Clinical Epigenetics

Quantifying the differentiation state of cells is an important task in regenerative medicine, cellular reprogramming and in elucidating how differentiation hierarchies are altered in aging and disease. For DNA methylation data (DNAm) there is however an accute shortage of methods for quantifying differentiation state. Here we use machine learning to build EpiDiff, a predictor of differentiation that yields a continuous absolute differentiation index (DI) when applied to a DNAm sample. We extensively validate EpiDiff in single-cells, sorted cells and bulk tissue, as well as in in-vitro differentiation, organoid, reprogramming and cellular rejuvenation experiments. In mixed samples, EpiDiff measures the extent of differentiation across all cellular lineages. In sorted cell populations, we find that DI increases with age and, underpinning this increase, we discover that many cell-types undergo a developmental epigenetic drift that is most prominent towards the mesenchymal lineage. When applied to normal-tissues, EpiDiff is predictive of carcinogenic exposure and cancer risk. In summary, EpiDiff is a unique, general and versatile tool that can accurately quantify the global differentiation state of a DNAm sample with broad applicability to many disciplines.

Objective: To investigate sex-specific associations between DNA methylation (DNAm) of neurodevelopmental, stress-response, and dopaminergic pathway genes and need for pharmacological treatment for Neonatal Opioid Withdrawal Syndrome (NOWS) among opioid-exposed newborns. Study Design: Buccal swabs were collected at birth from 181 infants in the multi-site Child and Family Study (CAFS). DNAm was measured via pyrosequencing at CpG sites within promoter regions of neurodevelopmental (BDNF), stress-response (AVP, NR3C1, OXTR, FKBP5, SLC6A4), dopaminergic (DRD2, DRD4), and opioid signaling (OPRM1) genes. Need for pharmacological treatment for NOWS was obtained from medical records. We estimated robust linear regression models to investigate sex-specific associations of DNAm and need for NOWS treatment. Estimated marginal means quantified sex-specific DNAm differences by treatment status. Results: After correction for multiple testing, five CpG sites within DRD4 were significantly associated with need for pharmacological treatment, with four sites showing higher DNAm in treated infants and one showing lower DNAm. Significant sex-specific associations were identified within DRD4 and AVP. Conclusions: Epigenetic variation across multiple biological pathways contributes to variability in NOWS severity among infants with prenatal opioid exposure. The relationship between epigenetic variation and need for NOWS treatment may vary depending on infant sex.

Background: Current recommendations limit the use of menopausal hormone therapy (MHT) principally to the management of menopausal symptoms, largely because of concerns regarding increased breast cancer (BC) risk. The impact of MHT use on systemic biological aging and blood methylome and its overlap with that of menopause timing remains incompletely understood. Methods: In females (N=78,209) of the Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial, we used Cox models to assess the associations of menopause timing (ordinal age at menopause; binary early-M [<45 years] vs non-early-M [[&ge;]45 years]) and MHT use with BC incidence, mortality, and survival. In a nested case-control subset with blood DNA methylome (DNAm; 758 cases, 745 controls), we related both exposures to epigenetic clocks and DNAm-based telomere length (DNAmTL) and used polygenic instruments to test both causal directions. Results: Ever MHT use was associated with higher BC incidence (aHR 1.17, 95% CI 1.10-1.24), particularly for hormone-receptor positive (HR+) subtypes (1.19, 1.11-1.27), whereas early-M was associated with lower HR+ incidence (0.88, 0.81-0.96) but not with overall incidence after adjustment (0.94, 0.88-1.01). However, ev-er MHT use was associated with lower BC mortality (0.72, 0.62-0.83) and better overall survival (0.87, 0.81-0.95). In the DNAm subset, non-early-M was associated with slower epigenetic aging and longer DNAmTL par-ticularly in cases. Higher cumulative aging and pace-of-aging markers predicted worse survival and partially mediated the early-M associations. Genetic analyses supported shared polygenic architecture between meno-pause timing and DNAm aging biomarkers rather than simple causation. MHT showed no broad epigenetic age acceleration and its profound methylome and immune-marker signatures largely did not overlap with those of menopause timing. Conclusions: Ever MHT use was associated with lower BC mortality and better overall survival despite higher BC incidence. Systemic aging detected more than a decade after menopausal transition correlates with early menopause. MHT use shows molecular signatures distinct to those seen for menopause timing.

This systematic review aimed to synthesize evidence on the association between DNA methylation (DNAm) age and all-cause and disease-specific mortality risks in adults. A systematic search of six databases from Jan 1 2011 to April 15 2026 identified articles assessing the association of DNAm age measures and all-cause or disease-specific mortality in adults from general or disease-specific populations. Effect sizes were pooled as hazard ratios (HRs) with 95% confidence intervals (CIs) using inverse-variance random-effects models. Of 42 023 records screened, 125 articles (380 705 participants) met the inclusion criteria, with 53 included in meta-analyses. Overall, 48 distinct DNAm clocks were evaluated. Higher DNAm ages were associated with higher risks of all-cause, cardiovascular, and cancer mortality risks. In general populations, GrimAge epigenetic age acceleration (EAA) showed consistent associations across mortality outcomes, with each 1 year higher GrimAge EAA associated with ~6-10% higher all-cause (31 cohorts, n=53 642, HR per SD: 1.46 [95% CI 1.38, 1.55], HR per 1-year: 1.09 [95% CI 1.08, 1.11], I^2=84.1%, p-value=1.21 x 10^(-14)), cardiovascular (6 cohorts, n=30 751, HR per SD: 1.55 [95% CI 1.38, 1.73], HR per 1-year: 1.10 [95% CI 1.07, 1.13], I^2=28.0%, p-value=1.71 x 10^(-4)), and cancer (5 cohorts, n=27 187, HR per SD: 1.31 [95% CI 1.15, 1.50], HR per 1-year: 1.06 [95% CI 1.03, 1.10], I^2=33.6%, p-value=4.76 x 10^(-3)) mortality. Clocks incorporating additional surrogates and technical refinements showed numerically larger pooled associations than their original counterparts. GrimAge2 (HR per SD: 1.65 [95% CI 1.53, 1.77] vs 1.46 [1.38, 1.55]) and PCGrimAge (1.56 [1.36, 1.78] vs 1.51 [1.32, 1.74]) showed higher pooled HR association with all-cause mortality than GrimAge. Further work is warranted to evaluate the responsiveness of DNAm clocks to interventions and potential clinical utility.

Background: Infants <30 weeks gestational age (very preterm (VPT)), are at risk of experiencing multiple serious neonatal morbidities. These morbidities impart serious biological stress, which may be reflected in dysregulated protein expression even after the morbidities have resolved. Recent studies suggest that DNA methylation-based predictors of circulating proteins may reflect the molecular effects of neonatal adversity. The objective of this study is to examine associations between DNA methylation-derived EpiScores, which are externally trained methylation signatures that proxy circulating protein levels, and neonatal morbidity burden in children born VPT. Buccal DNA methylation was obtained at NICU discharge in 537 infants from the NOVI cohort. A total of 111 EpiScores were calculated and tested for association with multimorbidity (0-1 vs. [&ge;] 2 morbidities) using adjusted linear regression models. Cross-tissue analyses in an external paired blood-buccal dataset (n=21) were used to identify EpiScores with moderate-to-strong correlations across tissues. Results: Eighteen EpiScores were nominally associated with multimorbidity (p < 0.05), with Melanoma-derived growth regulatory protein (MIA) with FDR < 0.05 (beta = 0.0023, p = 0.0004). In cross-tissue analyses, 35 EpiScores yielded r > 0.50 (p<0.05), 11 of which showed nominal associations with multimorbidity, including MIA. Overall, the morbidity-associated EpiScores reflected immune, inflammatory, metabolic, and growth-related pathways. Conclusions: Buccal DNA methylation-derived EpiScores capture biological signatures associated with neonatal morbidity burden in very preterm infants.

BackgroundClonal hematopoiesis of indeterminate potential (CHIP) is associated with ageing and atherosclerotic coronary artery disease (CAD), but evidence has largely come from peripheral blood. Whether somatic mutational profiles differ between arterial tissue and blood, and whether hematopoietic clones are represented in arterial tissue, remain poorly understood. MethodsWe performed deep whole-exome sequencing on 302 blood granulocytes and 263 arterial tissues from patients undergoing coronary artery bypass graft surgery, including 221 matched blood-tissue pairs, with mean sequencing depths of 130.5X and 120.8X, respectively. Somatic variants were identified using Mutect2. Associations with age and CAD complexity, assessed using SYNTAX score, were evaluated using multivariable regression. Primary analyses focused on variants with variant allele fractions of 10-25%. ResultsCHIP was detected in 24/302 (7.9%) blood granulocytes, predominantly involving DNMT3A, TET2, and ASXL1. In contrast, somatic mutations in CHIP-associated genes in arterial tissues showed a distinct profile dominated by CALR, SETDB1, and PDSS2. Somatic mutation carrier status increased with age in blood ({beta} = 0.07, p = 0.02) and arterial tissues ({beta} = 0.06, p = 0.04). Blood CHIP was associated with lower SYNTAX score ({beta} = -1.05, p = 2.66 x 10-3), partly driven by DNMT3A carriers ({beta} = -1.06, p = 0.04), whereas arterial CALR mutations were associated with higher SYNTAX score ({beta} = 1.14, p = 0.03). Among 221 matched pairs, only four identical variants, involving CHEK2, DNMT3A, GNB1, and SRSF1, were detected in both compartments. Genome-wide analyses showed compartment specificity, with bile acid metabolism enriched among arterial tissue-specific mutations (PAdj = 0.038). ConclusionBlood and arterial tissues in CAD harbour distinct somatic mutational landscapes with limited cross-compartment sharing. These findings suggest that cardiovascular somatic mutations may reflect both hematopoietic and arterial tissue-associated processes and motivate cell-resolved and spatial studies to define their origins and roles in cardiovascular ageing.

Background. Polygenic risk scores (PRS) capture inherited susceptibility to asthma, whereas methylation risk scores (MRS) may reflect disease-associated epigenetic variation. We assessed whether these scores differ in patients requiring biologic therapy and whether MRS change after mepolizumab initiation. Methods. Cross-sectional analyses in the GEMAS study included 699 participants with genotype data (428 with asthma, 271 controls) and 668 with blood DNA methylation data (408 with asthma, 260 controls). We evaluated 35 existing asthma PRS and derived six MRS from published epigenomic asthma studies. Longitudinal MRS changes after mepolizumab initiation were assessed in 16 GEMAS patients and were replicated in 20 patients from the MEGA study. Results. Twenty-eight PRS differentiated biologic-treated patients from controls (areas under the curve [AUC], 0.68-0.75), but none distinguished biologic-treated and non-treated patients after multiple-testing correction. MRS was higher in asthma without biologic than in controls (odds ratio [OR], 1.64; 95% CI, 1.34-1.99) and lower in biologic-treated than in asthma without biologic patients (OR, 0.54; 95% CI, 0.35-0.81). MRS did not differ significantly between biologic-treated patients and controls. Following mepolizumab initiation, MRS decreased at 6 and 12 months in GEMAS (p=4.81x10-5 and p=2.40x10-5, respectively). The 6-month decrease was also observed in MEGA (p=3.25x10-9). MRS epigenetic markers were predominantly hypermethylated, opposite to their described pattern in asthma risk. Conclusions. Asthma PRS did not differ significantly between biologic-treated and non-biologic-treated patients, but asthma MRS were lower in biologic-treated patients. The MRS decreased after mepolizumab initiation in two independent cohorts, consistent with a reversal of asthma-associated epigenetic patterns.

Proteomic aging clocks have emerged as biomarkers of aging, but most rely on cross-sectional data. Here, we present a proteomic aging clock based on longitudinal measurements of liquid chromatography-mass spectrometry plasma proteomics at up to three time points in the population-based KORA cohort, comprising 9,105 samples from 4,100 individuals in the final dataset aged 25-88 years. The model predicts chronological age and yields a measure of proteomic age acceleration associated with lifestyle and clinical risk factors. Risk factor-stratified analyses reveal shared proteomic signatures among cardiometabolic exposures and distinct signatures for smoking and physical activity. Within individuals, dyslipidemia and impaired kidney function track transitions to increases in age acceleration, while higher age acceleration is associated with increased all-cause mortality. Mediation analysis suggests that risk factors are linked to mortality indirectly through age acceleration. Affected proteins and pathways highlight extracellular matrix remodeling, complement and coagulation pathways, and liver-derived plasma proteins as key contributors to aging. Mendelian randomization identifies proteins with evidence consistent with a causal role in aging-related traits. Together, these findings are consistent with biological aging being dynamically responsive to changes in modifiable risk factors.

Despite recent evidence of the ability of systemic and organ-specific proteomic aging clocks to predict a large range of age-related diseases, their utility in cancer research remains largely underexplored. In this study, we evaluated the predictive ability of systemic and organ-specific proteomic aging clocks for (i) all-cause mortality, (ii) cancer-related mortality, and (iii) cancer incidence in a sample of Finnish twins (N = 401, mean age at baseline 62.3 years) with Olink proteomic data. Participants were followed for a mean of 10.6 years (SD +- 1.6), with estimates from four systemic and 18 organ-specific proteomic aging clocks calculated at baseline. Cox proportional hazards regression models adjusted for sex and age at baseline identified 15 proteomic aging clocks as significant predictors of all-cause mortality (Ncases = 28) after multiple testing correction (FDR < 0.05), with 11 remaining significant after lifestyle adjustment (Ncases = 27). For several clocks, effect sizes were large, with hazard ratios (HR) approximately doubling per one standard deviation (SD) increase in clock estimates. In predicting cancer-related deaths among participants without a prior cancer diagnosis at baseline (Ncases = 9), only the Immune clock showed a significant positive association after multiple testing correction in basic (HR = 2.94, 95% CI: 1.88-4.59) and lifestyle-adjusted models (HR = 3.31, 95% CI: 1.78-6.17). No associations with cancer incidence (Ncases = 34 basic, Ncases = 31 adjusted) survived multiple testing correction, although several nominal associations were observed. In conclusion, our findings suggest that proteomic aging clocks are strong predictors of all-cause and cancer-specific mortality, independent of lifestyle factors. Proteomic aging clocks may further serve as valuable tools for stratifying cancers by mortality risk.

Palmitate-associated lipotoxic stress activates the endoplasmic-reticulum stress sensor protein IRE1, but how IRE1 signaling influences genotoxic-stress responses in triple-negative breast cancer remains unclear. Here, we investigated IRE1 and XBP1 signaling in MDA-MB-231 cells exposed to palmitate and etoposide. Under combined lipotoxic and genotoxic stress, XBP1 depletion increased DNA-damage accumulation in IRE1 wild-type cells but not in IRE1-deficient cells, whereas IRE1 re-expression reduced DNA damage. Pharmacologic IRE1 RNase inhibition also increased etoposide-associated DNA damage, supporting a protective role for IRE1 RNase-dependent signaling. IRE1 status and XBP1 manipulation differentially affected H2A.X and {gamma}H2A.X abundance, indicating context-dependent regulation of chromatin-associated DNA-damage signaling. At the RNA level, H2A.X was enriched in IRE1 immunoprecipitates, and the H2A.X-linked DNA-damage-response transcripts HUWE1 and BRCA2 also associated with IRE1 under combined stress. These findings link palmitate-activated IRE1-XBP1 signaling to genome-protective responses during genotoxic stress and identify a network of IRE1-associated DNA-damage-response transcripts in triple-negative breast cancer cells. Direct IRE1-mediated cleavage of these transcripts remains to be established.

Background: Sex differences in asthma are well recognized, but sex-associated airway DNA methylation (DNAm) patterns and their relationships with gene expression remain incompletely characterized. We therefore conducted cis- and trans-expression quantitative trait methylation (eQTM) analyses using sex-stratified and CpG-by-sex interaction models. Methods: We analyzed nasal airway epithelial DNAm and transcriptomic data from 298 participants in the CAAPA discovery cohort. Asthma-associated differentially methylated CpGs (DMCs) were identified using sex-combined and sex-stratified models. Cis- and trans-eQTM analyses were then performed in participants with asthma using sex-combined, sex-stratified, and CpG-by-sex interaction models. To prioritize asthma-associated regulatory relationships, eQTMs that were also significant in non-asthmatic controls were excluded from downstream analyses. Replication in an independent bronchial epithelial cohort was defined by concordant effect direction and P < 0.05. Replicated targets underwent pathway and network analyses. Findings: Asthma-associated DMCs were predominantly hypomethylated in females and hypermethylated in males. Among trans-eQTMs, 379 associations were shared across all four models, whereas the majority were model-specific, indicating extensive sex-dependent regulatory architecture. We replicated 3, 1, 9, and 2 cis-eQTMs and 96, 84, 216, and 41 trans-eQTMs in the sex-combined, female-stratified, male-stratified, and interaction models, respectively. Sex-combined targets implicated innate immune and inflammatory signaling (TNF, IRF8); female-stratified targets implicated cytoskeletal remodeling, focal adhesion, and PI3K-Akt signaling (ITGA10); male-stratified targets implicated transcriptional regulation and post-translational modification (MOV10, HDAC7, CSF1, KAT2A); and interaction targets implicated lipid-mediator metabolism and inflammatory signaling and resolution (CYP2C9, LTB4R, CCL19). Our sex-dependent analyses showed that the majority of eQTMs resided within the trans-regulatory architecture, suggesting that sex-dependent gene expression differences are associated predominantly with trans rather than cis regulatory mechanisms. Pathway analyses revealed enrichment of innate immunity in the sex-combined model, structural remodeling in females, transcriptional control in males, and inflammatory resolution in the sex-interaction model. Interpretation: Sex-specific and sex-dependent airway methylation-expression associations were largely undetected by sex-combined analysis. Sex-aware analytical models may help resolve epigenetic mechanisms underlying sex differences in asthma biology.

Recent lifespan frameworks of aging theorize that pubertal development and cellular aging are governed by overlapping pathways, but the time lag between adolescence and older adulthood complicates the study of shared molecular mechanisms. Here we compare a DNA-methylation-based epigenetic index of pubertal development to epigenetic clocks, which were designed to measure biological aging, as a putative biomarker of adult aging and health in two adult cohorts: 3,642 older Americans in the Health and Retirement Study (HRS; age range, 56 to 100 years; 2,106 females) and 18,676 adults from Generation Scotland (GS; age range, 18 to 98 years; 10,974 females). Epigenetic puberty was correlated with chronological age in both cohorts, moderately in the older HRS sample (r = 0.51 in females, r = 0.51 in males) and strongly across the wider adult age range of GS (r = 0.82 in females, r = 0.86 in males). In both cohorts, age-residualized epigenetic puberty was associated with accelerated biological aging as measured by epigenetic clocks and other aging biomarkers (standardized coefficients: HRS, 0.13 to 0.47, all P < 0.005; GS, 0.05 to 0.40, all P < 0.001). Epigenetic puberty was linked with multiple health outcomes: mortality in HRS in both sexes (ORs, 1.39 and 1.46, both P [&le;] 0.001) and in GS among females (HR, 1.12, P = 0.003); 10-year onset of diabetes, any cancer and lung disease in GS (HRs, 1.12 to 1.19, all P < 0.005); and with multimorbidity, functional limitations and BMI in females in HRS (standardized coefficients, 0.10 to 0.16, all P < 0.001). It also accounted for a unique, albeit smaller, proportion of variance in aging-related outcomes beyond that explained by epigenetic clocks. These findings indicate that the epigenetic puberty index reflects pro-aging underlying biology, showing overlapping molecular pathways between pubertal development and cellular aging, and support a lifespan-based approach to studying biological aging.

Rationale: The role of DNA methylation (DNAm) markers in the upper-airway microbiome related to asthma exacerbations despite inhaled corticosteroid (ICS) treatment is unexplored. Objectives: To identify whole-blood DNAm markers associated with the upper-airway microbiome related to asthma exacerbations despite ICS treatment. Methods: We analyzed salivary, nasal, and pharyngeal microbiome in 242 asthma patients (GEMAS) for discovery. We tested associations between whole-blood DNAm at 703,505 CpGs and 21 exacerbation-related microbiome traits. Replication for the nasal microbiome was evaluated in 272 (Project Viva) and 66 (SysPharmPediA) children with and without asthma. We analyzed differentially methylated regions (DMRs), gene enrichment, associations with blood gene expression (RNA-seq, n=119), and DNAm predictors of plasma proteins. Measurements and Main Results: Whole-blood DNAm at 73 CpGs and 550 DMRs was associated with 17 exacerbation-related microbiome traits (false discovery rate [FDR]<0.05), including genes implicated in immune and inflammatory responses and the 17q12-q21 asthma locus ORMDL3. Most CpGs were associated with Campylobacter (pharyngeal) and Leptotrichia (nasal) abundance. Ten DNAm markers were replicated (p<0.05), including the corticosteroid insensitivity-related gene PTPRR associated with nasal bacterial richness. Enrichment analyses identified genes related to diabetes, obesity, smoking, TGF-{beta}, and Wnt signaling and regulated by trichostatin A, NF-{kappa}B, and the glucocorticoid receptor (FDR<0.05). The CpG cg18994033, associated with pharyngeal Tannerella, was associated with ITM2C whole-blood expression. Nine DNAm-predicted plasma proteins involved in inflammation, tissue remodeling, and TGF-{beta} signaling were associated with seven exacerbation-related microbiome traits, including Streptococcus and Selenomonas. Conclusions: Whole-blood DNAm markers implicated in inflammation, immunity, and asthma comorbidities are associated with the upper-airway microbiome linked to asthma exacerbations.

Menopause timing links reproductive lifespan with later life health, motivating investigation of its molecular and hematological correlates. We combined Generation Scotland analyses of women sampled at or after reported menopause (n = 1,444) and initially menstruating women followed for GP ascertained menopause onset (n = 1,725; 251 events) with bidirectional and multivariable Mendelian randomization. Higher age adjusted GrimAge V1, GrimAge V2 and DunedinPACE corresponded to 0.34 to 0.40 years earlier menopause per SD in the retrospective cohort at nominal P < 0.05. Prospective associations were nonsignificant, and cohort and primary bidirectional aging-related genetic associations did not survive multiple-testing correction. Genetically predicted later menopause was associated with higher neutrophil percentage and count and lower lymphocyte percentage in women; these associations and female vs. male contrasts survived correction. CRP conditional on menopause timing was associated with higher GrimAge and PhenoAge acceleration and shorter leukocyte telomere length after correction. None of 36 estimated inflammatory indirect effects reached P < 0.05. These findings highlight blood-cell composition as a prominent correlate of reproductive timing and identify selected methylation-aging signatures for further study. Together, they position reproductive hematological relationships as a specific avenue for understanding the connection between menopause and systemic aging.

Background: Hypertension prevalence rises sharply in females after menopause, exceeding that of age-matched males in later life, conferring greater relative cardiovascular disease risk in females than in males. However, the underlying mechanisms remain poorly understood. Method: We studied multi-tissue RNA-sequencing data from 193 CVD-free participants aged >55 years in the GTEx database and extended the findings to 1,605 age-matched Framingham Heart Study participants. Results: We identified a dominant female hypertension co-expression signature in blood, expressed at lower levels in females with uncontrolled high blood pressure than in males (sex-by-hypertension interaction) in both cohorts. Genes contributing to this signature were enriched for post-transcriptional modification and insulin signalling and regulated by ETS family transcription factors (TFs). Ten ETS TFs showed the same female-specific hypertension association and together explained the signature?s expression. Moreover, in females, but not males, lower blood signature scores were associated with a pro-inflammatory transcriptome in the artery and kidneys. Conclusions: Collectively, we identified the ETS-transcriptomic axis as a potential mechanism explaining sex differences in human hypertension.

Somatic mutations in the de novo DNA methyltransferase DNMT3A are frequent in clonal hematopoiesis, but how they alter the function of differentiated myeloid cells remains unclear. Here, we used isogenic human embryonic stem cell-derived macrophage models to define the consequences of DNMT3A dysfunction during myeloid differentiation. DNMT3A-mutant macrophages selectively upregulated bivalent Polycomb target genes, accompanied by DNA hypomethylation, reduced H3K27me3 and increased promoter accessibility. Despite broad epigenetic changes across bivalent promoters, transcriptional derepression occurred at a subset of loci characterized by lower baseline DNA methylation and higher H3K27me3, identifying pre-existing chromatin state as a determinant of transcriptional response. This Polycomb-associated program was conserved in murine macrophages and enriched for genes involved in cell migration and wound repair. DNMT3A-mutant macrophages exhibited enhanced migration and preferential early recruitment to injured tissue. These findings link clonal hematopoiesis-associated epigenetic alterations to selective transcriptional reprogramming and altered function of differentiated myeloid cells.

Multiple sclerosis (MS) is approximately three times more common in females than in males, but sex-linked epigenetic mechanisms remain incompletely understood. We tested whether X-chromosome DNA methylation differs in females with MS and whether associated sites preferentially map to genes normally subject to X-chromosome inactivation (XCI). An X-chromosome-focused epigenome-wide association study was performed in whole blood from three datasets comprising 496 females with MS and 509 female controls, with independent evaluation in isolated CD4+ T cells (80 cases, 76 controls). At FDR < 0.01, 3 182 X-chromosome CpGs were hypomethylated in MS (mean {Delta}{beta} = -0.035). Hypomethylated CpGs were strongly enriched in non-escape genes normally subject to XCI relative to escape genes (OR 6.77; p = 1.55x10-57) and mapped to immune and chromatin-related processes. Exploratory cis-mQTL analysis identified strong local genetic effects at a small subset of loci, including WAS, IRAK1 and TLR7. In CD4+ T cells, 2 080 of the 3,182 whole-blood hypomethylated CpGs (65.4%) were also significantly hypomethylated. These findings identify a reproducible X-chromosome hypomethylation signature in female MS and support direct investigation of inactive-X regulation, XCI escape and X-linked immune gene dosage.

Background: Alzheimer's disease (AD) is the leading contributor to dementia burden, and the risk of developing it is impacted by a multitude of factors. Among these factors are metabolic conditions like type-2 diabetes (T2D) and metabolic syndrome (MetS), along with ethnicity, which interacts both with AD and the metabolic comorbidities. Previous studies have established associations between methylation patterns at specific CpG sites and risk for AD, T2D and MetS individually, but the underlying etiology that is responsible for interactions between metabolic conditions and AD risk remains unresolved. Objective: We aimed to examine methylation patterns among Mexican American (MA) and Non-Hispanic White (NHW) individuals in the context of AD, alongside T2D and MetS, to identify CpG sites associated with disease-specific and interaction-dependent methylation effects related to those comorbidities. Methods: DNA methylation data from 551 patients of MA or NHW ancestry who were enrolled in the Texas Alzheimer's Research and Care Consortium (TARCC) were available for analysis. Participants were stratified into groups by AD/T2D status or AD/MetS score and Beta-values from the Illumina MethylationEPIC chip array were obtained for each patient. Differential methylation status was analyzed using the lumi and cate packages in R. Results: Five CpG sites had statistically significant differential methylation patterns, including two (cg06322660 and cg25514677) which exhibited significant interactions between AD and T2D status or AD and MetS score respectively, with cg06322660 being significant in the NHW cohort and cg25514677 being significant in the MA cohort. The association at cg25514677 was replicated in an independent MA cohort.

AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSIntroductionC_ST_ABSPolyunsaturated fatty acid (PUFA) status is an important marker of metabolic health across the lifespan, and omega-3 (n-3) PUFA were shown to have anti-inflammatory and cardioprotective effects. The omega-3 index, a composite of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), is widely used to assess n-3 PUFA supplementation status, and product-to-precursor fatty acid ratios are used as proxy indices of desaturation and elongation. Previous data indicate a higher proportion of n-3 PUFA with age. Whether the same pattern can be found in an NHANES cohort, and whether long-chain n-3 status relates to phenotypic age (PhenoAge), a composite measure of biological age, has not been established. MethodsWe analyzed erythrocyte fatty acid profiles measured by electron capture negative-ion mass spectrometry in erythrocytes of participants of the National Health and Nutrition Examination Survey (NHANES) 2021-2023. Adults aged 20-79 years with a complete 21-fatty-acid panel were included (n = 4,863) and stratified into five age groups (20-34, 35-44, 45-54, 55-64, 65-79 years). In the fasting subsample with a measured fasting glucose (n = 2,822) we additionally computed PhenoAge according to Levine and assessed PhenoAge acceleration (PhenoAge regressed on chronological age) in relation to EPA and DHA. ResultsPercentage of summarized PUFA and n-6 PUFA decreased with age while percentage of n-3 PUFA and EPA + DHA increased. In contrast, total saturated fatty acids did not differ across age groups. EPA and DHA rose with age, whereas linoleic acid (LA), dihomo-{gamma}-linolenic acid (DGLA) and -linolenic acid (ALA) declined. The delta-5-desaturase (D5D) index (AA/DGLA) and the AA/LA ratio were positively associated with age, while elongation-related proxies ELOVL2 (DTA/AA, DPA/EPA) and ELOVL5 (DGLA/GLA) were inversely associated. Higher EPA + DHA was associated with lower PhenoAge acceleration with the most pronounced effect of - 4,7 years in the group with highest ([&ge;]8%) EPA+DHA content. DiscussionAge-related shifts in erythrocyte PUFA composition and in desaturase and elongase proxy indices reported previously in a clinical cohort from Germany are reproduced in a large US population. In addition, long-chain n-3 status was inversely associated with PhenoAge acceleration.

The mammalian BRG-/BRM-associated factor (BAF) chromatin remodeling complexes are crucial regulators of hematopoietic stem and progenitor cell (HSPC) fate. Expression of the ncBAF subcomponent, BRD9, is altered in both normal aging and myeloid malignancies. We find that in adult human HSPC, BRD9 regulates the differentiation of myeloid progenitors. Upon degradation of BRD9 in these cells, ncBAF is displaced from the chromatin, leading in turn to enhanced recruitment of cBAF to bona fide CEBPA target sites. With the shift from ncBAF to cBAF, HSPC differentiation results in increased generation of myeloid-derived suppressor cells (MDSC) that secrete elevated levels of IL-8. Soluble factors from these myeloid cells, which have lost BRD9, enhance the stemness of breast cancer cells in vitro. In contrast, bromodomain inhibition of BRD9 results in minimal alterations of ncBAF binding and myeloid differentiation, indicating that BRD9 acts as a barrier to human MDSC differentiation in a bromodomain-independent manner.