Clinical Epigenetics

BackgroundAgeing is a sex-specific process characterised by a progressive decline in physiological integrity. DNA methylation represents a primary epigenetic hallmark of ageing, yet sex-specific patterns of epigenetic ageing within and across tissues remain poorly understood. This study aims to address these gaps through an integrated analysis of sex-moderated epigenetic ageing across eight human tissues. MethodsA total of 137 DNA methylation datasets comprising over 36,000 individuals aged 10-114 years were analysed using a meta-analytic workflow to identify age-associated differentially methylated positions (aDMPs) and regions (aDMRs), meta-regression to assess sex moderation, and pathway enrichment analyses to interpret functional relevance. FindingsIndividual tissues displayed distinct age-related methylation trajectories, but some DMP sites showed consistent hyper- or hypomethylation across tissues. Across tissues, we identified 68,630 aDMPs (10%) robustly associated with ageing. Age-associated changes at the regional level were less common, with only 80 robust age-associated aDMRs detected across tissues, representing 0.09% of analysed regions. Sex moderation was observed for only 16 aDMPs (0.002%), indicating that sex effects on age-associated DNA methylation are largely tissue-specific rather than shared across tissues. InterpretationOur findings indicate that age-associated DNA methylation changes predominantly occur at isolated CpG sites rather than extended genomic regions and are strongly dependent on tissue and genomic context. The minimal overlap of sex-moderated methylation signals across tissues suggests that age-related sex differences at the epigenetic level are more likely attributable to tissue- and cell-type-specific variation rather than to broadly conserved epigenetic mechanisms shared across tissues. FundingThis study was funded by an Australian Research Council (ARC) Discovery project (DP200101830). Severine Lamon was funded by an ARC Future Fellowship (FT210100278). Nir Eynon was funded by NHMRC Investigator Grant (APP1194159), and a Hevolution/AFAR New Investigator Award in Aging Biology and Geroscience Research. Mandhri D. Abeysooryia was supported by an Australian Government Research Training Program (RTP) Scholarship. Research in context Evidence before this studyDNA methylation is widely recognised as a central epigenetic hallmark of ageing. Previous research has demonstrated that some age-related methylation changes are conserved across tissues, forming the basis of pan-tissue epigenetic clocks. Most studies to date have primarily examined age effects in isolation. Although biological sex influences ageing trajectories and susceptibility to nearly all age-related diseases, sex-moderated epigenetic ageing has received limited investigation. Specifically, pan-tissue clocks, including GrimAge and PhenoAge, are "sex-aware" but were trained and validated in mixed-sex cohorts, limiting their capacity to disentangle tissue-specific sex effects. Consequently, it remains unclear whether sex-moderated epigenetic ageing signals are shared across tissues or are tissue-specific. Added value of this studyThis study provides a large-scale, comprehensive multi-tissue analysis of sex-moderated epigenetic ageing, integrating 137 DNA methylation datasets across eight human tissues and more than 36,000 male and female individuals spanning the lifespan. Our findings show that while age-associated methylation changes are widespread at the CpG level, sex-moderated effects are rare and largely tissue-specific, with minimal overlap across tissues. Implications of all the available evidenceTogether, the available evidence indicates that epigenetic ageing is predominantly driven by shared, conserved age-related methylation changes, whereas sex differences in epigenetic ageing are modest and context dependent. These sex-related effects are more likely to reflect tissue- and cell-type-specific variation rather than widespread, shared mechanisms. This underscores the need to develop sex-specific epigenetic clocks and to conduct longitudinal cohort and intervention studies to more precisely characterise sex-specific dynamics of epigenetic ageing across tissues.

BackgroundColorectal cancer (CRC) is a molecularly heterogeneous disease shaped by both genetic and epigenetic alterations. Approximately 15% of CRCs display widespread CpG island hypermethylation, known as the CpG Island Methylator Phenotype (CIMP). CIMP-high (CIMP-H) tumours frequently exhibit MLH1 promoter hypermethylation, leading to mismatch repair deficiency (MMRd) and microsatellite instability (MSI). However, DNA methylation patterns associated with MSI, independent of CIMP and MLH1 silencing, and the influence of clinical variables such as anatomical location and patient age on the CRC methylome remain poorly characterised. MethodsWe performed epigenome-wide DNA methylation profiling of 259 primary CRC tissue samples using the Illumina EPICv2 array, comparing differential methylation between MSI and microsatellite stable (MSS) CRC, adjusting for tumour purity, MLH1 promoter methylation, CIMP status, and anatomical location, to account for known confounders. We further evaluated the independent effects of anatomical location and patient age on global methylation patterns. ResultsEpigenome-wide differential methylation between MSS and MSI CRC was dominated by MLH1 promoter hypermethylation. After adjusting for MLH1 hypermethylation and CIMP status, we identified a distinct set of 656 CpG sites associated with MMRd independent of MLH1 silencing. These included hypermethylation at LRP6, GSK3{beta}, and CDK12, implicating altered WNT signalling and transcriptional regulation pathways. Comparison of MSI subgroups revealed the co-occurrence of MLH1 hypermethylation with promoter hypermethylation at TXNRD1. Anatomical location showed a strong independent effect on methylation patterns, while we observed only modest effects of patient age on the CRC methylome after adjustment for confounders. ConclusionsWe identified a distinct methylation profile distinguishing MSS and MSI CRC, including MLH1-independent markers of MMRd, as well as novel differentially methylated loci within MSI subgroups. We further showed that anatomical location has a strong independent impact on the CRC methylome. Together, these findings refine the molecular characterisation of CRC and highlight potential epigenetic markers that could inform patient stratification and precision oncology.

BackgroundX chromosome inactivation (XCI) is the mechanism which randomly silences one X chromosome to equalise gene expression between 46, XX females and 46, XY males. Though XCI is expected to result in a random pattern of mosaicism across tissues, some females display a significantly unbalanced ratio in immune cells, termed XCI-skew, in which [&ge;]75% of cells have the same X inactivated. XCI-skew is associated with adverse health outcomes and its prevalence increases with age - particularly after midlife - yet the specific risk factors have yet to be identified. The menopausal transition, which is driven by profound shifts in sex hormone levels, has significant impact on chronic disease risk yet the molecular and cellular effects are incompletely understood. We hypothesised that the menopausal transition may impact XCI-skew. MethodsUsing XCI data measured in blood-derived DNA from 1,395 females from the TwinsUK population cohort, along with questionnaires, genetic data, and sex hormone measures, we carried out a cross-sectional study to assess the impact of the menopausal transition and sex hormones on XCI-skew. ResultsWe demonstrate that early menopause (<45yrs) is associated with increased risk of XCI-skew. In subset analyses across those who had a surgically induced or natural menopause, we find the association restricted to those who underwent a surgical menopause. We next identify a low polygenic score (PGS) for testosterone levels is significantly associated with XCI-skew, which we replicate in an independent dataset (n=149), while a PGS for age at natural menopause is not associated. Finally, using longitudinal measures across two time points spanning [~]18 years we show XCI-skew is a stable cellular phenotype that typically increases over time. DiscussionThese data represent the first environmental and genetic risk factors of XCI-skew, both of which implicate endogenous sex hormone levels, particularly testosterone. We propose XCI-skew may have clinical relevance in postmenopausal females.

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.

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.

ImportanceAge-related eye diseases, such as cataract, glaucoma, age-related macular degeneration (AMD), and diabetic retinopathy (DR), are leading causes of irreversible vision loss globally. Chronic inflammation is a shared pathogenic pathway, but the role of systemic inflammatory drivers like clonal hematopoiesis of indeterminate potential (CHIP) is unknown. ObjectiveTo investigate the association of CHIP, including its major genetic subtypes and clone sizes, with the risk of four major age-related eye diseases. Design, Setting, and ParticipantsThis was a prospective cohort study conducted using data from the UK Biobank, a large-scale, population-based cohort. A total of 436,469 participants free of the four eye diseases at baseline were included in the analysis. Data were collected from 2006 to 2010, with follow-up extending to March 2022. ExposuresCHIP status was ascertained from whole-exome sequencing data, defined by the presence of a somatic driver mutation with a variant allele fraction of 2% or greater. Main Outcomes and MeasuresThe primary outcomes were incident cases of cataract, glaucoma, AMD, and DR, identified through linked electronic health records. Associations were assessed using multivariable Cox proportional hazards regression models. ResultsOf 436,469 participants (mean [SD] age, 56.4 [8.1] years; 54.5% women), 14,110 (3.2%) had CHIP. Over a median follow-up of 13.1 years, CHIP was significantly associated with an increased risk of incident cataract (Hazard Ratio [HR], 1.08; 95% CI, 1.03-1.14), AMD (HR, 1.12; 95% CI, 1.04-1.21), and DR (HR, 1.41; 95% CI, 1.20-1.64). No significant association was found with glaucoma (HR, 1.08; 95% CI, 0.99-1.17). The risk for AMD was primarily associated with smaller clones (VAF <10%), while the risk for DR was highest with non-DNMT3A mutations. Systemic inflammation, particularly neutrophil count, partially mediated the associations. Conclusions and RelevanceIn this study, CHIP was independently associated with a higher risk of developing cataract, AMD, and DR, but not glaucoma. These findings establish a link between hematopoietic somatic mutations and the pathogenesis of several major age-related eye diseases, suggesting that CHIP-driven inflammation is a potential target for risk stratification and prevention. Key PointsO_ST_ABSQuestionC_ST_ABSIs clonal hematopoiesis of indeterminate potential (CHIP) associated with the risk of major age-related eye diseases? FindingsIn this cohort study of 436,469 participants, CHIP was associated with an increased risk of incident cataract (HR, 1.08; 95% CI, 1.03-1.14), age-related macular degeneration (HR, 1.12; 95% CI, 1.04-1.21), and diabetic retinopathy (HR, 1.41; 95% CI, 1.20-1.64), but not glaucoma. MeaningThese findings identify CHIP as an independent, non-ocular risk factor for cataract, AMD, and diabetic retinopathy, suggesting that systemic inflammation driven by CHIP contributes to the pathogenesis of these conditions and may represent a novel target for preventive strategies.

BackgroundGroup 3 (MYC-driven) medulloblastoma (MB) is a highly aggressive brain tumor with poor-prognosis and limited treatment options. We previously identified protein-arginine methyltransferase-5 (PRMT5) as a promising target in Group 3 MB with its control on MYC protein stability. In this follow up study, we further mechanistically investigated PRMT5 control on MYC transcription and targeted it pharmacologically for therapeutic proof-of-concept. MethodsUsing pharmacogenetic inhibition approaches against PRMT5 in MYC-amplified (Group 3) MB cell line and neurosphere models in vitro and in vivo, we investigated molecular mechanism(s) and anti-cancer efficacy of PRMT5 inhibition. ResultsOur experiments demonstrated that PRMT5 epigenetically regulates MYC transcription in MYC-amplified MB cells by binding to the proximal-promoter region of the MYC gene and contributing to the enriched symmetric-dimethylation of histone H4R3 in the same region. We further showed that PRMT5 is recruited to the MYC promoter by its interaction with BRD4, the major BET-protein responsible for MYC transcription. PRMT5 inhibition caused the suppression of MYC-induced transcriptional programs and target genes, with widespread disruption of splicing across the transcriptome, particularly affecting metabolism-related gene products. Pharmacologic inhibition of PRMT5 using a panel of selective small-molecule inhibitors demonstrates suppression of cell growth/survival in a MYC-dependent manner in MB cells. Moreover, our in vivo analyses of PRMT5 inhibition, in mice treated with one of the potent pharmacologic inhibitors, particularly a lipid-decorated form of it, demonstrated reduced cerebellar tumor growth with suppressed MYC expression and prolonged survival of mice with MYC-amplified MB xenografts. ConclusionsOur findings establish a functional link between PRMT5 and MYC-mediated transcriptional regulation, suggesting a promising therapeutic approach targeting the PRMT5-MYC axis for MYC-driven MB. Key PointsO_LIPRMT5 acts as an epigenetic regulator of MYC transcription, RNA splicing and associated energy metabolism in MYC-driven MB. C_LIO_LIPRMT5 inhibition selectively suppresses cell growth/survival in MYC-driven MB. C_LIO_LIPRMT5 inhibition reduces tumor burden and prolongs survival in a MYC-driven MB mouse model. C_LI Importance of the StudyGroup 3 medulloblastoma is a highly aggressive pediatric brain tumor marked by MYC amplification, malignant clinical behavior, and poor survival outcomes despite intensive multimodal therapy. Because MYC remains largely undruggable, there is an urgent need for effective and less toxic treatment options for affected children. This study identifies protein arginine methyltransferase 5 (PRMT5) as a key epigenetic regulator of MYC transcription and MYC-dependent oncogenic programs in Group 3 MB. We show that PRMT5 is recruited to the MYC promoter via BRD4, sustains MYC-driven transcription and RNA splicing networks associated with metabolism, and supports MB tumor growth. Importantly, pharmacologic inhibition of PRMT5 using a selective brain-penetrant inhibitor suppresses MYC expression, reduces cerebellar tumor burden, and prolongs survival in MYC-amplified MB models. These findings provide a strong translational rationale for PRMT5 inhibition as a targeted therapeutic strategy for high-risk MB, with the potential to improve outcomes while reducing treatment-related toxicity.

Introduction Lung cancer is rare before age 45, and its inherited genetic basis remains poorly defined. Methods We performed whole-genome sequencing in 171 predominantly young-onset lung cancer patients and integrated these data with whole-exome sequencing from six major lung cancer consortia, yielding 9,065 patients. After quality control, analyses focused on 6,545 individuals of European ancestry, the largest ancestral group. We compared the prevalence of rare pathogenic and likely pathogenic (P/LP) germline variants between 186 young-onset (age <45 years) and 6,359 older patients at gene and gene-set levels using Fisher's exact test, stratified by histology, sex, and smoking status. Polygenic risk scores (PRS) derived from common variants were also evaluated. Results Young-onset patients carried a higher burden of rare germline P/LP variants in DNA damage response (DDR) genes (including BRIP1, ERCC6, MSH5), and in cilia-related genes, notably GPR161. At the pathway level, DDR genes were significantly enriched (OR=1.66, p=0.007), with the strongest signal in the Fanconi Anemia pathway and among females (OR=1.96, p=0.01). Enrichment was also observed in inborn errors of immunity pathways, with strongest signals in antibody deficiency and the complement system genes. Young-onset patients additionally exhibited higher lung cancer PRS. Conclusion Young-onset lung cancer exhibits a distinct germline genetic architecture, characterized by enrichment of rare P/LP variants in DDR, cilia-related, and immune pathways, and an elevated lung cancer PRS. These findings support a greater role for inherited susceptibility in early-onset disease and have implications for risk stratification, earlier screening, and precision prevention.

Background: Extreme-phenotype comparisons allowed the discovery of novel asthma genetic risk loci. However, this approach remains unexplored in epigenome-wide association studies (EWAS). We aimed to identify bulk and cell-specific methylation markers of asthma with severe exacerbations across diverse ancestry groups. Methods: We conducted a meta-EWAS of 739,543 CpGs in whole blood among 1,192 African American and Latino pediatric populations, comparing non-asthmatics and asthma exacerbators. Genome-wide CpGs were followed up for replication in a meta-analysis across 1,516 ethnically diverse participants and in a cross-tissue evaluation of 393 nasal samples. We conducted differentially methylated region (DMRs), cell-type-deconvoluted, and quantitative trait loci analyses (whole-genome sequencing n=1,668; RNA-seq n=1,209). We examined enrichment in traits, pathways, and druggable genes, and analyzed DNAm predictors of plasma proteins and aging. Results: DNAm at 505 CpGs and 119 DMRs in whole blood were associated with asthma exacerbations (p<9x10-8, {lambda}=1.05). We replicated 25 CpGs in blood cells, cross-validated 7 in nasal samples, and detected 42 cell-specific DNAm markers mainly driven by T cells. DNAm at 134 CpGs was associated with gene expression in whole blood, including 118 associations with T-cell receptor genes, and 446 CpGs were regulated by [&ge;]1 genetic variant. We found enrichment for previous associations with environmental exposures, immune disorders, immune and inflammatory pathways, and druggable genes by developmental drugs. 21 methylation-predicted plasma proteins, involved in host defense, and one lung aging clock were associated with asthma exacerbations. Conclusions: The first meta-EWAS of extreme asthma phenotypes identified hundreds of novel DNAm markers, suggesting novel methylation biomarkers and candidate drugs for asthma and supporting the role of T cells.

Long-term follow-up of the CASSIOPEIA trial (NCT02541383) demonstrated superior progression-free survival (PFS) with daratumumab, both in combination with bortezomib, thalidomide, and dexamethasone during induction and consolidation, and during maintenance therapy, in transplant- eligible patients newly diagnosed with multiple myeloma (MM). However, outcomes among CASSIOPEIA patients remain heterogeneous across treatment groups. Measurable residual disease (MRD) is a strong indicator of the depth and duration of therapeutic response and is independently associated with both PFS and overall survival (OS), but it does not fully capture the biological diversity of MM. We performed a risk prediction analysis based on transcriptomic subgroups in CASSIOPEIA patients. A subset of 628 patients was characterized using RNA sequencing and consensus clustering identified five transcriptomic subtypes of MM. Long-term follow-up allowed the definition of three transcriptomic risk categories, with estimated 72-month PFS rates of 70%, 51%, and 27% for low, intermediate, and high-risk groups, respectively, among patients who received daratumumab in at least one treatment phase. In these patients, MRD negativity rates after consolidation and six months later were significantly higher in the low and high-risk groups compared with the intermediate-risk group. In the high-risk group, MRD status was not associated with PFS or OS. This suggests that, although daratumumab administered during both the induction/consolidation and maintenance phases improves the clinical outcomes of patients with activation of NSD2 or overexpressing members of the MAF family, highly aggressive minor clones may rapidly expand. These findings emphasize the need for novel therapeutic strategies in this high-risk population.

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.

The BCL-2 inhibitor venetoclax (VEN) in combination with hypomethylating agents (HMAs) has improved treatment responses in acute myeloid leukaemia (AML), but the mechanisms underlying their synergy remain unclear. We investigated the role of DNA demethylation in the enhanced cytotoxicity of VEN-HMA combinations. Using AML cell lines, we compared the effects of azacitidine (AZA), decitabine (DAC), cytarabine (ARA-C) and the DNMT1-selective inhibitor GSK-3685032 (GSK5032) with VEN. As expected, VEN showed strong synergy with AZA, DAC, and the DNA-damaging agent ARA-C, but not with GSK5032, despite the latter inducing extensive DNA demethylation. Genome-wide methylation profiling confirmed that loss of DNA methylation did not correlate with increased cytotoxicity or synergy with VEN. Moreover, combining GSK5032 with ARA-C did not enhance cytotoxicity, indicating that DNA demethylation and DNA damage do not act additively. Instead, synergy was consistently associated with the DNA damage-inducing properties of AZA, DAC, and ARA-C. Extensive DNA demethylation tended to antagonize VEN activity, suggesting that the epigenetic effects of HMAs may limit their synergistic potential. Overall, our findings demonstrate that DNA damage-related cytotoxicity, rather than DNA demethylation, is the dominant mechanism driving VEN-HMA synergy and provide evidence that VEN-mediated cytotoxicity arises primarily from genotoxic stress, supporting refinement of treatment strategies.

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.

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.

BackgroundThe composition and function of the gut microbiome have been shown to contribute to both health and disease. One of the most powerful modulators of microbial composition and function is diet. Materials & MethodsUsing the E{micro}-TCL1 murine model of B-cell chronic lymphocytic leukemia (CLL), we assigned male and female mice to a high-fat, high-carbohydrate Western diet (HF) or standard chow (CH) diet. ResultsMice consuming a HF diet had significantly shorter survival than those consuming a CH diet, irrespective of sex, with female mice exhibiting particularly poor outcomes. We also observed a significant increase in splenic involvement by CLL in the HF diet-fed mice at time of sacrifice. Mice receiving the HF diet demonstrated immediate and profound effects on the gut microbiome, marked by reduced alpha diversity and significantly different community composition as measured by beta diversity. Notably, there was a sustained increase in Akkermansia muciniphila and Bacteroidetes thetaiotaomicron in HF diet-fed mice, coupled with a corresponding increase in microbiome functional pathways related to arginine and histidine biosynthesis, chitin degradation, and nucleotide biosynthesis. DiscussionCollectively our data provides evidence of the profound and sustained impact of a high-fat Western diet upon the gut microbiome community and CLL pathogenesis in the E{micro}-TCL1 murine model of CLL.

Glycosylation is a key structural modification of immunoglobulin G (IgG) that modulates its effector functions and has multiple roles in balancing inflammation. Altered IgG glycosylation has been reported in many diseases, often years before clinical manifestation, suggesting its causal role and biomarker potential. Here, we analyzed IgG glycome composition in 20,405 individuals from 42 different studies processed at the Genos Glycoscience Research Laboratory between 2008 and 2025. Across nearly all diseases, specific IgG glycome profiles reflected accelerated biological aging. Accelerated glycan aging was strongly associated with increased risk of all-cause mortality, independent of established clinical risk factors and potential confounders. Moreover, interventions known to reduce mortality risk, including hormone replacement therapy, therapeutic plasma exchange and caloric restriction, were associated with reversal of glycan aging. Given their role in modulating low-grade systemic inflammation, IgG glycans may represent a functional link between chronic inflammation, aging, disease susceptibility and all-cause mortality.

BackgroundMetabolically healthy obesity (MHO) is unstable, with up to 80% of individuals progressing to metabolically abnormal obesity (MAO), yet mechanisms underlying this transition remain unclear. African Americans bear a disproportionate burden of obesity-related cardiovascular disease. Circulating extracellular vesicles (EVs) mediate inter-organ communication and may drive MAO-related vascular dysfunction. MethodsAdults of African ancestry were classified as metabolically healthy lean (MHL, n=14), MHO (n=9), or MAO (n=16). Plasma-derived EVs were characterized and their microRNA cargo profiled. Human coronary artery endothelial cells were treated with EVs from each group to assess nitric oxide signaling, oxidative stress, inflammatory activation, and mitochondrial dynamics. ResultsMHO participants exhibited preserved insulin sensitivity and lower inflammation compared with MAO despite comparable adiposity. EVs from MHO carried a distinct microRNA signature enriched in miR-148a-5p, miR-181c-5p, and miR-1255a, linked to antioxidant and matrix regulatory pathways. MAO EVs were enriched in miR-3613-3p, miR-6842-3p, and miR-326, targeting inflammation and insulin resistance pathways. Compared with both MHL and MHO EVs, MAO EVs suppressed endothelial nitric oxide synthase phosphorylation and reduced nitric oxide bioavailability, with increased reactive oxygen species and ICAM-1 expression. MHO EVs induced an intermediate phenotype with disrupted mitochondrial morphology, supporting a graded continuum of endothelial stress. ConclusionsMHO represents a biologically active intermediate state. Circulating EVs from MHO individuals convey molecular signals that impair endothelial and mitochondrial function, predisposing to vascular injury and progression toward MAO. EV-associated microRNAs are mechanistic mediators and candidate biomarkers of metabolic and vascular deterioration in obesity. CLINICAL PERSPECTIVEO_ST_ABSWhat Is New?C_ST_ABSO_LIThis study systematically investigated extracellular vesicles derived from metabolically healthy obese individuals to define direct vesicle effects on endothelial function using integrated omics coupled to functional outputs. C_LIO_LIExtracellular vesicles from metabolically healthy obesity convey a distinct molecular and biological signature that distinguishes lean and metabolically abnormal obesity. C_LIO_LIMetabolic health status, rather than obesity alone, drives extracellular vesicle-mediated endothelial nitric oxide signaling, oxidative stress, inflammation, and mitochondrial dynamics. C_LI What Are the Clinical Implications?O_LIThese findings explain why some individuals with obesity exhibit preserved vascular function while others develop early endothelial dysfunction. C_LIO_LIStratifying obesity by metabolic health status improves cardiovascular risk assessment beyond body mass index alone. C_LIO_LITargeting extracellular vesicle signaling pathways represents a novel strategy to prevent metabolically healthy individuals from progressing to metabolically abnormal obesity. C_LI

Biological sex regulates fundamental neurobiology, as well as the etiology and prevalence of neuropsychiatric disorders. Cyclin-dependent kinase 5 (Cdk5) is a neuronally enriched kinase that regulates synaptic plasticity, neuronal homeostasis, and hippocampal-dependent memory. While Cdk5 protein activity is necessary and sufficient to promote memory in male rodents, its role in females and its gene regulation in either sex remain poorly understood. In males, Cdk5 protein inhibition impairs fear memory. We previously showed that fear conditioning activates Cdk5 gene expression and increases permissive chromatin acetylation in male, but not female hippocampus. We hypothesize that Cdk5 gene repression would impair fear memory in males. We developed an excitatory neuron-specific, CRISPR/dCas9-HDAC3 epigenetic editing tool to target histone acetylation at the endogenous Cdk5 promoter. This strategy reduced histone acetylation and decreased Cdk5 mRNA, protein, and kinase activity in both sexes. Interestingly, Cdk5 repression in hippocampal neurons impaired fear and spatial memory in both male and female mice. Targeted deacetylation also evicted the transcription factor CREB1 from the Cdk5 promoter, revealing a link between histone acetylation and Cdk5 transcriptional activation. These findings demonstrate that Cdk5 acetylation in neurons is necessary for hippocampal memory in both sexes, providing new insight into sex-specific epigenetic regulation of memory.

Background: The 2017 American College of Cardiology/American Heart Association (ACC/AHA) guideline lowered diagnostic threshold for hypertension, encouraging earlier treatment initiation in the U.S. compared to UK, where the National Institute for Health and Care Excellence (NICE) guideline recommends higher thresholds. No comparative study evaluating how different hypertension guidelines and physical activity are jointly associated with mortality outcomes in two countries. Aims: This study compared hypertension prevalence, treatment uptake, blood pressure (BP) levels, and mortality between the UK Biobank (UKBB) and the U.S. National Health and Nutrition Examination Survey (NHANES). We evaluated whether moderate-to-vigorous physical activity (MVPA) modifies mortality risk among different hypertension subgroups (normotensive, medicated hypertension, and unmedicated hypertension). Methods: We harmonized demographic, biomarker, lifestyle, and accelerometer data from UKBB (n=63,452) and NHANES (n=7,397). Comprehensive weighting methods were applied in both cohorts. Accelerometry data was classified using a validated two-stage machine learning Random Forest algorithm. Associations between MVPA and all-cause mortality were examined with restricted cubic spline regression and visualized using Kaplan-Meier survival curves. Results: NHANES showed a higher proportion of treated hypertension (29.9%) and lower average blood pressure (SBP/DBP: 122.2/70.7 mmHg) compared to UKBB (11.7% treated; SBP/DBP: 136.0/81.3 mmHg). Despite lower BP levels, cardiovascular mortality was higher in UKBB (10.3 per 10,000 person-years) compared to NHANES (4.0 per 10,000 person-years). In both cohorts, greater MVPA was linked to lower mortality risk, with the strongest association observed among medicated hypertensives. Notably, NHANES participants with treated hypertension and low MVPA (<10.7 minutes/day) experienced a steeper survival decline, falling to 74% by year 8, compared to 91% in normotensives and 79% in untreated hypertensives. Conclusion: Despite higher treatment prevalence and lower average BP levels in NHANES, mortality remained higher compared with UKBB, suggesting that differences in mortality patterns may relate to broader cardiometabolic profiles and PA patterns beyond pharmacological management alone. Across both cohorts, higher levels of MVPA were associated with lower all-cause mortality, with the strongest associations were observed among individuals with medicated hypertension.

Prognostic stratification in multiple myeloma (MM) relies on staging systems that assign patients to fixed categories at diagnosis and discard the temporal information that accumulates during treatment. We developed a dynamic multimodal framework that predicts residual overall survival using observation windows ranging from 1 to 18 months post-diagnosis. The model integrates DeepInsight-transformed gene expression representation, longitudinal laboratory measurement trajectories across 10 analytes, and treatment history for three drug classes through an adaptive fusion mechanism that accounts for missing clinical observations. On the MMRF CoMMpass cohort (n = 752), five-fold cross-validation yielded a concordance index (C-index) of 0.773 {+/-} 0.024 and a time-dependent AUC at a 1-year prediction horizon (tdAUC1yr) of 0.789 {+/-} 0.021, outperforming all evaluated baseline methods including DeepSurv (0.633 {+/-} 0.095) and random survival forests (0.636 {+/-} 0.024) on matched cross-validation splits. Modality ablation identified longitudinal laboratory measurements as the strongest individual contributor (C-index 0.693); the DeepInsight spatial encoding of gene expression yielded higher discrimination than a multilayer perceptron (MLP) baseline operating on the same features (0.624 vs. 0.596). Kaplan-Meier analysis showed significant prognostic group separation at all primary landmarks (log-rank p < 0.001; hazard ratios 3.46-3.93). A distilled student model retaining only the DeepInsight representation and five baseline clinical features achieved C-index 0.672 and tdAUC1yr 0.740 on an independent microarray cohort (GSE24080, n = 507) without retraining. Interpretability analysis identified prognostic associations consistent with established myeloma biology, including ubiquitin-proteasome pathway genes, endoplasmic reticulum stress markers, and Interferon Alpha Response pathway enrichment.