Epigenetics

Epigenetics may play a crucial role in livestock adaptation to environmental challenges like heat stress. In recent years, a growing number of studies have investigated the epigenetic mechanisms underlying dairy cow adaptation to heat stress. However, there is still limited knowledge about the effects of heat stress on immune cells and immune-related phenotypes. Herein we aim to identify heat-stress induced DNA methylation variations on blood methylome potentially affecting regulatory regions and associated phenotypes. Blood samples were collected and peripheral blood mononuclear cell (PBMC) isolated from four cows before (D0) and after (D14) a 14-d heat stress challenge (cyclical THI 72-82) and, from four cows kept in thermoneutral conditions (THI 61-64). Heat-stressed cows had ad libitum access to diets supplemented with adequate levels of vitamin D and Ca (12,000 IU/kg of vitamin D and 0.73% Ca, respectively). To eliminate confounding effects due to differences in nutrient intake, cows maintained under thermoneutral conditions were pair-fed (PF) to their heat-stressed counterparts and received adequate concentrations of vitamin D and Ca as well. Reduced representation bisulphite sequencing (RRBS) was used to profile PBMCs methylome. Differential methylation analysis was performed using methylKit and DSS softwares ({Delta}meth [&ge;] 25%, adjusted p-value < 0.01), retaining only commonly detected differentially methylated cytosines (DMCs). A total of 2,908 DMCs were identified when comparing pre- and post-heat stress samples. After excluding 649 DMCs that were also detected under thermoneutral conditions, as these changes were likely associated with feed restriction inherent to the pair-feeding design rather than with heat stress per se, 2,259 heat stress-specific DMCs remained, predominantly hypomethylated. About half of the DMCs are annotated in intronic and intergenic regions; known to harbor regulatory elements. By intersecting the DMRs with publicly available functional annotation data, we observed hypomethylation on regulatory regions putatively affecting cows immune system. As an example, we identified a loss of methylation within an enhancer region of the MSN gene, which is involved in lymphocyte homeostasis, and a loss of methylation in the promoter region of MECP2, a well-established epigenetic regulator with a central role in chromatin organization and gene expression. These findings highlight the impact of heat stress on dairy cow immunity and provide new insights into its epigenetic regulation under environmental stress. Interpretative summaryThis study examined DNA methylation changes induced by heat stress in dairy cows to elucidate epigenetic mechanisms of thermal adaptation. Using RRBS on PBMCs, 2,259 heat stress-specific differentially methylated cytosines were identified, predominantly hypomethylated and enriched in regulatory regions. Functional annotation highlighted immune-related pathways, including hypomethylated regulatory regions near genes (e.g., MSN, ZBTB33, SLC25A5, GNAS, FAM3A, and MECP2) associated with immune function. These findings indicate that heat stress induces targeted epigenetic modifications potentially affecting immune regulation in dairy cows.

DNA methylation is a key epigenetic mechanism influencing gene regulation and cellular identity. In skeletal muscle, methylation contributes to fiber-type specification, metabolic programming, and satellite cell function, with evidence of sex-specific differences. Here, we investigated whether spatial regionalization of gene expression along the proximal-distal axis of the tibialis anterior (TA) is mirrored by corresponding patterns of DNA methylation. Using MeDseq on TA sections from muscles previously analyzed by spatial transcriptomics, we profiled methylation across transcriptional start sites (TSS), gene bodies, and regulatory elements. Despite robust spatial differences in transcriptomes, methylation patterns were largely uniform along the proximal-distal axis, indicating that DNA methylation does not underlie regional gene expression in adult TA muscle. In contrast, sex emerged as the primary determinant of methylation variation. Male muscles exhibited widespread hypermethylation at TSS, gene-bodies and regulatory regions, corresponding with sex-specific transcriptional programs, including glycolytic fiber enrichment in males and oxidative fiber markers in females. Notably, chromatin- and methylation-associated regulators such as Setd7, Gsk3a, and Bmyc were upregulated in males, suggesting mechanisms linking transcriptional control to epigenetic state. These findings highlight that while spatial gene expression is transcriptionally driven, sex-specific epigenetic programs dominate adult skeletal muscle, underscoring the need to consider sex in multi-omic studies of muscle biology.

Background Prenatal exposure to pesticides and psychosocial factors often co-occurs, particularly in low- and middle-income settings, yet their joint effects on epigenetic age acceleration (EAA) in early life remain unknown. We investigated the joint associations of prenatal pesticides metabolites and psychosocial factors on EAA in the first five years of life in the South African Drakenstein Child Health Study. Methods In 643 mothers, we measured 11 urinary pesticide metabolites and seven psychosocial factors during the second trimester of pregnancy. Child DNA methylation was measured in whole blood at ages 1, 3, and 5 years. EAA was estimated using the Horvath, Skin & Blood Horvath (skinHorvath), and Wu epigenetic clocks. Longitudinal associations were estimated using generalized estimating equations, adjusted for confounders. Joint mixture associations were evaluated using weighted quantile sum regression (WQS) and quantile g-computation (QGCOMP). Results The joint prenatal exposure mixture was positively associated with Wu ({beta} per one quintile increase in the mixture [95% CI]: 0.41 years [0.15, 0.80]), skinHorvath (0.11 years [0.06, 0.16]), and Horvath EAA (0.31 years [0.20, 0.46]) over time using WQS. Psychosocial factors, particularly food insecurity, physical interpersonal violence, and stress biomarkers, contributed most to the total mixture effect for all clocks. Pyrethroid metabolites PBA and TDCCA were top pesticide contributors to Wu EAA. Pathway enrichment analyses of clock-specific CpGs revealed distinct biological architectures, with the Wu clock enriched for neurodevelopmental and immune pathways, and metabolic pathways for the Horvath clock. Discussion Joint prenatal exposure to pesticides and psychosocial factors was associated with increased EAA across early childhood, with psychosocial factors contributing the most to the total effect. These findings highlight the importance of assessing chemical and non-chemical stressors jointly and clock-specific biological interpretation in epigenetic aging research.

BackgroundGene expression changes in response to developmental and environmental cues rely on cis-regulatory sequence elements (cREs). BRG1/BRM-Associated Factors (BAF) chromatin remodeling complexes maintain chromatin accessibility at many cREs, enabling binding by transcription factors (TFs). However, cREs exhibit a broad range of sensitivity to loss of BAF function, and the basis of this variability remains unknown. ResultsTo identify the characteristics of BAF-dependent cREs, we mapped chromatin accessibility changes following acute pharmacologic BAF inhibition in GM12878 lymphoblastoid cells. We integrated these results with over 100 TF and histone modification ChIP-seq datasets and used machine learning to identify features that predict chromatin accessibility changes. We found that Activator Protein 1 (AP-1) factors and lymphoid lineage-defining TFs including RUNX3 and PU.1 predicted BAF-dependence. Strikingly, we found that cREs bearing the chromatin signature of "primed" enhancers - enriched for H3K4me1 but lacking H3K27ac - were significantly more sensitive to BAF inhibition than typical active enhancers. As primed enhancers are known to facilitate transcriptional responses to stimuli, we tested the requirement of BAF activity in these responses. Acute BAF inhibition was sufficient to prevent both chromatin and transcriptional responses to interferon gamma and dexamethasone. cREs which normally gained accessibility in response to stimulation failed to do so with BAF inhibition, and these cREs were linked to genes with suppressed transcriptional induction. ConclusionsCollectively, our results demonstrate a requirement for continuous BAF activity to enable stimulus response and suggest that defective signal responsiveness may be a pathogenic mechanism in disease states caused by loss-of-function mutations in BAF subunits.

Psychosocial stress is a significant risk factor for mental and physical illness, and emerging evidence suggests that altered oral microRNAs (miRNAs) and microbiome may act as biomarkers or mediators of stress responses. This study investigated stress-associated molecular changes in saliva from 113 male police officers. Based on repeated administrations of the Karasek Demand/Control and Effort/Reward Imbalance questionnaires, subjects were stratified by perceived stress response (SR) to homogeneous occupational stressors into low, intermediate, or high responders. Salivary miRNA profiles were analyzed using small RNA sequencing, and microbiome composition was assessed through shotgun metagenomics. Eighteen miRNAs were significantly differentially expressed between high- and low-SR groups, with four miRNAs with increasing (miR-10400-5p, miR-1290, miR-6074-5p, and miR-9902) and fourteen with decreasing (including miR-21-5p and mirR-142-3p) levels in the high SR group (adj.p<0.05). The identified salivary miRNAs showed a progressive alteration from low- to high-SR groups. Functional enrichment analysis indicated that dysregulated miRNA targets are involved in apoptosis, cellular stress responses, and metabolic regulation. Distinct salivary microbial communities were also observed across SR groups. Several taxa displayed progressive abundance shifts, with Prevotella baroniae and Schaalia odontolytica increasing and Actinomyces naeslundii and Capnocytophaga ochracea decreasing in the high SR group. Functional predictions revealed, in this group, a significant enrichment of inositol degradation pathways, paralleled by a reduction in bacteria involved in L-tryptophan and thiamine biosynthesis. These findings suggest that salivary miRNAs and microbiota profiles may serve as non-invasive biomarkers of psychosocial stress and provide insight into molecular mechanisms linking chronic stress to physiological and behavioral outcomes.

Stressful life events impact individual's functionality and contribute to disease outcomes, yet the biological pathways underlying life stress remain unclear. We characterized the metabolomic profiles of stressful life events using data from 3,264 participants (5,163 observations) of the Dutch NESDA cohort. 98 metabolites were identified, with upregulated metabolites overrepresented in phosphatidylethanolamine and downregulated metabolites overrepresented in fatty acid metabolism. 92 of these metabolites were available in the Dutch NEO cohort (N=599): 11 were significantly replicated including six lipids (e.g., three bile acids (glycochenodeoxycholate 3-sulfate)), one carbohydrate, and one xenobiotic. 21 overlapping metabolites were additionally available in the Chinese GBCS cohort (N=200): 10-undecenoate (11:1n1) (fatty acid) and glycochenodeoxycholate 3-sulfate (bile acid) showed consistent associations across both Dutch and Chinese cohorts. Stressful life events are associated with metabolic dysregulation, particularly involving fatty acid and bile acid pathways, highlighting promising biological targets to reduce the impact of stress on mental and somatic health.

Long-chain n-3 polyunsaturated fatty acids (n-3 PUFAs) are candidate preventive agents for breast cancer. With emerging evidence of epigenetic regulation of the tumor microenvironment, tissue-level epigenetic effects may represent an important target for cancer prevention. In a randomized Phase II sub-study (high-dose 5 g/day vs low-dose 1 g/day for 12 months; n = 17; Clinicaltrials.gov: NCT02295059), DNA methylation (DNAm) of the breast environment was profiled by reduced-representation bisulfite sequencing (RRBS). DNAm was assessed genome-wide, at individual gene promoters, and for locus-level heterogeneity which has been linked to epigenetic dysregulation that can precede breast cancer. Both doses induced promoter DNAm changes, but their responses diverged: low-dose samples showed increased CpG variance and more differentially methylated promoters without pathway enrichment, whereas high-dose samples had reduced DNAm heterogeneity and promoter enrichment in inflammation signaling pathways. Many overlapping differentially methylated promoters changed in opposite directions between doses. The finding that high-dose n-3 PUFA affects DNAm fidelity in the breast adipose suggests a new potential mechanism for n-3 PUFA-mediated prevention of breast cancer development. Together with the dose-specific, directionally discordant DNAm responses in breast adipose, this study has important implications for both advancing n-3 PUFA for breast cancer prevention and dose selection in future n-3 PUFA supplementation trials.

Childhood socioeconomic position (SEP) can have lifelong effects on health. Many studies have used adult height as a surrogate marker for early-life conditions. In this study, we derived the non-genetic component of height, calculated as the residual from sex-specific standardized height regressed on genetically predicted height, as a surrogate for childhood SEP, using data from the Hispanic Community Healthy Study/Study of Latinos (2008-2011). A positive residual would indicate favorable early-life conditions promoting growth, while a negative residual indicates early-life adversity that may stunt the development. The height residual was associated with early-life variables such as parental education, year of birth, US nativity and age at first migration to the US (50 states/DC), supporting the validity of height residual as a surrogate for early-life conditions. Furthermore, a height residual was positively associated with better cardiovascular health (CVH) and cognitive function among middle-aged and older adults. Interestingly, among <35 years old, the height residual was negatively associated with the "Lifes Essential 8" clinical CVH scores. These results suggest the non-genetic component of height as a surrogate for childhood environment, with predictive value for CVH and cognitive function.

Ehmt2 is a key H3K9 methyltransferase that regulates genome silencing and structural integrity during animal development. In addition to this canonical function, Ehmt2 has also been implicated in neural tissues mediating both direct and indirect transcriptional activation, and exon splicing, to facilitate proper neural cell differentiation and survival. Several germline loss-of-function animal models have been developed showing both conserved and divergent phenotypes that range from embryonic lethality to behavioural deficits in adult, fertile animals. Here, we generated the first maternal-zygotic ehmt2 loss of function mutant in zebrafish using CRISPR-Cas9 mutagenesis. An assessment of the pattern of H3K9 methylation in mutant embryos by ChIP-seq indicates that there are aberrant levels of this repressive mark, including reduction in discrete 5 non-coding regions of genes, but with no significant change in the overall pattern distribution of these marks across the genome. Global transcriptome and morphological analyses demonstrated that mutant embryos displayed greater variation in the timing of developmental progression that is, on average, slower compared to controls. Despite this, mutant embryos ultimately survive and are fertile. Through examination of progenitor cell dynamics and gene expression profiles, we found that the delay in embryonic development was associated with longer rates of S-M phases of the progenitor cell cycle in mutants leading to deficits in tissue growth. Finally, our data suggest a robust network of epigenetic regulators can potentially compensate for Ehmt2 loss of function and permit embryonic development and survival in ehmt2 mutant zebrafish. Our work establishes a zebrafish ehmt2 loss of function model that will facilitate examination of the complex and varied roles of Ehmt2 in vertebrate development.

Background: Pre-stroke physical activity may protect against post-stroke cognitive impairment (PSCI) via neuroplastic mechanisms including BDNF signalling. However, evidence in stroke survivors and the modifying role of the BDNF Val66Met polymorphism remain limited. Methods: In this prospective single-centre cohort, 97 patients with ischaemic stroke underwent detailed neuropsychological assessment during index hospitalisation and at 6-month follow-up. Pre-stroke activity was quantified as weekly MET-minutes (IPAQ scale). Serum BDNF and Val66Met genotype were measured. Associations between METs and cognitive outcomes (baseline, follow-up) were assessed with Spearman correlations and adjusted multivariable linear regression. Results: Higher pre-stroke METs correlated with superior baseline performance across global cognition (MoCA), verbal learning/recall (CVLT indices), attention and executive measures. After adjustment, CVLT long-delay free recall (LDFR) and TMTA remained significant ({beta} for CVLT LDFR {approx}0.000097 per MET-min/week, p < 0.05). At 6 months, METs were associated with multiple CVLT indices (SDCR, SDFR, LDFR) in adjusted models. All associations indicated positive correlation between physical activity and better cognitive outcome. Mean serum BDNF did not correlate with METs (mean 27,261 +/- 7,967 pg/mL) and did not differ from controls. Val/Val (GG) carriers of Val66Met genotype of BDNF gene performed better cognitively than Met allele carriers, but the genotype did not correlate with serum BDNF level. Conclusions: Greater self-reported pre-stroke physical activity was associated with better early and 6-month cognitive outcomes after ischaemic stroke, whereas peripheral BDNF levels were not correlated. Val66Met polymorphism of BDNF gene correlates with the cognitive outcome in stroke survivors but does not enhance BDNF level, indicating effect on activity rather than quantity.

Introduction: Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is a common congenital malformation with complex etiology involving both genetic and environmental factors. Epigenetic mechanisms may mediate environmental contributions, but separating genetic from environmental effects remains challenging. Methods: We present an epigenome-wide association study with 32 monozygotic and 22 dizygotic twin pairs discordant for NSCL/P on blood and saliva samples. Differential methylation analysis was conducted using linear models to identify CpG sites showing significant methylation differences between affected and unaffected twins followed by functional annotation and pathway enrichment analysis. Results: The top-ranked finding is a differentially methylated region comprising two CpG sites at the CYP26A1 locus, cg12110262 (P = 3.21x10-7) and cg15055355 (P = 1.39x10-3). CYP26A1 is essential for retinoic acid catabolism and craniofacial patterning. The chromatin regulator ANKRD11, which causes KBG syndrome featuring cleft palate was the second best hit. Differentially methylated CpG sites showed significant enrichment in craniofacial enhancers and overlap with multiple GWAS-validated cleft genes including VAX1, PVRL1, SMAD3, and PRDM16. Conclusions: Our findings implicate retinoic acid signaling and chromatin regulation in NSCL/P etiology and demonstrate the value of discordant twin designs for distinguishing environmental from genetic epigenetic contributions to complex malformations.

Trait-selective harvesting by fisheries can impose strong selective pressures on fish populations, driving changes in life history traits affecting fisheries productivity and ecosystem functioning. While the genetic consequences of harvesting have been extensively studied, the extent to which phenotypic variation reflects genomic evolution versus environmentally-induced plasticity remains unclear. Epigenetic mechanisms, such as DNA methylation, may mediate between these processes, serving as a rapid and reversible response to the selective pressures imposed by harvesting. In this study, we implemented an improved laboratory and bioinformatics protocol, epiGBS3, to examine genomic variation and DNA methylation patterns in the marine fish Xyrichtys novacula. The study spanned three replicated geographical areas each comprising two adjacent locations: an intensively exploited fishery and a no-take Marine Protected Area (ntMPA). A nested analysis design across the three areas revealed strong gene flow and no evidence of genetic structure. Nevertheless, nucleotide diversity was significantly reduced in fisheries relative to ntMPAs. We also found that DNA methylation levels differed between protected and exploited sites after controlling for age, suggesting that fishing may influence epigenetic changes independently of fisheries-induced age-truncation effects. This represents one of the first lines of evidence that fisheries can potentially shape epigenetic variation, supporting DNA methylation as contributor to local adaptation under high gene flow and strong anthropogenic selection.

Postpartum depression (PPD) arises during a period of profound endocrine and immune reorganisation, yet it is unclear whether women who develop PPD show distinct trajectories of immune-related DNA methylation compared to euthymic mothers. In a longitudinal cohort, women with PPD (n = 17) and healthy postpartum controls (n = 24) were followed from birth to 12 weeks postpartum, with repeated assessment of depressive symptoms and perceived stress and whole-blood sampling at 2-3 days (T0) and 12 weeks (T4) for Infinium MethylationEPIC array profiling. Healthy postpartum women showed a widespread gain in DNA methylation from T0 to T4 with strong enrichment of genes involved in neutrophil activation, chemokine signalling and interleukin-1 production, consistent with a normative immune-epigenetic down-tuning after childbirth. Women with PPD also exhibited immune-related changes, but with fewer differentially methylated CpGs and increased variance at sites that were stably hypermethylated in controls, indicating an attenuated and more heterogeneous epigenetic response. Although no CpG reached epigenome-wide significance in direct case-control contrasts, longitudinal consistency analyses highlighted a small set of CpGs with reproducible PPD-associated hypermethylation in stress- and signalling-related genes, including FKBP5 and AVP, suggesting that disrupted immune-epigenetic adaptation and altered regulation at these loci may contribute to postpartum vulnerability.

The zebrafish forebrain is a central hub for cognitive and social behaviors, yet a comprehensive, region-specific DNA methylation reference for this tissue is not available. To address this gap, we generated a genome-wide methylation map of the adult zebrafish forebrain using Oxford Nanopore Technologies (ONT) long-read sequencing. Forebrains from six individuals were profiled, enabling direct detection of multiple DNA base modifications at single-base resolution. The resulting dataset includes CpG-associated 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC), as well as non-CpG 5mC and N6-methyladenine (6mA), with 96.8% genome coverage. CpG methylation was widespread, with 64.2% of CpG sites classified as highly 5mC-modified. In contrast, 5hmC and non-CpG methylation were markedly less abundant, and 6mA was detected at very low levels. CpG islands showed a bimodal distribution of methylation, promoter regions displayed elevated variability compared to gene bodies, and CC-context non-CpG methylation exhibited significant strand asymmetry. This resource provides a high-resolution epigenomic baseline for the adult zebrafish forebrain.

Large-scale genomic studies have identified biomarkers of adult cognitive functioning and educational attainment, yet the developmental pathways connecting these biomarkers to adult outcomes remain unclear. Drawing on four cohorts, we examined the developmental correlates of an epigenetic index of adult cognitive function ( Epigenetic-g) alongside polygenic indices of cognition and education. Epigenetic-g and polygenic indices were uncorrelated and captured distinct variation in childrens cognitive and academic performance. Longitudinal analyses revealed that Epigenetic-g is plastic in early childhood, reaching moderate stability by adolescence, and, unlike polygenic indices, is not related to longitudinal cognitive growth. Twin models indicated that Epigenetic-g captures genetic and unique environmental variation relevant to cognitive and academic achievement that is not identified by current polygenic indices. Epigenetic indices relevant to psychological development can be generated from DNA methylation studies of adults, with most variation in these indices emerging early in life.

Background: Vascular smooth muscle cells (VSMCs) phenotypic plasticity can modulate atherosclerosis progression. Although several gene regulatory steps towards pro-inflammatory phenotypes have been well-studied, epitranscriptomic changes during this transition and their regulatory roles remain unexplored. Methods and Results: Primary human VSMCs were stimulated with TGF-{beta}1 to induce an atheroprotective, contractile, and matrix-producing state and with IL1-{beta} plus PDGF-BB to induce a highly energetic, pro-inflammatory state, confirmed by Illumina bulk RNA sequencing and proteomics. Untargeted screening of mRNA base modifications using Oxford Nanopore Technologies direct RNA sequencing and xPore analysis revealed enhanced uridine modification within a GUUUU motif in pro-inflammatory VSMCs. Modified uridines were enriched in 3'-UTR and accessible RNA structures, with implications on Poly(A) tail dynamics and miRNA binding. Conclusions: Atheroprotective and pro-atherogenic treatments induce distinct epitranscriptomic landscapes composed of different modification types, often co-localized in the same transcript. Modified uridines in mRNAs are abundant in a high-energy, pro-inflammatory VSMC state and associated with post-transcriptional regulation. In summary, epitranscriptomics adds a novel regulatory layer to VSMC phenotypic transitions critical for atherosclerosis development and progression.

BackgroundConventional models of human ribosomal DNA (rDNA) array organization have historically depended on transcription-centric boundaries, partitioning the unit into a [~]13 kb rDNA transcription region and a monolithic [~]31 kb intergenic spacer (IGS). While our previous identification of Duplication Segment Units (DSUs) mapped these arrays based on an intuitive analysis of the microsatellite density landscape of the complete reference human genome, our present deep mining of this landscape has revealed a more accurate rDNA Gene Unit Pattern. Methods & ResultsIn this study, we conducted a deep mining analysis of our previously established microsatellite density landscape of the T2T-CHM13 assembly, focusing specifically on nucleolar organizing regions (NORs). We suggest a more accurate rDNA Gene Unit Pattern containing a (CTTT)n microsatellite aggregation ahead of the rDNA gene and a (CT)n microsatellite aggregation behind the gene, rather than a pattern featuring an IGS region inserted between two rDNA genes. ConclusionsA correct rDNA gene pattern of the human genome probably includes a (CTTT)n microsatellite aggregation ahead of the gene and a (CT)n microsatellite aggregation behind it, which possibly constitute cis- and trans-regulating regions; the (CTTT)n and (CT)n microsatellite aggregations may provide two different local stable DNA structures for regulatory protein binding.

BackgroundAdvanced ageing has been associated with an increased risk of serious disease endpoints in people with HIV (PWH). We conducted a longitudinal analysis to assess advanced proteomic ageing during untreated HIV infection and the effect of antiretroviral therapy (ART) on it by comparing the plasma proteome before and after ART initiation. Methods416 protein abundance estimates were used to train a linear regression model predicting chronological age on 727 samples from Swiss HIV Cohort Study (SHCS) participants on long-term suppressive ART (median ART duration, 11.7 years). Advanced ageing was defined as age predicted by the proteomic ageing clock (PAC) minus chronological age. We evaluated the effect of successful ART on advanced proteomic ageing in an independent set of 80 PWH who had 4 longitudinal samples available, that is 2 samples during untreated HIV infection (>3 years apart, median interval between samples, 8{middle dot}08 years (IQR 4{middle dot}83-11{middle dot}09)) and 2 samples during suppressive ART (>3 years apart, median interval between samples, 9{middle dot}81 years (7{middle dot}16-11{middle dot}01)). FindingsIn the longitudinal test cohort, participants showed significantly higher proteomic age during untreated HIV infection than during suppressive ART, with a mean difference of 5.99 years (95% CI 4.25, 7.72), p = 0.0001. Thus, ART was associated with a marked reduction in proteomic advanced ageing. Although proteomic age remained higher than chronological age at all time points, linear interpolation of per-participant advanced ageing showed progressive normalisation towards chronological age during long-term suppressive ART. We validated these findings with our previously published epigenetic ageing study in the same cohort and extended those observations to the functional proteome, showing that proteomic data can capture acute immune signatures. Further, mediation analysis suggests that reversal of advanced ageing under ART is not driven by CD4+ or CD8+ T cell counts, indicating that the proteome captures ageing signals beyond immune reconstitution. InterpretationsIn a longitudinal study spanning more than 17 years, the advanced proteomic ageing observed during untreated HIV infection showed immediate and persistent deceleration under suppressive ART, demonstrating the importance of minimising the duration of untreated HIV infection. FundingSwiss HIV Cohort Study Research in contextO_ST_ABSEvidence before this studyC_ST_ABSCurrent guidelines recommend prompt antiretroviral therapy (ART) initiation after HIV diagnosis, making it now difficult to quantify the potential effects of untreated HIV on advanced ageing. Biological ageing clocks serve as proxies for individual-level disease impact and are associated with serious disease endpoints in people with HIV (PWH). We searched PubMed for English-language reports from database inception to February 24, 2026, using combinations of the terms "HIV infection," "antiretroviral therapy," "proteomic ageing," "proteomic clocks," "proteomic advanced ageing," and "age advancement." We identified one study reporting that virally suppressed HIV infection is associated with a significant increase in proteomic ageing. We have previously shown in the well established longitudinal SHCS cohort with blood samples spanning >17 years and available both pre-ART and post-ART, that telomere length attrition and epigenetic ageing is accelerated during untreated HIV infection and that initiation of successful ART is associated with a significant reduction in accelerated ageing. Added value of this studyTo our knowledge, this is the first study to examine the impact of untreated HIV on the proteome using a proteomic ageing clock. Our results demonstrate that proteomic age is elevated before ART initiation and decreases significantly following successful viral suppression on ART. This reduction was not mediated by standard immunological markers (CD4+ and CD8+ T-cell counts,CD4:8 ratio). Compared with our previous epigenetics study, the proteome appears more responsive: advanced ageing increases more sharply during untreated HIV infection and is faster to decrease after ART initiation. Implications of all the available evidenceOur findings demonstrate the importance of prompt ART initiation for PWH and reveal HIV-related ageing signals in the proteome that extend beyond immune reconstitution. Further, given the established association between advanced ageing and serious disease endpoints, this evidence motivates future studies into persistent advanced ageing to enable identification and stratification of high-risk PWH.

Mental health conditions, including perinatal suicidality, remains a significant health burden representing a leading cause of maternal mortality in the United States. Although the etiology of perinatal suicidal ideation (SI) is not well understood, DNA methylation may provide meaningful mechanistic insights and/or serve as clinical biomarkers during the peripartum period. Using data provided by the Swedish BASIC cohort, we performed a retrospective analysis of DNA methylation changes associated with perinatal SI at three perinatal timepoints (17- and 38-weeks gestation and 8 weeks post-partum) through a targeted and genome-wide approach. Targeted analysis of a priori genes revealed 1, 10, and 4 significantly differentially methylated probes at each timepoint and implicated genes associated with the hypothalamic-pituitary-adrenal axis. Genome-wide results identified 465, 2,880, and 510 differentially methylated probes and 7, 25, and 12 differentially methylated regions at each timepoint. Pathway analysis at 38-weeks gestation identified vitamin digestion and absorption as the top term differentially methylated in perinatal SI. Additionally, genes implicated in estrogen and oxytocin signaling were also significantly differentially methylated. Post-partum ideation-risk was successfully predicted using the top ten genome-wide differentially methylated probes at 17 weeks (AUC=66.9%), with prediction accuracy highest when DNA methylation and depression severity were combined (AUC=93.2%). Furthermore, the prediction accuracy for identifying novel SI in the post-partum period increased to 86.2% with 17-week biomarkers. Our results deliver novel insights regarding the role of DNA methylation and perinatal SI, with biomarkers providing both mechanistic insights and clinical usefulness, contributing to the field of perinatal psychiatry and epigenetics.

BackgroundDespite extensive cataloging of carcinogenic exposures by the International Agency for Research on Cancer (IARC) and pharmacogenomic variation by resources such as PharmVar and CPIC, few platforms unify exposure, metabolic activation and detoxification, DNA damage, and genetic annotation within a single interactive visualization framework. This gap limits systematic evaluation of gene-environment interactions in cancer risk assessment. MethodsWe developed the Carcino-Genomic Knowledge Graph, ExposoGraph, an interactive knowledge-graph platform for carcinogen metabolism and DNA damage pathways. The reference graph integrates curated data and annotations from IARC, KEGG, PharmVar, CPIC, CTD, and supporting literature/resources. The current reference graph contains 96 nodes across 5 entity types (Carcinogens, Enzymes, Metabolites, DNA Adducts, and Pathways) and 102 edges across 6 relationship types (activates, detoxifies, transports, forms adduct, repairs, and pathway). ResultsThe first-generation reference graph captures metabolic activation and detoxification pathways for 9 carcinogen classes spanning 15 index carcinogens. It represents 36 enzymes across Phase I activation (n=14), Phase II conjugation and detoxification (n=14), Phase III transport (n=3), and DNA repair (n=5). Interactive exploration supports carcinogen-class filtering, node- and edge-type filtering, metadata-based search, and detailed hover/detail views with provenance and pharmacogenomic annotations. The androgen branch highlights cross-pathway connectivity by linking androgen metabolism to estrogen quinone formation and DNA adduct generation through CYP19A1-mediated aromatization and downstream catechol estrogen chemistry. In the optional androgen-focused extension, additional receptor, tissue, and variant context further connects this branch to androgen receptor signaling and genotype-specific annotations. ConclusionsExposoGraph provides a first-generation integrated, interactive framework linking carcinogenic exposures to metabolic fates and genetic modulators. The platform supports hypothesis generation for gene-environment interaction studies and may inform future individualized risk modeling, while remaining a research-use framework rather than a clinically validated risk-assessment tool.