Clinical Epigenetics

BackgroundFathers adolescent smoking and overweight affect respiratory health in offspring, suggesting that paternal puberty exposures may influence offspring biological ageing through preconception epigenetic mechanisms. MethodsWe analyzed epigenetic age acceleration using four validated epigenetic clocks derived from blood DNA methylation in 892 RHINESSA offspring (mean age 27 years), linked to parental data on smoking and body shapes from RHINE/ECRHS. Linear regression examined parental smoking initiation ([≤]15 or >15 years) and overweight body shape (childhood/puberty or age 30) in relation to offspring epigenetic age acceleration, adjusting for offspring sex, age and parental socioeconomic status. Sensitivity analyses accounted for offspring smoking and BMI. ResultsPCHorvath ({beta} 1.53; 95% CI 0.02, 2.9), PCGrimAge (1.21; 0.03, 2.1), DunedinPACE (0.04; -0.001, 0.1) and PCPhenoAge (1.92; -0.3, 4.2) were accelerated in daughters of fathers who started smoking [≤]15 years. Likewise, PCHorvath (2.25; 1.2, 3.3), PCGrimAge (1.36; -0.2, 2.9), DunedinPACE (0.07; 0.01, 0.1) and PCPhenoAge (3.11; 1.8, 4.4) were accelerated in daughters and sons of fathers who had been overweight in childhood and puberty. These results remained largely unchanged after additional adjustments or stratification in sensitivity analyses. No associations were found for maternal smoking or overweight in puberty. ConclusionsEpigenetic ageing is accelerated in offspring of fathers who smoked or were overweight in puberty, independent of offspring lifestyle. These findings suggest that adolescent boys environment and lifestyle may be critical for next-generation health. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC="FIGDIR/small/26352444v1_fig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@1eea189org.highwire.dtl.DTLVardef@1af41f4org.highwire.dtl.DTLVardef@1132932org.highwire.dtl.DTLVardef@f5ba2c_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1.C_FLOATNO Graphical abstract Legend to graphical abstract Figure Fathers smoking or overweight during puberty was associated with accelerated epigenetic aging in offspring (n=892), independent of the offsprings own lifestyle. No such pattern was observed for maternal puberty exposures, or when paternal exposures occurred after puberty. Male puberty may be a critical window for next-generation health. C_FIG

Aberrant DNA methylation is a hallmark of cancer, but its clinical interpretation remains debated. UHRF1, a key epigenetic adaptor for DNA methylation maintenance and chromatin bivalency regulation in embryonic stem cells, is frequently overexpressed yet shows context-dependent prognostic behaviour. By integrating bulk and single-cell transcriptomics, CpG-resolution methylation, developmental chromatin states, immune profiling and clinical outcomes across gastric (STAD), clear-cell renal (KIRC) and adrenal (ACC) carcinomas, we identified a four-class UHRF1-embryonic morphogenesis (UHRF1-EM) framework resolving this paradox. This axis revealed an inverse prognostic pattern: whilst across all three tumours EM-low and EM-high states mark better or worse prognosis, respectively, UHRF1-high levels associate with favourable outcome in STAD (UH-EML), and unfavourable in KIRC and ACC (UH-EMH). The classification proved reproducible and independently prognostic after adjustment for stage and molecular subtypes, outperforming existing classifiers and exceeding pathological stage in KIRC and ACC. Multivariable models incorporating UHRF1-EM yielded uniformly positive {Delta}C-indices. Hypermethylation associated with the UHRF1-EM axis was enriched at ESC bivalent developmental loci (EM and oncofoetal genes), but not at housekeeping cell-cycle sites. In STAD, this pattern was related to oncofoetal gene downregulation and best prognosis, whereas in KIRC and ACC it matched with gene-body/enhancer methylation, higher EM expression, immunosuppressive microenvironments and worst prognosis. Together, these findings establish the UHRF1-EM axis as a clinically robust molecular classifier and support a mechanistic model in which tumour-specific epigenetic engagement of developmental loci may contribute to the prognostic inversion, providing a foundation for further mechanistic experimental validation.

BackgroundThe Developmental Origins of Adult Disease (DOAD) theory predicts that prenatal and early life events shape adult health outcomes. Birth weight is a useful indicator of the foetal experience, and has been associated with multiple adult health outcomes. DNA methylation (DNAm) is one plausible mechanism behind the relationship of birth weight to adult health. MethodsThe Generation Scotland study allows data linkage to historic Scottish birth cohorts, and birth records held through the NHS Information and Statistics Division. Data linkage with these sources yielded a sample of 4, 710 individuals. Health measures were related to birth weight in regression models. An epigenome-wide association study (EWAS) was performed in a subgroup (n=1, 395), relating adult DNAm from whole blood to birth weight, with replication in an independent sample (n=362). Associations between birth weight and epigenetic clocks were also assessed. FindingsHigher birth weight was significantly associated with reduced incidence of depression and osteoarthritis, higher body mass index, and higher general intelligence (absolute standardised effect size range 0{middle dot}04 to 0{middle dot}30, p(FDR)<0{middle dot}05). Meta-analysis of discovery and replication EWAS studies yielded one genome-wide significant CpG site (p=5{middle dot}97x10-9), cg00966482. Significant associations between birth weight and Grim Age (p=0{middle dot}0014) and DNAm-derived telomere length (p=3{middle dot}3x10-4) are also described. InterpretationOur results demonstrate associations between birth weight and adult health outcomes, with particularly striking effects for depression risk. It also provides support for an association between birth weight and DNAm, describing the first significant EWAS site associated with birth weight in an adult sample. FundingWellcome Trust Strategic Award 104036/Z/14/Z Research in ContextO_ST_ABSEvidence before this studyC_ST_ABSThe associations between birth weight and various adult health outcomes have been well established. DNA methylation is a plausible mechanism through which early life experiences may continue to affect health throughout the lifecourse; however, evidence for birth weight associations with DNA methylation in adulthood has not yet been robustly established. This is likely due to small sample sizes of previous samples, as well as the use of poor-quality birth weight data, such as binary low/normal variables or retrospective self-report. Alternatively, work has attempted to describe the persistence into adulthood of DNA methylation at sites identified at birth. Added value of this studyWe investigated genome-wide differential DNA methylation patterns from whole blood using data linkage-derived, continuous birth weight data, in the largest reported adult sample (n=1, 395) with replication (n=362) and meta-analysis. Meta-analysis revealed one epigenome-wide significant CpG site, to our knowledge the first significant EWAS result reported for birth weight in a an adult sample. In addition, we found associations between birth weight and GrimAge and a DNA methylation-derived measure of telomere length, demonstrating accelerated biological ageing in lower birth weight individuals. Together, these results suggest differential methylation exists in adulthood related to birth weight, and this may be relevant to health and mortality. Implications of all the available evidenceAlthough CpG sites differentially methylated with birth weight at parturition may not remain so throughout life, the adult epigenome may still provide information on the impact of birth weight on health outcomes. The adult epigenome, therefore, may represent a useful archive of the foetal experience which results in birth weight variability, and this information may provide clinically useful information in mid-life.

BackgroundEpigenetic (gestational) age acceleration (E(G)AA) is associated with environmental exposures and health outcomes in humans. However, E(G)AA is the residual term from a regression of epigenetic age (outcome) on chronological (gestational) age (predictor) and therefore strongly obscured by noise from multiple sources. Here, we propose a simple procedure, based on regression, principal component analysis (PCA), and the Lasso, that amplifies E(G)AA signals. More specifically, we first regress given (gestational) age against each CpG used for epigenetic (gestational) age prediction. The CpGs are typically taken from one of several epigenetic clocks available. PCA is subsequently performed on the resulting matrix of residual vectors for each CpG as it projects the E(G)AA signal onto perpendicular principal components (PCs), thereby separating signal from noise. Finally, we use the Lasso to select PCs associated with an outcome of interest. We apply our method to previous studies: EAA in patients with Downs syndrome and Werners syndrome and EGAA of newborns exposed to prenatal smoking as well as associations with maternal BMI. ResultsThe extracted EAA components computed using our proposed procedure revealed a significant association with Downs syndrome (PB<0.05, Bonferroni adjusted for multiple testing) as well as for Werners Syndrome (PB<0.05). For EGAA we find a significant association with maternal prenatal smoking (PB<0.05, also Bonferroni adjusted) and maternal BMI (PB<0.05). Additionally, by examining the loadings of the PCs of interest, and contrary to residual EGAA, our method can identify implicated CpGs. ConclusionsOur findings suggest that our proposed procedure leads to a remarkable amplification of the E(G)AA signal. Furthermore, our method reveals that E(G)AA is a composite signal that can be driven by multiple independent factors.

BackgroundInflammatory bowel diseases (IBDs) are chronic inflammatory disorders with a dysregulated immune response partly influenced by environmental factors. DNA methylation (DNAm), a key epigenetic mechanism, is implicated in the etiology of complex diseases, including IBD. Epigenetic clocks, which use DNAm patterns to estimate biological aging, have been increasingly linked to various health and disease states. Previous studies have associated DNAm with IBD, and first- and second-generation epigenetic clocks with IBD subtypes. ResultsIn a discovery IBD cohort (n=149) with 8-year clinical follow-up data, we explored the relationship between DNAm variation, second- and third-generation epigenetic clocks, and IBD clinicopathological outcomes, including disease subtype, activity, and recurrence. One CpG site was significantly differentially methylated (Benjamini-Hochberg adjusted p-value<0.05) in patients with clinical recurrence of disease over the long term (i.e., after the first year of study) compared to non-recurrence (no treatment escalation after 8 years). Next, we assessed DNAm aging signatures and IBD outcomes using logistic regression. Individuals with IBD exhibited significantly increased epigenetic aging, as measured by GrimAge, GrimAge2, and DunedinPACE, compared with controls. These associations were replicated in two independent IBD cohorts (GSE87648 (n=377) and GSE112611 (n=238)). Additionally, in UC patients, the active disease group was associated with higher age acceleration (GrimAge (U=669, p=0.003)) and higher pace of aging (DunedinPACE (t=3.233, 0.002)) compared to the inactive group. In the discovery cohort, DunedinPACE outperforms CRP measures in discriminating activity in UC patients with an AUC, sensitivity and specificity of 0.71, 69.5% and 68.7% respectively, highlighting its potential as a useful biomarker of activity in UC. ConclusionsOverall, we present strong evidence that dynamic age-related DNAm changes can be used to differentiate between IBD (including separately by subtype) and controls. Furthermore, our study provides important new evidence that DunedinPACE may have utility as a biomarker for monitoring disease recurrence in IBD patients and may be a strong marker of disease activity in UC patients. Overall, this suggests that blood-based DNAm signatures could serve as biomarkers for detection and monitoring of IBD.

Background: Psychosocial stress is a key risk factor for coronary heart disease (CHD), particularly in postmenopausal women who face both a high stress burden and elevated cardiovascular risk. DNA methylation (DNAm), a critical epigenetic modification bridging environment and health, remains understudied as a contributor to stress-related CHD. Methods: We conducted an epigenome-wide association study (EWAS) of stress in the Women's Health Initiative (WHI), an ancestrally diverse cohort of postmenopausal women (n=3,857). At screening visit, participants completed a questionnaire assessing stressful life events and provided whole blood for DNAm. Incident CHD was then longitudinally ascertained (follow-up mean/SD: 16.7/8.4 years), and DNAm signatures were evaluated as CHD predictors using Cox regression. Predictive models were independently validated in the Jackson Heart Study (JHS; n=3,053) and Multi-Ethnic Study of Atherosclerosis (MESA; n=870). The bulk-level DNAm associations were computationally deconvolved at the cell-type-specific level using tensor composition analysis (TCA). Results: The EWAS in WHI identified 841 stress-related DNAm sites (99 hypermethylated, 742 hypomethylated with stress) after FDR correction, with 13 significant after Bonferroni correction, including sites located on immune and CHD-related genes (e.g., TNF, ALDH2). Methylation risk scores (MRSs) integrating the 841 FDR-significant sites (MRS841) and 13 Bonferroni-significant sites (MRS13) predicted incident CHD (HR=1.33-1.37; p[&le;]0.0008) and mediated 16.5-17.7% of the association between stress and CHD. In JHS and MESA, MRS13 independently predicted CHD (HR=1.34; p=0.036), whereas MRS841 was suggestively associated with CHD (HR=1.27; p=0.087). TCA indicated that the greatest number of stress-related sites predictive of CHD was specifically in monocytes (133 total), with directions consistent with bulk-level associations (9 hypermethylated, 124 hypomethylated with stress). Conclusion: Our study supports methylation risk scores as novel biomarkers of stress-related CHD and uncovers epigenetic regulation in monocytes as a potential underlying mechanism. These findings highlight biological pathways linking stress and disease and may promote personalized interventions in high-risk populations.

BackgroundSmall intestinal neuroendocrine tumours (SI-NETs) are the most common malignancy of the small intestine and around 50% of patients present in clinic with multifocal disease. Recent investigations into the genomic architecture of multifocal SI-NETs have found evidence that these synchronous primary tumours evolve independently of each other. They also have extremely low mutational burden and few known driver genes, suggesting that epigenetic dysregulation may be driving tumorigenesis. Very little is known about epigenetic gene regulation, metabolism and ageing in these tumours, and how these traits differ across multiple tumours within individual patients. MethodsIn this study, we performed the first investigation of genome-wide DNA methylation in multifocal SI-NETs, assessing multiple primary tumours within each patient (n=79 primary tumours from 14 patients) alongside matched metastatic tumours (n=12) and normal intestinal epithelial tissue (n=9). We assessed multifocal SI-NET differential methylation using a novel method, comparing primary tumours with matched normal epithelial tissue and an enterochromaffin-enriched cell line to enrich for tumour-specific effects. This method reduced the identification of false positive methylation differences driven by cell composition differences between tumour and normal epithelial tissue. We also assessed tumour ageing using epigenetic clocks and applied metabolic predictors in the dataset to assess methylation variation across key metabolic genes. ResultsWe have identified 12,392 tumour-specific differentially methylated positions (Bonferroni corrected p<0.05) which were enriched for neural pathways. The expression levels of the genes associated with top sites were also found to be significantly altered in SI-NETs. Age acceleration was observed across SI-NETs and a variability in epigenetic age of tumours within each patient, which we believe is reflecting the order in which tumours have developed. This is supported by the correlation of age acceleration with somatic mutational count in the tumours. We have identified SI-NET associated alterations to the methylation patterns in key metabolic genes compared to matched normal tissue, which is more pronounced in metastatic tumours and tumours harbouring chromosome 18 loss of heterozygosity, indicating metabolic differences in these tumour subtypes. ConclusionsWe have identified accelerated ageing and changes to regulation of metabolic genes, alongside an epigenetic signature of multifocal SI-NETs. These findings add to our understanding of multifocal SI-NET biology and their molecular differences which may be instrumental in the development of these elusive tumours.

There is converging evidence that young blood conveys cells, vesicles and molecules able to revitalize function and restore organ integrity in old individuals. Here, we assessed the effects of young rat plasma on the lifespan, epigenetic age and healthspan of old female rats. Beginning at 25.3 months of age, a group of 9 rats (group T) was intraperitoneally injected with plasma from young rats (2 months) until their natural death. A group of control rats of the same age, received no treatment. Blood samples were collected every other week. Survival curves showed that from age 26 to 30 months, none of the T animals died, whereas the survival curve of C rats began to decline at age 26 months. The external appearance of the T rats was healthier than that of the C counterparts. Blood DNA methylation (DNAm) was assessed using the HorvathMammalMethylChip320. Blood DNAm age versus chronological age showed that DNAm age in young animals increased faster than chronological age then slowed down progressively, entering a plateau after 27 months. Immediately after the start of the treatment, the DNAm age (i.e., epigenetic age) of the treated rats fell below the DNAm age of controls and remained consistently lower until the end of their lives. Assessment of each experimental group showed that the blood DNA methylation levels of 1638 CpGs were different between treated and control blood samples (false discovery rate q-value<0.05). Of these, 1007 CpGs exhibited increased methylation, with age while 631 CpGs showed decreased methylation levels. When rats were grouped according to the similarities in their differential blood DNA methylation profile, samples from the treated and control rats clustered in separate groups. Analysis of promoter differential methylation in genes involved in systemic regulatory activities revealed specific GO term enrichment related to the insulin-like factors (IGFs) pathways as well as to cytokines and chemokines associated with immune and homeostatic functions. We conclude that young plasma therapy may constitute a natural noninvasive intervention for epigenetic rejuvenation and health enhancement, readily translatable to the clinic.

In 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.

BackgroundAging is linked to hypermethylation of CpG sites on promoters and enhancers, along with loss of methylation in intergenic zones. That such changes are not necessarily a continuous process is exemplified by the extensive changes in DNA methylation during development with another significant time of change during adolescence. However, the relation between age and DNA methylation during adult life has not been systematically evaluated. In particular, potential changes in methylation trends in the same CpGs over the years that may occur with aging remain largely unexplored. MethodsHere we set out to determine the average trends by age of the CpG sites represented in the Illumina 450 platform, based on data from 2143 subjects of the age range of 20 to 80 years, compiled from 24 different cohorts. Using several mathematical procedures, we initially separated stationary probes from probes whose methylation changes with age. Among the latter, representing [~]20% of the probes, we then focused on the identification of CpG sites with switch points, i.e., a point where a stable trend of change in the age-averaged methylation is replaced by another linear trend. ResultsUsing several mathematical modeling steps, we generated a machine learning model that identified 5175 CpG sites with switch points in age-related changes in the trend of methylation over the years. Switch points reflect acceleration, deceleration or change of direction of the alteration of methylation with age. The 5175 switch points were limited to 2813 genes in three waves, 80% of which were identical in men and women. A medium-size wave was seen in the early forties, succeeded by a dominant wave as of the late fifties, lasting up to 8 years each. Waves appeared[~]4-5 years earlier in men. No switch points were detected on CpGs mapped to the X chromosome. ConclusionIn non-stationary CpG sites, concomitant switch points in age related changes in methylations can be seen in a defined group of sites and genes, which cluster in 3 age- and sex-specific waves.

Psychological trauma is associated with significant alterations of biological functions and is correlated with epigenetic changes specifically of DNA methylation. Trauma therapy is aiming at relieving the impact of trauma and is in initial studies also correlated with changes in DNA methylation. In this study we explored the changes in whole blood DNA methylation of participants of a program focusing on individual, ancestral and collective trauma processing and meditation in a large group setting of 1.6 years duration. Based on accompanying questionnaires, training participants report slight improvements in anxiety, depression and overall life satisfaction and some mystical experiences. 3227 CpGs and 253 genes were found to be differentially methylated during the training. Although these genes are not involving any of the known trauma related genes and relevant gene ontology terms, they comprise a large number of genes involved in the nervous function, as well as in cellular and developmental functions, the immune system and metabolism. Also, epigenetic aging is predicted to slow down during training. In summary this pilot study yielded additional findings showcasing the potential correlation of trauma therapy and alterations of DNA methylation.

BACKGROUNDCalorie restriction (CR) increases healthy lifespan and is accompanied by slowing or reversal of aging-associated DNA methylation (DNAm) changes in animal models. In the Comprehensive Assessment of Long-term Effects of Reducing Intake of Energy (CALERIE) human trial we evaluated associations of CR and changes in whole-blood DNAm. METHODSCALERIE randomized 220 healthy, non-obese adults in a 2:1 allocation to two years of CR or ad libitum (AL) diet. The average CR in the treatment group through 24-months of follow-up was 12%. Whole blood (baseline, 12 and 24 month) DNAm profiles were measured. Epigenome-wide association study (EWAS) analysis tested CR-induced changes from baseline to 12- and 24-months in the n=197 participants with available DNAm data. RESULTSNo CpG-site-specific changes with CR reached epigenome-wide significance (FDR<0.05). Secondary analyses of CpG sites identified in published EWAS suggest, we found that CR induced DNAm changes opposite those associated with body mass index (BMI) and smoking (p<0.003 at 12- and 24-month follow-ups). In contrast, CR altered DNAm at chronological-age associated CpG sites in the direction of older age (p<0.003 at 12- and 24-month follow-ups). CONCLUSIONAlthough individual CpG site DNAm changes in response to CR were not identified, analyses of sets CpGs identified in prior EWAS revealed CR-induced changes to blood DNAm. Altered CpG sets were enriched for insulin-production, glucose-tolerance, inflammation, and DNA-binding and -regulation pathways, several of which are known to be modified by CR. DNAm changes may contribute to CR effects on aging.

Analyses of 3,370 normal human tissues of ectodermal, endodermal and mesodermal origins identified 12,587 regions averaging [~]585 bp with significant differences in DNA methylation levels within identical tissues. These methylation variants (MeVars) occurred in 8,037 genes enriched in neurological disorders and cancers of which, majority were tissue-specific rather than being systemic. This somatic variation was reduced by reprogramming in vitro into iPSCs and in vivo during spermatogenesis. Analysis of prefrontal cortices showed a higher incidence of MeVars in the candidate genes in controls than schizophrenia patients wherein a subset showed significantly altered transcript levels. Similar effects were observed for oral tissues and skin fibroblast cells. MeVars showed significant association with SINE1, simple and low complexity repeats, H3K27me3, H3k9me3 and H3K4me1 modifications and EZH2, SUZ12 and REST binding sites. Collectively, MeVars have postzygotic origins with an ability to reset during reprogramming, adding a new dimension in the form of epigenetic diversity and its relevance to disease susceptibility in humans.

DNA methylation (DNAm) is influenced by genetic and environmental factors, and can be used to understand interindividual variability in genomic regulation. Co-methylation between DNAm sites is a known phenomenon, but the architecture of relationships between the approximately 450,000 (450k) sites commonly measured in epidemiological studies has not been described. We investigate whether interindividual co-methylation structure amongst the 450k sites changes with age, whether it differs between UK-born White (n=849, 910, 921 and 424) and Pakistani ancestry (n=439) individuals, and how it relates to genome regulation. We find stability between birth and adolescence, across cohorts, and between two ethnic groups. Highly correlated DNAm sites in close proximity are heritable, but these relationships are weakly influenced by nearby genetic variants, and are enriched for transcription factor (TF) binding sites related to regulation of short RNAs transcribed by RNA polymerase III. Highly correlated sites that are distant, or on different chromosomes (in trans), are driven by common and unique environmental factors, with methylation at these sites less likely to be driven by genotype. Trans co-methylated DNAm sites are enriched for multiple TF binding sites and for inter-chromosomal chromatin contact sites, suggesting DNA co-methylation of distant sites may relate to long-range cooperative TF interactions. We conclude that DNA co-methylation has a stable structure from birth to adolescence, and between UK-born White and Pakistani individuals. This stable structure might have implications for future design and interpretation of epigenetic studies. We hypothesise that co-methylation may have roles in genome regulation in humans, including 3D chromatin architecture.

Background: Suicide is a major public health concern and a highly complex, heterogeneous phenotype. Increasing evidence implicates epigenetic mechanisms, particularly DNA methylation (DNAm), in suicidal behavior. Methods: Building on previous epigenome-wide association studies (EWASs), we conducted the largest EWAS to date in postmortem dorsolateral prefrontal cortex (Brodmann area 9), analyzing DNAm and epigenetic aging (EA) in 199 suicide decedents (SD) and 190 age- and sex-matched non-psychiatric controls (NPC) using the Infinium MethylationEPIC BeadChip Array v2.0. Results: Bulk tissue analysis identified no significant differentially methylated positions or regions. In contrast, cell type-specific analysis using DNAm-deconvoluted cell proportions identified 605 differentially methylated cytosines in individual cell types (DMCTs) in excitatory neurons, 10 in inhibitory neurons, and 28 in oligodendrocyte precursor cells. Sex-stratified analyses identified mainly male-specific DMCTs, most of which were found in excitatory neurons, while comparison of violent and non-violent suicide identified additional DMCTs in glial cell types. Excitatory neuron DMCTs were enriched for synaptic, small GTPase signaling, and neurodevelopmental pathways, and overlapped genes previously associated with suicidal behavior, including MAD1L1. No significant differences in EA acceleration were observed overall or by sex or suicide mechanism. Conclusions: These findings indicate that suicide-associated DNAm patterns are primarily neuron-specific and may remain undetectable in bulk tissue, highlighting the importance of cell type-specific approaches to elucidate biological mechanisms underlying suicide.

Post-traumatic stress disorder (PTSD) is associated with increased cardiovascular disease (CVD) risk, yet the epigenetic mechanisms underlying this link remain unclear. We investigated whether DNA methylation (DNAm) within Conserved Regions of Systemic Interindividual Variation (CoRSIVs), genomic regions showing stable within-individual, but variable between-individual methylation, mediates the association between PTSD symptom severity (PTSS) and CVD. We analyzed blood-derived DNAm from three cohorts (DNHS: discovery; GTP and NHS: replication), focusing on 7,694 CoRSIV CpGs profiled with the Illumina MethylationEPIC BeadChip. Logistic regression related CpGs to PTSS and CVD, adjusting for demographic and trauma-related covariates. CpGs nominally associated (p<0.05) with both PTSS and CVD in DNHS were then tested using causal mediation analysis. In DNHS, 27 CpGs were nominally associated with both PTSS and CVD, with seven showing nominal mediation (p<0.05). Across cohorts, six of these seven displayed mediation effects in a consistent direction in at least one replication cohort, and three CpGs showed concordant mediation directions across all three cohorts. Notably, cg07941916 (C5orf56/IRF1-AS1) and cg20545458 (intergenic) exhibited positive mediation in DNHS with the same direction in GTP, implying that higher PTSS is associated with methylation changes that correspond to higher CVD risk, whereas all mediation effects in NHS were negative, consistent with its healthier, lower-risk profile. These loci map to immune and inflammatory pathways, alongside other mediators annotated to neuronal/stress-aging and autonomic processes. Overall, DNAm variation within CoRSIVs may partially mediate PTSD-related CVD risk and nominates specific CpGs as hypothesis-generating epigenetic biomarkers that require validation in larger, ancestrally diverse longitudinal cohorts.

DNA methylation is an established biomarker of human ageing, and analysing CpGs grouped by transcript as functional units may reveal new insights into the processes of ageing. In this study, we analyzed the GSE87571 dataset (714 samples from 14-94 years) to assess the relationship between transcript-level methylation profiles and chronological age in human blood. This approach led to the creation of Epitage, a curated set of 48 transcripts from 13 genes identified through machine learning as having methylation profiles that strongly correlate with age (R2 [&ge;] 0.8). This analysis highlighted transcripts from the genes KCNS1, SPTBN4, and VTRNA1-2, which have been only rarely mentioned as age-related methylation markers in humans, suggesting them as underexplored candidates for future investigation. In addition, the list includes genes already implicated in aging or related pathways, such as ELOVL2, FHL2, KLF14, TRIM59, MIR29B2CHG, CALB1, OBSCN, PRRT1, OTUD7A, and SYNGR3. To validate models efficiently while ensuring reproducibility, we developed ugPlot, an open-source R package with a graphical user interface (GUI) that automates routine steps for training and testing hundreds of machine-learning models. The tool also streamlines dataset import and manipulation, reducing human error and generating publication-ready plots. Epitage thus provides a focused and accessible starting point for experimental and translational studies into the roles of DNA methylation and transcript regulation in human ageing.

DNA methylation influences gene expression and is altered in many cancers, but the relationship between DNA methylation and cancer outcomes is not yet fully understood. If methylation of specific genes is associated with better or worse outcomes, it could implicate genes in driving cancer and suggest therapeutic strategies. To advance our understanding of DNA methylation in cancer biology, we conducted a pan-cancer analysis of the relationship between methylation and overall survival. Using data on 28 tumor types from The Cancer Genome Atlas (TCGA), we identified genes and genomic regions whose methylation was recurrently associated with survival across multiple cancer types. While global DNA methylation levels are associated with outcome in some cancers, we found that the gene-specific associations were largely independent of these global effects. Genes with recurrent associations across cancer types were enriched for certain biological functions, such as immunity and cell-cell adhesion. While these recurrently associated genes were found throughout the genome, they were enriched in certain genomic regions, which may further implicate certain gene families and gene clusters in affecting survival. By finding common features across cancer types, our results link DNA methylation to patient outcomes, identify biological mechanisms that could explain survival differences, and support the potential value of treatments that modulate the methylation of tumor DNA.

Variation in DNA methylation (DNAm) is associated with multiple biological processes that track growth and development, ageing and age-related diseases. However, there is little understanding of what constitutes typical patterns of DNAm variation and how these patterns change across the life course. In this study, we synthesised a map of the human methylome across the life course, focussing on changes in variability and mean DNAm. Harmonizing DNAm datasets across eight longitudinal and cross-sectional UK-based studies, we meta-analysed n=13,215 blood samples from n=7,037 unique individuals from birth to 98 years of age. Changes in CpG-specific variability and means were described across the life course using a meta-regression framework. CpG-specific associations of variability or mean DNAm in relation to the likelihood of association with 100 traits linked to environmental exposures, health and disease were tested within and across ten developmental age bins across the life course. Age was linked to DNAm variability at 29,212 CpG sites. On average, we observed a 1.26 fold increase in DNAm variability per year across the life course. 33,730 CpGs displayed changes in mean DNAm, with 64% of these loci showing decreases in DNAm over time. CpG sites linked to traits were in general more variable across the life course. Our study provides, for the first time, a map of the human methylome across the life course, which is publicly accessible through a searchable online database. This resource allows researchers to query CpG-specific trajectories from birth to old age and link these to health and disease.

Age at menarche, a key milestone in female reproductive development, has declined globally and is associated with cancer and other health outcomes. We investigated epigenetic mechanisms underlying pubertal timing by analysing genome-wide DNA methylation in blood from 3,429 women (mean age 56 years) using the Illumina HumanMethylation450 BeadChip. In the discovery cohort, comprising 479 participants from the Australian Mammographic Density Twins and Sisters Study and 2,614 from the Melbourne Collaborative Cohort Study, we identified 63 differentially methylated regions. Of these, the TRIM61 region was replicated (P<0.05) in 336 women from the European Prospective Investigation into Cancer and Nutrition-Italy, showing consistent positive effects for each CpG and for the region overall. Mendelian randomisation suggested that TRIM61 methylation causally influences age at menarche and regulates the expression of nearby genes, including RP11-366M4.11. Functional annotation revealed the replicated region overlaps with active regulatory elements, suggesting that methylation at these sites may influence the expression of nearby genes through modulation of chromatin accessibility and transcriptional regulation. These findings identify a novel, causally implicated epigenetic mechanism at TRIM61, where methylation changes in active regulatory regions may alter chromatin accessibility and gene expression to influence pubertal timing. By integrating epigenome-wide association, Mendelian randomisation, and functional annotation, this work provides molecular evidence for novel regulatory pathways underlying age at menarche, offering new mechanistic insights into female reproductive development and its links to long-term health.