for the participants in the Dose‐Response to Exercise in postmenopausal Women (DREW) trial and analyses were performed to determine whether an FTO variant was associated with adiposity and cardiorespiratory fitness (CRF) before and after 6 months of moderate intensity exercise in white women (n = 234). The A/A homozygotes for rs8050136 had a higher BMI (kg/m²) compared to C/C homozygotes at baseline (32.8 (0.6) vs. 31.0 (0.4), respectively; P < 0.05) and at follow‐up (31.9 (0.6) vs. 30.4 (0.5), respectively; P < 0.05). Weight loss occurred after exercise, but there was no significant genotype by exercise interaction over time. Exploratory analyses among women exposed to moderate intensity exercise meeting, or exceeding, the physical activity recommendation found that those homozygous A/A lost significantly more weight than the C allele carriers (?3.3 (0.7) kg vs. ?1.4 (0.4) kg and ?1.5 (0.5) kg, respectively; P < 0.05). CRF, defined as VO_2peak (oxygen consumption), increased after exercise and the magnitude of the increase was similar for each genotype. In conclusion, women genetically predisposed to being obese experienced weight loss and CRF benefits with moderate intensity exercise, with additional weight loss observed when the women met or exceeded the physical activity recommendations.     

Circulating MicroRNAs and Aerobic Fitness – The HUNT-Study

Aerobic fitness, measured as maximal oxygen uptake (VO_2max), is a good indicator of cardiovascular health, and a strong predictor of cardiovascular mortality. Biomarkers associated with low VO_2max may therefore represent potential early markers of future cardiovascular disease (CVD). The aim of this study was to assess whether circulating microRNAs (miRs) are associated with VO_2max-level in healthy individuals. In a screening study, 720 miRs were measured in serum samples from healthy individuals (40–45 yrs) with high (n = 12) or low (n = 12) VO_2max matched for gender, age and physical activity. Candiate miRs were validated in a second cohort of subjects with high (n = 38) or low (n = 38) VO_2max. miR-210 and miR-222 were found to be higher in the low VO_2max-group (p<0.05). In addition, miR-21 was increased in male participants with low VO_2max (p<0.05). There were no correlations between traditional risk factors for CVD (blood pressure, cholesterol, smoking habit, or obesity) and miR-21, miR-210 and miR-222. DIANA-mirPath identified 611 potential gene-targets of miR-21, miR-210 and miR-222, and pathway analysis indicated alterations in several important signaling systems in subjects with low VO_2max. Potential bias involve that blood was collected from non-fasting individuals, and that 8 performed exercise within 24 h before sampling. In conclusion, we found that miR-210, miR-21, and miR-222 were increased in healthy subjects with low VO_2max. The lack of association between these three miRs, and other fitness related variables as well as traditional CVD risk factors, suggests that these miRs may have a potential as new independent biomarkers of fitness level and future CVD.     

The Relation of Body Mass Index,Cardiorespiratory Fitness,and All‐Cause Mortality in Women

Objective: To examine the relation of body mass index (BMI), cardiorespiratory fitness (CRF), and all‐cause mortality in women. Research Methods and Procedures: A cohort of women (42.9 ± 10.4 years) was assessed for CRF, height, and weight. Participants were divided into three BMI categories (normal, overweight, and obese) and three CRF categories (low, moderate, and high). After adjustment for age, smoking, and baseline health status, the relative risk (RR) of all‐cause mortality was determined for each group. Further multivariate analyses were performed to examine the contribution of each predictor (e.g., age, BMI, CRF, smoking status, and baseline health status) on all‐cause mortality while controlling for all other predictors. Results: During follow‐up (113,145 woman‐years), 195 deaths from all causes occurred. Compared with normal weight (RR = 1.0), overweight (RR = 0.92) and obesity (RR = 1.58) did not significantly increase all‐cause mortality risk. Compared with low CRF (RR = 1.0), moderate (RR = 0.48) and high (RR = 0.57) CRF were associated significantly with lower mortality risk (p = 0.002). In multivariate analyses, moderate (RR = 0.49) and high (RR = 0.57) CRF were strongly associated with decreased mortality relative to low CRF (p = 0.003). Compared with normal weight (RR = 1.0), overweight (RR = 0.84) and obesity (RR = 1.21) were not significantly associated with all‐cause mortality. Discussion: Low CRF in women was an important predictor of all‐cause mortality. BMI, as a predictor of all‐cause mortality risk in women, may be misleading unless CRF is also considered.     

Lower than predicted resting metabolic rate is associated with severely impaired cardiorespiratory fitness in obese individuals

Obese individuals have reduced cardiorespiratory fitness as compared with leaner counterparts. Regular exercise maintains or increases fitness and lean body mass. Lean body mass, in turn, has a direct impact on resting metabolic rate (RMR). Given these relationships, we sought to evaluate the association between RMR and cardiorespiratory fitness in obese individuals. We evaluated 64 obese individuals (78% female) with direct assessment of RMR and cardiorespiratory fitness via breath‐by‐breath measurement of oxygen consumption and carbon dioxide production at rest and during exercise. The mean age and BMI were 47.4 ± 12.2 years and 47.2 ± 9.2 kg/m², respectively. The majority of subjects, 69%, had a measured RMR above that predicted by the Harris‐Benedict equation. Compared with the higher RMR group, those with a lower than predicted RMR had increased BMI, with values of 52.9 vs. 44.7 kg/m², P = 0.001, respectively. Analysis of those demonstrating significant effort during cardiopulmonary exercise testing (peak respiratory exchange ratio ≥1.10) revealed a significantly higher peak oxygen uptake (VO₂ peak) in the higher RMR group (17.3 ± 3.5 ml/min/kg) compared with the lower RMR group (13.6 ± 1.9 ml/min/kg), P = 0.003. In summary, a lower than predicted RMR was associated with a severely reduced VO₂ peak and a higher BMI in this cohort. These data suggest that morbid obesity may be a vicious cycle of increasing BMI, reduced cardiorespiratory fitness, muscle deconditioning, and lower RMR. Collectively, these responses may, over time, exacerbate the imbalance between energy intake and expenditure, resulting in progressive increases in body weight and fat stores.     

Maternal smoking during pregnancy and cord blood DNA methylation: new insight on sex differences and effect modification by maternal folate levels

Maternal smoking during pregnancy may affect newborn DNA methylation (DNAm). However, little is known about how these associations vary by a newborn’s sex and/or maternal nutrition. To fill in this research gap, we investigated epigenome-wide DNAm associations with maternal smoking during pregnancy in African American mother-newborn pairs. DNAm profiling in cord (n = 379) and maternal blood (n = 300) were performed using the Illumina HumanMethylation450 BeadChip array. We identified 12 CpG sites whose DNAm levels in cord blood were associated with maternal smoking, at a false discovery rate <5%. The identified associations in the GFI1 gene were more pronounced in male newborns than in females (P = 0.002 for maternal smoking × sex interaction at cg18146737). We further observed that maternal smoking and folate level may interactively affect cord blood DNAm level at cg05575921 in the AHRR gene (P = 5.0 × 10^?4 for interaction): compared to newborns unexposed to maternal smoking and with a high maternal folate level (>19.2 nmol/L), the DNAm level was about 0.03 lower (P = 3.6 × 10^?4) in exposed newborns with a high maternal folate level, but was 0.08 lower (P = 1.2 × 10^?8) in exposed newborns with a low maternal folate level. Our data suggest that adequate maternal folate levels may partly counteract the impact of maternal smoking on DNAm. These findings may open new avenues of inquiry regarding sex differences in response to environmental insults and novel strategies to mitigate their intergenerational health effects through optimization of maternal nutrition.     

Epigenomic association analysis identifies smoking-related DNA methylation sites in African Americans

Cigarette smoking is an environmental risk factor for many chronic diseases, and disease risk can often be managed by smoking control. Smoking can induce cellular and molecular changes, including epigenetic modification, but the short- and long-term epigenetic modifications caused by cigarette smoking at the gene level have not been well understood. Recent studies have identified smoking-related DNA methylation (DNAm) sites in Caucasians. To determine whether the same DNAm sites associate with smoking in African Americans, and to identify novel smoking-related DNAm sites, we conducted a methylome-wide association study of cigarette smoking using a discovery sample of 972 African Americans, and a replication sample of 239 African Americans with two array-based methods. Among 15 DNAm sites significantly associated with smoking after correction for multiple testing in our discovery sample, 5 DNAm sites are replicated in an independent cohort, and 14 sites in the replication sample have effects in the same direction as in the discovery sample. The top two smoking-related DNAm sites in F2RL3 (factor II receptor-like 3) and GPR15 (G-protein-coupled receptor 15) observed in African Americans are consistent with previous findings in Caucasians. The associations between the replicated DNAm sites and smoking remain significant after adjusting for genetic background. Despite the distinct genetic background between African Americans and Caucasians, the DNAm from the two ethnic groups shares common associations with cigarette smoking, which suggests a common molecular mechanism of epigenetic modification influenced by environmental exposure.     

Adiposity and age explain most of the association between physical activity and fitness in physically active men

Background

To determine if there is an association between physical activity assessed by the short version of the International Physical Activity Questionnaire (IPAQ) and cardiorespiratory and muscular fitness.

Methodology/Principal Findings

One hundred and eighty-two young males (age range: 20–55 years) completed the short form of the IPAQ to assess physical activity. Body composition (dual-energy X-Ray absorptiometry), muscular fitness (static and dynamic muscle force and power, vertical jump height, running speed [30 m sprint], anaerobic capacity [300 m running test]) and cardiorespiratory fitness (estimated VO₂max: 20 m shuttle run test) were also determined in all subjects.Activity-related energy expenditure of moderate and vigorous intensity (EEPA_moderate and EEPA_vigorous, respectively) was inversely associated with indices of adiposity (r = −0.21 to −0.37, P<0.05). Cardiorespiratory fitness (VO₂max) was positively associated with LogEEPA_moderate (r = 0.26, P<0.05) and LogEEPA_vigorous (r = 0.27). However, no association between VO₂max with LogEEPA_moderate, LogEPPA_vigorous and LogEEPA_total was observed after adjusting for the percentage of body fat. Multiple stepwise regression analysis to predict VO₂max from LogEEPA_walking, LogEEPA_moderate, LogEEPA_vigorous, LogEEPA_total, age and percentage of body fat (%fat) showed that the %fat alone explained 62% of the variance in VO₂max and that the age added another 10%, while the other variables did not add predictive value to the model [VO₂max  = 129.6−(25.1× Log %fat) − (34.0× Log age); SEE: 4.3 ml.kg⁻¹. min⁻¹; R² = 0.72 (P<0.05)]. No positive association between muscular fitness-related variables and physical activity was observed, even after adjusting for body fat or body fat and age.

Conclusions/Significance

Adiposity and age are the strongest predictors of VO₂max in healthy men. The energy expended in moderate and vigorous physical activities is inversely associated with adiposity. Muscular fitness does not appear to be associated with physical activity as assessed by the IPAQ.     

DNA methylation-based biomarkers for ageing long-lived cetaceans

Epigenetic approaches for estimating the age of living organisms are revolutionizing studies of long-lived species. Molecular biomarkers that allow age estimates from small tissue biopsies promise to enhance studies of long-lived whales, addressing a fundamental and challenging parameter in wildlife management. DNA methylation (DNAm) can affect gene expression, and strong correlations between DNAm patterns and age have been documented in humans and nonhuman vertebrates and used to construct “epigenetic clocks”. We present several epigenetic clocks for skin samples from two of the longest-lived cetaceans, killer whales and bowhead whales. Applying the mammalian methylation array to genomic DNA from skin samples we validate four different clocks with median errors of 2.3–3.7 years. These epigenetic clocks demonstrate the validity of using cytosine methylation data to estimate the age of long-lived cetaceans and have broad applications supporting the conservation and management of long-lived cetaceans using genomic DNA from remote tissue biopsies.     

Characterization of age signatures of DNA methylation in normal and cancer tissues from multiple studies

Background

DNA methylation (DNAm) levels can be used to predict the chronological age of tissues; however, the characteristics of DNAm age signatures in normal and cancer tissues are not well studied using multiple studies.

Results

We studied approximately 4000 normal and cancer samples with multiple tissue types from diverse studies, and using linear and nonlinear regression models identified reliable tissue type-invariant DNAm age signatures. A normal signature comprising 127 CpG loci was highly enriched on the X chromosome. Age-hypermethylated loci were enriched for guanine–and-cytosine-rich regions in CpG islands (CGIs), whereas age-hypomethylated loci were enriched for adenine–and-thymine-rich regions in non-CGIs. However, the cancer signature comprised only 26 age-hypomethylated loci, none on the X chromosome, and with no overlap with the normal signature. Genes related to the normal signature were enriched for aging-related gene ontology terms including metabolic processes, immune system processes, and cell proliferation. The related gene products of the normal signature had more than the average number of interacting partners in a protein interaction network and had a tendency not to interact directly with each other. The genomic sequences of the normal signature were well conserved and the age-associated DNAm levels could satisfactorily predict the chronological ages of tissues regardless of tissue type. Interestingly, the age-associated DNAm increases or decreases of the normal signature were aberrantly accelerated in cancer samples.

Conclusion

These tissue type-invariant DNAm age signatures in normal and cancer can be used to address important questions in developmental biology and cancer research.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-997) contains supplementary material, which is available to authorized users.     

Importance of Both Fatness and Aerobic Fitness on Metabolic Syndrome Risk in Japanese Children

Associations between body mass index (BMI), peak oxygen consumption (VO_2peak), and metabolic syndrome (MetS) risk factors have not been adequately studied in Japanese children. Here the relationships between these parameters and the threshold aerobic fitness level necessary for low MetS risk were determined. The participants (299 children; 140 boys and 159 girls, aged 9.1 ± 0.3 years) were divided into four groups using the medians of predicted VO_2peak (_pVO_2peak) and BMI. MetS risk scores were calculated using z-scores. Receiver Operating Characteristic analysis was used to determine the threshold aerobic fitness level necessary for low MetS risk. The MetS risk score of the High BMI group was significantly higher than that of the Low BMI group for both sexes (p < 0.0001). However, the High BMI/High Fitness group had a significantly lower MetS risk score than the High BMI/Low Fitness group for both sexes. The _pVO_2peak cut-off values for low MetS risk were 47.9 and 44.9 ml/kg/min for boys and girls, respectively. Our results suggest that improvements in both fatness and aerobic fitness are important for decreasing MetS risk. We also confirmed the _pVO_2peak of cut-off values necessary for low MetS risk in Japanese children.