Trends in DNA methylation with age replicate across diverse human populations

AbstractAging is associated with widespread changes in genome-wide patterns of DNA methylation. Thousands of CpG sites whose tissue-specific methylation levels are strongly correlated with chronological age have been previously identified. However, the majority of these studies have focused primarily on cosmopolitan populations living in the developed world; it is not known if age-related patterns of DNA methylation at these loci are similar across a broad range of human genetic and ecological diversity. We investigated genome-wide methylation patterns using saliva and whole blood derived DNA from two traditionally hunting and gathering African populations: the Baka of the western Central African rainforest and the ≠Khomani San of the South African Kalahari Desert. We identify hundreds of CpG sites whose methylation levels are significantly associated with age, thousands that are significant in a meta-analysis, and replicate trends previously reported in populations of non-African descent. We confirm that an age-associated site in the gene ELOVL2 shows a remarkably congruent relationship with aging in humans, despite extensive genetic and environmental variation across populations. We also demonstrate that genotype state at methylation quantitative trait loci (meQTLs) can affect methylation trends at some known age-associated CpG sites. Our study explores the relationship between CpG methylation and chronological age in populations of African hunter-gatherers, who rely on different diets across diverse ecologies. While many age-related CpG sites replicate across populations, we show that considering common genetic variation at meQTLs further improves our ability to detect previously identified age associations.

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The effect of age on DNA methylation in whole blood among Bangladeshi men and women

BMC Genomics ◽

10.1186/s12864-019-6039-9 ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 1

Author(s):

Rick J. Jansen ◽

Lin Tong ◽

Maria Argos ◽

Farzana Jasmine ◽

Muhammad Rakibuz-Zaman ◽

...

Keyword(s):

Dna Methylation ◽

Whole Blood ◽

Cpg Islands ◽

Chronological Age ◽

Cpg Sites ◽

Age Related ◽

Genome Wide ◽

A Genome ◽

Effect Of Age ◽

Age Related Changes

Abstract Background It is well-known that methylation changes occur as humans age, however, understanding how age-related changes in DNA methylation vary by sex is lacking. In this study, we characterize the effect of age on DNA methylation in a sex-specific manner and determine if these effects vary by genomic context. We used the Illumina HumanMethylation 450 K array and DNA derived from whole blood for 400 adult participants (189 males and 211 females) from Bangladesh to identify age-associated CpG sites and regions and characterize the location of these age-associated sites with respect to CpG islands (vs. shore, shelf, or open sea) and gene regions (vs. intergenic). We conducted a genome-wide search for age-associated CpG sites (among 423,604 sites) using a reference-free approach to adjust for cell type composition (the R package RefFreeEWAS) and performed an independent replication analysis of age-associated CpGs. Results The number of age-associated CpGs (p < 5 x 10− 8) were 986 among men and 3479 among women of which 2027(63.8%) and 572 (64.1%) replicated (using Bonferroni adjusted p < 1.2 × 10− 5). For both sexes, age-associated CpG sites were more likely to be hyper-methylated with increasing age (compared to hypo-methylated) and were enriched in CpG islands and promoter regions compared with other locations and all CpGs on the array. Although we observed strong correlation between chronological age and previously-developed epigenetic age models (r ≈ 0.8), among our top (based on lowest p-value) age-associated CpG sites only 12 for males and 44 for females are included in these prediction models, and the median chronological age compared to predicted age was 44 vs. 51.7 in males and 45 vs. 52.1 in females. Conclusions Our results describe genome-wide features of age-related changes in DNA methylation. The observed associations between age and methylation were generally consistent for both sexes, although the associations tended to be stronger among women. Our population may have unique age-related methylation changes that are not captured in the established methylation-based age prediction model we used, which was developed to be non-tissue-specific.

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Age-related DNA methylation changes are sex-specific: a comprehensive assessment

10.1101/2020.01.15.905224 ◽

2020 ◽

Cited By ~ 2

Author(s):

Igor Yusipov ◽

Maria Giulia Bacalini ◽

Alena Kalyakulina ◽

Mikhail Krivonosov ◽

Chiara Pirazzini ◽

...

Keyword(s):

Dna Methylation ◽

Sex Differences ◽

Meta Analysis ◽

Large Fraction ◽

Age Related ◽

Genome Wide ◽

Epigenetic Age ◽

Age Dependent ◽

Males And Females ◽

Methylation Patterns

AbstractIn humans, females live longer than males but experience a worse longevity, as genome-wide autosomal DNA methylation differences between males and females have been reported. So far, few studies have investigated if DNA methylation is differently affected by aging in males and females. We performed a meta-analysis of 4 large whole blood datasets, comparing 4 aspects of epigenetic age-dependent remodeling between the two sexes: differential methylation, variability, epimutations and entropy. We reported that a large fraction (43%) of sex-associated probes undergoes age-associated DNA methylation changes, and that a limited number of probes shows age-by-sex interaction. We experimentally validated 2 regions mapping in FIGN and PRR4 genes, and showed sex-specific deviations of their methylation patterns in models of decelerated (centenarians) and accelerated (Down syndrome) aging. While we did not find sex differences in the age-associated increase in epimutations and in entropy, we showed that the number of probes showing age-related increase in methylation variability is 15 times higher in males compared to females. Our results can offer new epigenetic tools to study the interaction between aging and sex and can pave the way to the identification of molecular triggers of sex differences in longevity and age-related diseases prevalence.

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Changes in DNA Methylation and Gene Expression of Insulin and Obesity-Related Gene PIK3R1 after Roux-en-Y Gastric Bypass

International Journal of Molecular Sciences ◽

10.3390/ijms21124476 ◽

2020 ◽

Vol 21 (12) ◽

pp. 4476

Author(s):

Marcela A S Pinhel ◽

Natália Y Noronha ◽

Carolina F Nicoletti ◽

Vanessa AB Pereira ◽

Bruno AP de Oliveira ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Weight Loss ◽

Gastric Bypass ◽

Related Gene ◽

Cpg Sites ◽

Genome Wide ◽

Genetically Determined ◽

Methylation Patterns ◽

Weight Loss Interventions

Weight regulation and the magnitude of weight loss after a Roux-en-Y gastric bypass (RYGB) can be genetically determined. DNA methylation patterns and the expression of some genes can be altered after weight loss interventions, including RYGB. The present study aimed to evaluate how the gene expression and DNA methylation of PIK3R1, an obesity and insulin-related gene, change after RYGB. Blood samples were obtained from 13 women (35.9 ± 9.2 years) with severe obesity before and six months after surgical procedure. Whole blood transcriptome and epigenomic patterns were assessed by microarray-based, genome-wide technologies. A total of 1966 differentially expressed genes were identified in the pre- and postoperative periods of RYGB. From these, we observed that genes involved in obesity and insulin pathways were upregulated after surgery. Then, the PIK3R1 gene was selected for further RT-qPCR analysis and cytosine-guanine nucleotide (CpG) sites methylation evaluation. We observed that the PI3KR1 gene was upregulated, and six DNA methylation CpG sites were differently methylated after bariatric surgery. In conclusion, we found that RYGB upregulates genes involved in obesity and insulin pathways.

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Genome-Wide DNA Methylation Analysis Shows Enrichment of Differential Methylation in “Open Seas” and Enhancers and Reveals Hypomethylation in DNMT3A Mutated Cytogenetically Normal AML (CN-AML)

Blood ◽

10.1182/blood.v120.21.653.653 ◽

2012 ◽

Vol 120 (21) ◽

pp. 653-653 ◽

Cited By ~ 2

Author(s):

Ying Qu ◽

Andreas Lennartsson ◽

Verena I. Gaidzik ◽

Stefan Deneberg ◽

Sofia Bengtzén ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Cpg Island ◽

Cpg Islands ◽

Differential Methylation ◽

Methylation Analysis ◽

Cpg Sites ◽

Genome Wide ◽

Genomic Regions ◽

Methylation Patterns

Abstract Abstract 653 DNA methylation is involved in multiple biologic processes including normal cell differentiation and tumorigenesis. In AML, methylation patterns have been shown to differ significantly from normal hematopoietic cells. Most studies of DNA methylation in AML have previously focused on CpG islands within the promoter of genes, representing only a very small proportion of the DNA methylome. In this study, we performed genome-wide methylation analysis of 62 AML patients with CN-AML and CD34 positive cells from healthy controls by Illumina HumanMethylation450K Array covering 450.000 CpG sites in CpG islands as well as genomic regions far from CpG islands. Differentially methylated CpG sites (DMS) between CN-AML and normal hematopoietic cells were calculated and the most significant enrichment of DMS was found in regions more than 4kb from CpG Islands, in the so called open sea where hypomethylation was the dominant form of aberrant methylation. In contrast, CpG islands were not enriched for DMS and DMS in CpG islands were dominated by hypermethylation. DMS successively further away from CpG islands in CpG island shores (up to 2kb from CpG Island) and shelves (from 2kb to 4kb from Island) showed increasing degree of hypomethylation in AML cells. Among regions defined by their relation to gene structures, CpG dinucleotide located in theoretic enhancers were found to be the most enriched for DMS (Chi χ2<0.0001) with the majority of DMS showing decreased methylation compared to CD34 normal controls. To address the relation to gene expression, GEP (gene expression profiling) by microarray was carried out on 32 of the CN-AML patients. Totally, 339723 CpG sites covering 18879 genes were addressed on both platforms. CpG methylation in CpG islands showed the most pronounced anti-correlation (spearman ρ =-0.4145) with gene expression level, followed by CpG island shores (mean spearman rho for both sides' shore ρ=-0.2350). As transcription factors (TFs) have shown to be crucial for AML development, we especially studied differential methylation of an unbiased selection of 1638 TFs. The most enriched differential methylation between CN-AML and normal CD34 positive cells were found in TFs known to be involved in hematopoiesis and with Wilms tumor protein-1 (WT1), activator protein 1 (AP-1) and runt-related transcription factor 1 (RUNX1) being the most differentially methylated TFs. The differential methylation in WT 1 and RUNX1 was located in intragenic regions which were confirmed by pyro-sequencing. AML cases were characterized with respect to mutations in FLT3, NPM1, IDH1, IDH2 and DNMT3A. Correlation analysis between genome wide methylation patterns and mutational status showed statistically significant hypomethylation of CpG Island (p<0.0001) and to a lesser extent CpG island shores (p<0.001) and the presence of DNMT3A mutations. This links DNMT3A mutations for the first time to a hypomethylated phenotype. Further analyses correlating methylation patterns to other clinical data such as clinical outcome are ongoing. In conclusion, our study revealed that non-CpG island regions and in particular enhancers are the most aberrantly methylated genomic regions in AML and that WT 1 and RUNX1 are the most differentially methylated TFs. Furthermore, our data suggests a hypomethylated phenotype in DNMT3A mutated AML. Disclosures: No relevant conflicts of interest to declare.

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Epigenetic influences on aging: a longitudinal genome-wide methylation study in old Swedish twins

10.1101/226266 ◽

2017 ◽

Author(s):

Yunzhang Wang ◽

Robert Karlsson ◽

Erik Lampa ◽

Qian Zhang ◽

Åsa K. Hedman ◽

...

Keyword(s):

Dna Methylation ◽

Monozygotic Twins ◽

Cross Sectional ◽

Age Related ◽

Genome Wide ◽

Illumina Humanmethylation450 ◽

Binding Factor ◽

Old Swedish ◽

Methylation Patterns ◽

Over Time

AbstractAge-related changes in DNA methylation have been observed in many cross-sectional studies, but longitudinal evidence is still very limited. Here, we aimed to characterize longitudinal age-related methylation patterns (Illumina HumanMethylation450 array) using 1011 blood samples collected from 385 old Swedish twins (mean age of 69 at baseline) up to five times over 20 years. We identified 1316 age-associated methylation sites (p<1.3×10−7) using a longitudinal epigenome-wide association study design. We measured how estimated cellular compositions changed with age and how much they confounded the age effect. We validated the results in two independent longitudinal cohorts, where 118 CpGs were replicated in PIVUS (p<3.9×10−5) and 594 were replicated in LBC (p<5.1×10−5). Functional annotation of age-associated CpGs showed enrichment in CCCTC-binding factor (CTCF) and other unannotated transcription factor binding sites. We further investigated genetic influences on methylation (methylation quantitative trait loci) and found no interaction between age and genetic effects in the 1316 age-associated CpGs. Moreover, in the same CpGs, methylation differences within twin pairs increased over time, where monozygotic twins had smaller intra-pair differences than dizygotic twins. We show that age-related methylation changes persist in a longitudinal perspective, and are fairly stable across cohorts. Moreover, the changes are under genetic influence, although this effect is independent of age. In addition, inter-individual methylation variations increase over time, especially in age-associated CpGs, indicating the increase of environmental contributions on DNA methylation with age.

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Genome-Wide DNA Methylation Analysis of Patients with Myelodysplastic Syndrome After Azacitidine Treatment.

Blood ◽

10.1182/blood.v114.22.600.600 ◽

2009 ◽

Vol 114 (22) ◽

pp. 600-600

Author(s):

Hyang-Min Byun ◽

Timothy Triche ◽

Hyeoung-Joon Kim ◽

Hee Nam Kim ◽

Yeo-Kyeoung Kim ◽

...

Keyword(s):

Dna Methylation ◽

Bone Marrow ◽

Who Classification ◽

Methylation Pattern ◽

Methylation Analysis ◽

Cpg Sites ◽

Genome Wide ◽

Methylation Patterns ◽

Dna Methylation Analysis ◽

Hypermethylated Genes

Abstract Abstract 600 Background: Azacitidine is hypothesized to exert its therapeutic effect in patients with myelodysplastic syndrome (MDS) through inhibition of DNA methylation. However to date no genomic DNA methylation pattern has been shown to predict response to azacitidine in patients with MDS, and no aberrantly silenced gene or group of genes has been shown to be reactivated by azacitidine that can be clearly linked to the beneficial clinical effect. We sought to identify the gene or group of aberrantly hypermethylated genes that are responsible for the therapeutic effect of azacitidine by retrospectively analyzing genome-wide DNA methylation profiles from bone marrow samples of a cohort of 113 patients with MDS treated with the DNA methylation inhibitor, azacitidine. Methods: Bone marrow aspirates were collected at time of diagnosis prior to treatment, after 4 cycles of azacitidine therapy and 8 cycles of therapy. DNA was isolated and bisulfite treated with the EZ-96 DNA Methylation-Gold Kit. DNA methylation analysis was performed on 27,578 CpG sites representing 14,475 genes (almost ¾ of known genes) using the Infinium Bead Array system for samples at the time of diagnosis, 4 and 8 cycles of therapy. Only 19,662 CpG sites were used for further analysis due to exclusion of CpG sites that were on the × chromosome, sites suspected of containing single nucleotide polymorphisms (SNP), and sites within DNA repeats. In total 91 samples were analyzed from 43 patients with MDS, which were selected to represent different disease classifications and responses to therapy, and bone marrow aspirates from 10 healthy control subjects without MDS. Results: Two-way hierarchical cluster analysis showed clear clustering of bone marrow samples taken from subjects without MDS. DNA methylation patterns from healthy controls clustered together, and pre and post azacitidine treatment samples from the same subject clustered together as well. Samples did not cluster by DNA methylation patterns for WHO classification, International Prognostic Scoring System (IPSS), cytogenetic abnormalities, or response to azacitidine. Supervised cluster analysis is ongoing. Global decreases in DNA methylation as measured by the average methylation for all 19,662 loci assayed did decrease with treatment and there was a trend for a larger decrease in DNA methylation in those patients who responded to azacitidine. Conclusion: In this pilot study of genome-wide DNA methylation analysis of MDS patients treated with azacitidine we find global decreases of DNA methylation. We were unable to identify a DNA methylation pattern or group of hypermethylated genes that would predict response to azacitidine. MDS samples did not cluster by WHO classification, IPSS or response to azacitidine. Larger translational studies are needed, but the possibility that DNA methylation decreases in patients treated with azacitidine serve as a pharmacological marker rather than a therapeutic target should also be considered Disclosures: Laird: Celgene: Consultancy. Yang:Celgene: Honoraria, Research Funding, Speakers Bureau.

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A Systematic Review and Meta-analysis of Environmental, Lifestyle, and Health Factors Associated With DNA Methylation Age

The Journals of Gerontology Series A ◽

10.1093/gerona/glz099 ◽

2019 ◽

Vol 75 (3) ◽

pp. 481-494 ◽

Cited By ~ 18

Author(s):

Joanne Ryan ◽

Jo Wrigglesworth ◽

Jun Loong ◽

Peter D Fransquet ◽

Robyn L Woods

Keyword(s):

Dna Methylation ◽

Meta Analysis ◽

Conclusive Evidence ◽

Chronological Age ◽

Biological Aging ◽

Robust Estimate ◽

Healthy Life ◽

Age Related ◽

Health Factors ◽

Dna Methylation Age

Abstract DNA methylation (DNAm) algorithms of biological age provide a robust estimate of an individual’s chronological age and can predict their risk of age-related disease and mortality. This study reviewed the evidence that environmental, lifestyle and health factors are associated with the Horvath and Hannum epigenetic clocks. A systematic search identified 61 studies. Chronological age was correlated with DNAm age in blood (median .83, range .13–.99). In a meta-analysis body mass index (BMI) was associated with increased DNAm age (Hannum β: 0.07, 95% CI 0.04 to 0.10; Horvath β: 0.06, 95% CI 0.02 to 0.10), but there was no association with smoking (Hannum β: 0.12, 95% CI −0.50 to 0.73; Horvath β:0.18, 95% CI −0.10 to 0.46). DNAm age was positively associated with frailty (three studies, n = 3,093), and education was negatively associated with the Hannum estimate of DNAm age specifically (four studies, n = 13,955). For most other exposures, findings were too inconsistent to draw conclusions. In conclusion, BMI was positively associated with biological aging measured using DNAm, with some evidence that frailty also increased aging. More research is needed to provide conclusive evidence regarding other exposures. This field of research has the potential to provide further insights into how to promote slower biological aging and ultimately prolong healthy life.

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Identification, Heritability, and Relation With Gene Expression of Novel DNA Methylation Loci for Blood Pressure

Hypertension ◽

10.1161/hypertensionaha.120.14973 ◽

2020 ◽

Vol 76 (1) ◽

pp. 195-205 ◽

Cited By ~ 1

Author(s):

Yisong Huang ◽

Miina Ollikainen ◽

Maheswary Muniandy ◽

Tao Zhang ◽

Jenny van Dongen ◽

...

Keyword(s):

Gene Expression ◽

Blood Pressure ◽

Dna Methylation ◽

Association Study ◽

Meta Analysis ◽

African Ancestry ◽

Cpg Sites ◽

Genome Wide ◽

Novel Association ◽

Peripheral Leukocytes

We conducted an epigenome-wide association study meta-analysis on blood pressure (BP) in 4820 individuals of European and African ancestry aged 14 to 69. Genome-wide DNA methylation data from peripheral leukocytes were obtained using the Infinium Human Methylation 450k BeadChip. The epigenome-wide association study meta-analysis identified 39 BP-related CpG sites with P <1×10 −5 . In silico replication in the CHARGE consortium of 17 010 individuals validated 16 of these CpG sites. Out of the 16 CpG sites, 13 showed novel association with BP. Conversely, out of the 126 CpG sites identified as being associated ( P <1×10 −7 ) with BP in the CHARGE consortium, 21 were replicated in the current study. Methylation levels of all the 34 CpG sites that were cross-validated by the current study and the CHARGE consortium were heritable and 6 showed association with gene expression. Furthermore, 9 CpG sites also showed association with BP with P <0.05 and consistent direction of the effect in the meta-analysis of the Finnish Twin Cohort (199 twin pairs and 4 singletons; 61% monozygous) and the Netherlands Twin Register (266 twin pairs and 62 singletons; 84% monozygous). Bivariate quantitative genetic modeling of the twin data showed that a majority of the phenotypic correlations between methylation levels of these CpG sites and BP could be explained by shared unique environmental rather than genetic factors, with 100% of the correlations of systolic BP with cg19693031 ( TXNIP ) and cg00716257 ( JDP2 ) determined by environmental effects acting on both systolic BP and methylation levels.

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Sexually divergent DNA methylation programs with hippocampal aging

10.1101/161752 ◽

2017 ◽

Cited By ~ 2

Author(s):

Dustin R. Masser ◽

Niran Hadad ◽

Hunter Porter ◽

Colleen A. Mangold ◽

Archana Unnikrishnan ◽

...

Keyword(s):

Dna Methylation ◽

Sex Differences ◽

Biological Aging ◽

Age Related ◽

Genome Wide ◽

Aging Response ◽

Genomic Location ◽

Methylation Patterns ◽

Genomic Methylation

SummaryDNA methylation is a central regulator of genome function and altered methylation patterns are indicative of biological aging and mortality. Age-related cellular, biochemical, and molecular changes in the hippocampus lead to cognitive impairments and greater vulnerability to neurodegenerative disease that varies between the sexes. The role of hippocampal epigenomic changes with aging in these processes is unknown as no genome-wide analyses of age-related methylation changes have considered the factor of sex in a controlled animal model. High-depth, genome-wide bisulfite sequencing of young (3 month) and old (24 month) male and female mouse hippocampus revealed that while total genomic methylation amounts did not change with aging, specific sites in CG and non-CG (CH) contexts demonstrated age-related increases or decreases in methylation that were predominantly sexually divergent. Differential methylation with age for both CG and CH sites was enriched in intergenic, and intronic regions and under-represented in promoters, CG islands and specific enhancer regions in both sexes suggesting that certain genomic elements are especially labile with aging, even if the exact genomic loci altered are predominantly sex-specific. Life-long sex differences in autosomal methylation at CG and CH sites were also observed. The lack of genome-wide hypomethylation, sexually divergent aging response, and autosomal sex differences at CG sites were confirmed in human data. These data reveal sex as a previously unappreciated central factor of hippocampal epigenomic changes with aging. In total, these data demonstrate an intricate regulation of DNA methylation with aging by sex, cytosine context, genomic location, and methylation level.

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Prediction of biological age and evaluation of genome-wide dynamic methylomic changes throughout human aging

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab112 ◽

2021 ◽

Author(s):

Mahmoud Amiri Roudbar ◽

Seyedeh Fatemeh Mousavi ◽

Siavash Salek Ardestani ◽

Fernando Brito Lopes ◽

Mehdi Momen ◽

...

Keyword(s):

Reproducing Kernel ◽

Cpg Islands ◽

Specific Pattern ◽

Chronological Age ◽

Global Methylation ◽

Aging Rate ◽

Cpg Sites ◽

Age Related ◽

Kernel Hilbert Spaces ◽

Methylation Patterns

Abstract The use of DNA methylation signatures to predict chronological age and aging rate is of interest in many fields, including disease prevention and treatment, forensics, and anti-aging medicine. Although a large number of methylation markers are significantly associated with age, most age-prediction methods use a few markers selected based on either previously published studies or datasets containing methylation information. Here, we implemented reproducing kernel Hilbert spaces (RKHS) regression and a ridge regression model in a Bayesian framework that utilized phenotypic and methylation profiles simultaneously to predict chronological age. We used over 450,000 CpG sites from the whole blood of a large cohort of 4,409 human individuals with a range of 10-101 years of age. Models were fitted using adjusted and un-adjusted methylation measurements for cell heterogeneity. Un-adjusted methylation scores delivered a significantly higher prediction accuracy than adjusted methylation data, with a correlation between age and predicted age of 0.98 and a root-mean-square error (RMSE) of 3.54 years in un-adjusted data, and 0.90 (correlation) and 7.16 (RMSE) years in adjusted data. Reducing the number of predictors (CpG sites) through subset selection improved predictive power with a correlation of 0.98 and an RMSE of 2.98 years in the RKHS model. We found distinct global methylation patterns, with a significant increase in the proportion of methylated cytosines in CpG islands and a decreased proportion in other CpG types, including CpG shore, shelf, and open sea (p < 5e-06). Epigenetic drift seemed to be a widespread phenomenon as more than 97% of the age-associated methylation sites had heteroscedasticity. Apparent methylomic aging rate (AMAR) had a sex-specific pattern, with an increase in AMAR in females with age related to males.

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