m6A modification has been shown to play a role in regulating HBV RNA expression. However, it remains unclear whether the m6A levels of HBV pregenomic RNA (pgRNA) are related to HBV replication and liver function. Serum HBV pgRNA-m6A levels were determined by T3 DNA ligase assay. HBV DNA copy numbers and gene expression were detected by TaqMan assay and RT-qPCR, respectively. Liver function was evaluated using clinical laboratory indicators. The TET-off stable HBV-producing cell line HepAD38 and targeted pgRNA demethylation by SunTag system (TRADES) were used for the site-specific m6A editing. Flow cytometry was used to measure the cytokine levels in the supernatant of cell culture. Serum HBV pgRNA-m6A levels were positively correlated with HBV DNA copy number, pgRNA expression and liver function indicators (all p < 0.05). Both pgRNA-m6A levels and pgRNA expression were significantly increased in patients with high virus load (HBV DNA > 1.0 × 107 IU/mL). Site-specific demethylation of pgRNA1907-m6A significantly reduced HBV DNA, hepatitis B e antigen (HBeAg) and HBV pgRNA, while induced levels of interferon alfa 2 (IFN-α2) and apolipoprotein B mRNA editing enzyme catalytic subunit 3A (APOBEC3A). pgRNA-m6A modification of HBV associates with viral replication and liver function indicators. Site-specific m6A demethylation of pgRNA provides novel insight into anti-HBV treatment.
Epithelial ovarian cancer (EOC) is a heterogenous disease with frequent late-stage diagnosis and high mortality rates, for which no reliable screening tests exist. In recent years, epigenetic biomarkers in the form of DNA methylation in CpG-rich regions have gained increased attention in the scientific community due to their robust nature and accessibility, allowing for diagnosis without the need for invasive surgery. In this study, we investigated the aberrant methylation of promoter regions in early stage EOC through non-parametric methods, with the purpose of characterizing candidate epigenetic biomarkers. The approach was used on a cohort of early stage EOC samples, and results were compared to existing programs for differential methylation. Significant regions were then used to construct a CpG panel for stratifying EOC histotypes through predictive classification in external data. Identified promoter regions were highly reproducible across cohorts, and the constructed CpG model stratified histotypes in external cohorts through predictive classification. Comparisons against other DMP and DMR callers showed a degree of homogeneity between results but also revealed promoter regions that were overlooked despite clear signs of aberrant methylation. Finally, EOC histotypes were found to differ in their methylation distribution types, and results indicate that methods sensitive to non-normally distributed data may be poorly suited to compare groups with different distribution types. The non-parametric approach identified aberrantly methylated promoter regions that were highly reproducible across cohorts. Results from predictive classification indicate that these regions may be useful for the purpose of EOC histotype stratification.
Environmental factors can influence the epigenetic inheritance of pathology across generations. Prior studies found various toxicants increased pathology in their descendants through epigenetic transgenerational inheritance. Previously, three generations of rats were exposed separately to vinclozolin (F0 generation), a jet fuel hydrocarbon mixture (F1 generation), and dichlorodiphenyltrichloroethane (DDT) (F2 generation), producing a transgenerational F5 generation. The current study extends this study by breeding this transgenerational F5 generation with wild-type rats to create maternal and paternal outcross lineages, labeled MOC and POC, respectively. In the current study, we examined the differential DNA methylated regions (DMRs) in the outcross F6 generation offspring to detect potential parent-of-origin lineage‑specific inheritance impacts. When comparing both outcross MOC and POC lineages of the F6 generation to a control outcross F3 generation from the same lineage, with no toxicant exposure, a higher number of DMRs were observed in the F6 generation lineages. Additionally, while there was some common overlap between the two MOC and POC outcross generations, only the F6 POC generation had overlaps with the F5 multigenerational exposure lineage generation of the previous study, which was also a paternal outcross. Since previous pathology analysis has been extensive, limited pathology (e.g. obesity) was performed in the current study to primarily confirm the transgenerational pathology in the F6 generation outcross lineages. Comparisons between the control same lineage F3 generation and both of the outcross F6 generations identified outcross‑specific results, suggesting sex-specific epigenetic inheritance after ancestral toxicant exposure. Therefore, both the oocyte and sperm facilitate epigenetic transgenerational inheritance.
Colorectal cancer (CRC) is a heterogeneous disease shaped by genetic and epigenetic alterations. Approximately 20% of CRCs exhibit widespread CpG island hypermethylation, termed the CpG Island Methylator Phenotype (CIMP), frequently accompanied by MLH1 promoter hypermethylation, deficient mismatch repair (dMMR) and microsatellite instability (MSI). However, methylation patterns associated with MSI, independent of CIMP and MLH1 silencing, and the influence of anatomical location and patient age on the CRC methylome remain incompletely defined. We performed epigenome-wide DNA methylation profiling of 259 sporadic CRCs using the Illumina EPICv2 array. Differential methylation between MSI and microsatellite stable (MSS) CRCs was assessed after adjustment for tumour purity and anatomical location, then MLH1 promoter methylation and CIMP status, to delineate MSI-associated methylation changes. Additionally, we evaluated the effects of anatomical location and age on methylation patterns. While differential methylation between MSS and MSI CRCs was dominated by MLH1 promoter hypermethylation, additional adjustment for MLH1 hypermethylation and CIMP identified 656 CpG sites associated with MSI, beyond the global methylator phenotype. These included hypermethylation at LRP6, GSK3β, and CDK12, identifying differential methylation of genes involved in WNT signalling and transcriptional regulation. Within MSI CRCs, we observed the co-occurrence of MLH1 hypermethylation with promoter hypermethylation at TXNRD1. Anatomical location was strongly associated with methylation, whereas age had more modest effects. These results identify methylation changes associated with sporadic MSI beyond CIMP status and MLH1 hypermethylation, reveal heterogeneity within MSI CRCs, and indicate that anatomical location is a major determinant of the CRC methylome, advancing molecular stratification of CRC.
Transcriptional activation of cell-type-specific genes is achieved by multiple mechanisms that guarantee chromatin accessibility at cis-regulatory elements and the long-range interactions between them. Generally, DNA methylation counteracts these processes and promotes gene silencing in vertebrates. CTCF is a conserved and essential multifunctional transcription factor relevant for establishing and maintaining chromatin architecture and accessibility, while its precise role in regulating DNA methylation remains to be determined. We focused on the highly abundant and previously studied erythroid-specific αD gene (HBAD) to systematically investigate the role of CTCF binding on DNA methylation, chromatin accessibility, and gene expression using a chicken erythroid cell differentiation system. The perturbation of CTCF binding at the intergenic region between the embryonic π and the adult αD gene resulted in DNA methylation propagation towards the αD gene, which was accompanied by decreased chromatin accessibility, GATA-1 binding, and gene expression. Notably, chromatin conformation analyses revealed that CTCF binding enables αD transcriptional activation independently of its architectural function. We observed a similar role of CTCF on DNA methylation and gene expression in the human orthologous gene HBA2. Our findings support a conserved role of CTCF in preventing DNA methylation spreading and gene silencing of cell-type-specific genes along differentiation.
Environmental disruption alters circadian clock gene expression, increasing the risk of adverse cardiac events and suggesting cardiomyocyte-specific circadian responses to external stimuli. Analyses of previously reported transcriptomic data revealed increased expression of Titin-cap (Tcap) in adult compared to embryonic myocytes and identified myosin light chain 2 (Myl2) as clock-controlled. Given cardiac sarcomeric roles of the encoded proteins, we hypothesized that extracellular cues driving postnatal cardiac maturation and hypertrophy influence time-of-day Tcap and Myl2 expression. Tcap induction was concomitant with neonatal myocyte binucleation, fetal gene suppression, and increased heart weight during the early phase of cardiac growth. Since norepinephrine stimulates β-adrenergic and α-adrenergic receptors, the latter driving clock-controlled transcriptional remodeling, phase‑response curves of the β‑adrenergic agonist isoproterenol (ISO) following α-adrenergic stimulation with phenylephrine (PE) were performed on neonatal rat ventricular myocytes (NRVM), revealing periodic myocyte hypertrophy and TCAP protein expression. PE entrenched ISO-mediated Tcap suppression, to which oscillatory Per2 and Myl2 transcription was impervious. Differential NRVM culture density revealed biomass-dependent changes in Per2 and Tcap transcription and hypertrophy timing. Hypoxia initiated myocyte atrophy and Bmal1-dependent Tcap transcription, reflected in decreased heart weight and increased Tcap expression in hypoxic neonatal rat hearts. Tcap depletion impaired Bmal1 and fetal hypertrophic gene expression, compromised hypoxia-mediated Myl2 transcriptional suppression, and aggravated hypoxia-induced atrophy. In summary, Tcap and Myl2 are circadian genes differentially influenced by environmental factors, including adrenergic stimulation, paracrine signaling, and O2 tension during postnatal cardiac maturation. These findings have implications for the distinct regulation of myocyte growth and maturation, by external cues during the postnatal period.
Osteosarcoma (OS) is the predominant primary malignant bone tumor in children and adolescents. Current treatments mainly include surgical resection combined with chemotherapy, but they still cannot effectively control tumor metastasis and recurrence, and may pose a risk of long-term complications. N6-methyladenosine (m6A) is the most widespread internal modification. It orchestrates various biological and disease-related events via the reversible m6A machinery comprising writers, erasers and readers. As a key epigenetic regulatory mechanism, m6A modification opens new avenues for deeper exploration of OS mechanisms and for developing new therapeutic targets and biomarkers. In this manuscript, we systematically explore the critical roles of m6A in OS cell proliferation, metastasis, metabolic reprogramming, programmed cell death, and tumor microenvironment regulation. Our aim is to provide a robust theoretical framework to underpin future basic studies and clinical applications in this field.
Endometriosis (EMs) is a common gynecological disorder affecting reproductive‑aged women, characterized by ectopic endometrial growth and chronic pelvic pain that severely impairs quality of life. Although its pathogenesis remains incompletely understood, accumulating evidence indicates that the tumor suppressor p53 and aberrant epigenetic modifications play critical roles in EMs initiation and progression. p53 expression is significantly reduced in ectopic lesions, leading to apoptosis resistance and hyperproliferation of endometrial cells. Importantly, p53 dysfunction contributes to EMs through at least four epigenetic mechanisms: (1) p53 transcriptionally represses DNA methyltransferases (DNMTs), and its loss indirectly promotes locus‑specific hypermethylation and silencing of tumor suppressors; (2) p53, via its interaction with histone modifiers, influences their recruitment to target genes, and p53 impairment synergizes with histone deacetylase dysregulation to create a pro‑proliferative, anti‑apoptotic microenvironment; (3) p53 functionally interacts with the chromatin remodeler ARID1A, and their co‑dysruption impairs chromatin accessibility and immune homeostasis; (4) p53 coordinates non‑coding RNA networks (e.g. lncRNA MALAT1, miR‑34a) that regulate epithelial-mesenchymal transition, angiogenesis, and apoptosis. This review systematically summarizes the p53‑mediated epigenetic regulatory network in EMs and highlights potential therapeutic opportunities targeting p53-epigenetic crosstalk. Future studies should investigate synergistic mechanisms among different epigenetic layers and validate these findings in multi‑center clinical cohorts.
Vertebrate limb development provides an excellent model for understanding how epigenetic mechanisms coordinate the integration of positional information and temporal signals to generate complex three-dimensional structures. An increasing body of evidence shows that chromatin-based mechanisms, including DNA methylation, histone modifications, and higher-order chromatin organization, define the competence of progenitor cells to respond to morphogenetic signals with spatial and temporal precision during limb development. This review explores how epigenetic mechanisms orchestrate and regulate the major phases of limb formation: from field specification and bud induction to morphogenesis, lineage differentiation, and programmed cell death. Here, we examine how chromatin remodeling, histone and DNA modifications, and enhancer - promoter interactions functionally converge with developmental signaling pathways to control gene expression programs that govern timing, positional identity, and cell fate decisions. Furthermore, this review highlights recent advances that link epigenetic landscapes with morphogenetic outcomes and discusses how comparative epigenomic approaches are reshaping our understanding of evolutionary diversification in limb morphology.
DNA methylation has traditionally been regarded as a stable epigenetic modification. However, emerging evidence indicates that oxidative and genotoxic stress can induce locus-specific methylation changes that modulate transcriptional responses. The contribution of such dynamic regulation to cardiac gene expression during myocardial ischemia/reperfusion injury (MIRI) remains incompletely understood. This study investigated whether altered methylation changes within the Gja1 promoter region are associated with connexin43 (Cx43) remodeling during MIRI. Male C57BL/6 mice were underwent global hypothermic I/R using a Langendorff-perfused heart model, with or without pretreatment using the DNA methyltransferase inhibitor 5-azacytidine (5-Aza, 3 μg/g body weight, i.p.). Gja1 promoter methylation was analyzed by BSP and MSP, while Dnmt1 enrichment was assessed by chromatin immunoprecipitation. Cx43 expression and localization were examined by qRT-PCR, Western blotting, and immunofluorescence, together with electrophysiological and histological analyses. MIRI was associated with Dnmt1 upregulation and nuclear enrichment, accompanied by altered methylation signals at selected CpG sites within the examined Gja1 promoter region and transcriptional repression. These changes coincided with reduced Cx43 expression, altered subcellular localization, impaired electrical conduction and increased arrhythmia susceptibility. Pretreatment with 5-Aza partially attenuated Gja1 promoter methylation signals and preserved Cx43 expression and localization during subsequent MIRI. These findings support an association between Dnmt1 enrichment, alteredGja1promoter CpG methylation, and Cx43 remodeling under reperfusion stress, suggesting that methylation-related epigenetic regulation may participate in Gja1 transcriptional responses during MIRI. Further temporal and gene-specific validation will be required to establish the kinetics and causal specificity of this pathway.
HIV persistence is facilitated by immune evasion strategies that reshape host immune responses. As the Interferon Gamma (IFNG) gene encodes a key immunoregulatory cytokine whose transcriptional competence is governed by promoter CpG methylation, we hypothesized that HIV plasma RNA would track with epigenetic remodeling at the IFNG promoter, altering IFNG mRNA transcription. DNA methylation at the IFNG promoter was quantified by bisulfite sequencing in PBMCs from people with HIV (PWH) with high (n = 16; >5000 copies/µL), medium (n = 18; 500 to 4999 copies/µL), or undetectable (n = 18; ≤50 copies/µL) plasma HIV RNA. Corresponding IFNG mRNA was quantified by RT-qPCR, with a sensitivity analysis adjusting for T cell abundance. High detectable plasma HIV RNA was associated with significant IFNG hypomethylation across 4 out of 5 CpG sites in the IFNG promoter compared to those with medium HIV RNA, while those with undetectable plasma HIV RNA showed no significant differences after adjusting for duration of infection. Accordingly, IFNG mRNA transcription was significantly elevated in participants with high plasma HIV RNA compared to medium (p = 0.037), which strengthened after modeling TCF7 expression as a covariate to account for varying T cell counts (p = 0.02). These findings provide the first in vivo evidence correlating HIV viral load with epigenetic transcriptional control of IFNG in peripheral blood.
Colorectal cancer (CRC) is a prevalent and highly lethal malignancy. However, the molecular mechanisms underlying its progression remain incompletely understood. Therefore, this study aimed to investigate the role and mechanisms of circKPNA2 in CRC progression. We used various techniques, including RNA sequencing, functional assays, RNA pull-down, and mass spectrometry, to examine the expression and function of circKPNA2. Our findings indicate that circKPNA2 is significantly upregulated in CRC tissues and cell lines. It contributes to tumour growth by promoting cell proliferation, migration, and invasion. We found that circKPNA2 specifically binds to the RIN1 protein and increases its levels, thereby activating the Ras signalling pathway and facilitating CRC progression. Additionally, we identified that METTL3 regulates the expression of circKPNA2 through N6-methyladenosine (m6A) methylation, which in turn affects CRC cell proliferation, migration, and invasion. These results deepen our understanding of CRC biology and underscore the potential of targeting circKPNA2 as both a therapeutic target and a diagnostic biomarker to improve CRC diagnosis and treatment.
Humans have coexisted with dogs for at least 20,000 years, yet the biological consequences of long-term human-dog co-residence remain poorly understood. We propose that sustained exposure to dogs may have contributed to context-dependent variation in human stress regulation, immune function, and socio-emotional neurobiology through environmentally responsive epigenetic mechanisms. Here, we define an epigenetic imprint as detectable differences in gene-regulatory marks, including DNA methylation at environmentally sensitive loci, consistent with developmental plasticity and early-life environmental calibration rather than germline inheritance. In this Commentary, we integrate evidence from genomics, neuroscience, microbiome research, evolutionary anthropology, and palaeoepigenetics to examine whether multispecies living environments may represent an under-recognised biological exposure shaping human regulatory biology. We further outline a framework to test whether archaeologically inferred dog co-residence is associated with epigenetic and regulatory signatures in ancient human populations while accounting for major ecological and demographic confounds. Overall, we argue that human-dog cohabitation provides a plausible and testable model for investigating how long-term social and ecological relationships may influence stress and immune regulation across populations.
Tumor recurrence and metastasis remain the principal causes of mortality in patients with head and neck squamous cell carcinoma (HNSCC). However, the key molecular drivers underlying HNSCC progression and their regulatory mechanisms have not yet been fully elucidated. In this study, we investigated the biological role of the long noncoding RNA MIR4435-2HG in HNSCC. Integrated analyses across multiple public databases demonstrated that MIR4435-2HG is significantly upregulated in HNSCC and is closely associated with pathological T stage, clinical stage, and histological grade. Through further bioinformatic screening and functional validation, upstream transcription factor 1 (USF1) was identified as a critical downstream effector of MIR4435-2HG. Mechanistically, MIR4435-2HG directly interacts with USF1 and promotes its protein stability by facilitating USF1 succinylation, thereby enhancing tumor cell migration and invasion through the induction of epithelial - mesenchymal transition. Moreover, dual-luciferase reporter assays and RT-qPCR analyses revealed that CREB1 transcriptionally upregulates MIR4435-2HG expression, establishing a positive feedback regulatory circuit. Collectively, our findings demonstrate that MIR4435-2HG promotes USF1 succinylation and stabilization, leading to the formation of a MIR4435-2HG - USF1-AKT - CREB1 signalling loop that drives epithelial - mesenchymal transition and facilitates the invasive and metastatic potential of HNSCC cells.
Cutaneous melanoma (CM) is highly invasive with limited prognostic tools, and the prognostic relevance of lactylation, a novel post-translational modification, remains unexplored. We developed a lactylation-related prognostic model using relative methylation orderings from The Cancer Genome Atlas (TCGA) melanoma cohort (n = 458), which was validated in two dependent cohorts (n = 241). Comprehensive analyses of immune infiltration, therapy efficacy, drug sensitivity, and tumour mutation burden were conducted between high- and low-risk groups. Results showed that 284 lactylation-related genes collected classified TCGA melanoma patients into two clusters with significant survival differences (Kaplan-Meier log-rank test, p = 0.046). Between the two clusters, 279 differentially methylated loci were identified (false discovery rate < 0.05 and |Δβ| >0.1). Based on these loci, 1,743 locus pairs were significantly associated with overall survival (Univariate Cox regression, false discovery rate < 0.05). From these significant pairs, the CM 11 locus-pair prognostic model (CM-LP11) consisting of 11 pairs was constructed, which could effectively stratify patients into high- and low-risk groups with significantly different overall survival across all datasets (all p < 0.05, log-rank test). The high-risk group exhibited an immunosuppressive microenvironment with reduced CD8+ T cells and B cells and increased monocytes (p < 0.05, Wilcoxon test). Functional analysis of methylation differences between risk groups showed significant immune response-related pathways such as antigen processing and presentation. The high- and low-risk patients also exhibited distinct sensitivity to cytotoxic chemotherapy, targeted therapy, and immunotherapy, with the low-risk group showing higher immunophenoscore, cytolytic activity, and tumor mutational burden. CM-LP11 represents a robust lactylation-related prognostic biomarker that predictive survival outcomes and therapeutic responses in CM patients, proving insights for personalized treatment strategies.
Colorectal cancer (CRC) is a leading cause of cancer-related deaths worldwide. Although epigenetic alterations are common in CRC, the epigenetic changes that occur during colorectal carcinogenesis remain unclear. Thus, we sought to elucidate the role of NOS1 methylation in colorectal carcinogenesis, which is essential for understanding disease pathology. We used the UCSC Xena database to comparatively analyze NOS1 expression and methylation status between tumour and adjacent normal tissues across 33 cancer types. Low expression and hypermethylation of NOS1 have been identified in 12 cancer types, with CRC demonstrating this characteristic epigenetic regulation. NOS1 promoter methylation status was examined using genomic DNA extraction and MassARRAY EpiTYPER methylation analysis. NOS1 hypermethylation was confirmed among CRCs in in-house dataset 1 (p < 0.001), and among CRCs and advanced adenomas in in-house dataset 2 (p < 0.001). An upward trend in methylation changes was identified from non-advanced adenoma to advanced adenoma to CRC (p for trend < 0.001). Quantitative real-time PCR was used to analyze NOS1 expression in in-house Dataset 3, and significantly low NOS1 expression was also identified in CRCs (p < 0.001). Kaplan-Meier estimator and Cox proportional hazard models were used to assess the prognostic and predictive roles of NOS1. NOS1 hypermethylation was significantly associated with better disease-specific survival (DSS) in CRC patients. NOS1 hypermethylation is an epigenetic driver of colorectal tumorigenesis and is associated with better survival.
Hepatocellular carcinoma (HCC) is a leading cause of cancer-related mortality worldwide, yet current surveillance with alpha-fetoprotein (AFP) and ultrasound (US) lacks sufficient accuracy, particularly for early-stage disease. This study aimed to develop and clinically validate a blood-based digital PCR (dPCR) assay targeting novel methylation biomarkers for HCC detection. Genome-wide methylation profiles from HCC, normal, and other cancer types were analysed to identify candidates, which were then screened and verified in cancer cell lines, primary tumour tissues, and plasma specimens. A total of 186 plasma samples were evaluated, including 66 healthy controls, 60 patients with chronic liver disease (CLD) without HCC, and 60 patients with HCC. FAR1 methylation emerged as an HCC-specific biomarker, showing significantly higher levels in liver cancer cell lines and HCC tumour tissues compared with controls. A dPCR assay targeting FAR1 achieved 70.0% sensitivity (42/60; 95% CI, 56.8%-81.2%) and 96.8% specificity (122/126; 95% CI, 92.1-99.1%), with an area under the curve (AUC) of 0.90 (95% CI, 0.85-0.96). Combining FAR1 with AFP improved sensitivity to 88.3% (53/60; 95% CI, 77.4%-95.2%) while maintaining 96.8% specificity. Notably, early-stage HCC (Barcelona Clinic Liver Cancer [BCLC] stage 0-A) was detected with 85.4% sensitivity (35/41; 95% CI, 77.4%-94.4%). This blood-based dPCR assay demonstrated high diagnostic performance, underscoring its potential as a noninvasive tool to enhance early detection and clinical management of HCC in high-risk populations.
Epigenetic aging prior to midlife is gaining interest as an intervenable period to address health and cognitive aging. Epigenetic changes may index DNA methylation aging rates, but methylation profiles may not be substitutable across tissues. We compared DNA methylation clocks and age acceleration in saliva, buffy coat (BC), and peripheral blood mononuclear cells (PBMC) collected in 91 individuals (7 unpaired, 20 siblings, 64 twins; 18 monozygotic (MZ), 14 dizygotic (DZ) pairs) from the Colorado Adoption/Twin Study of Lifespan behavioral development and cognitive aging (CATSLife1; Mean age = 30.90 years [range = 28.07-41.13]; 50.5% female). Across 15 DNA methylation clocks, chronological age and DNA methylation ages were moderately associated (mean Spearman correlations: r = 0.37, Saliva; r = 0.40, BC; r = 0.34, PBMC). In mixed-effects models, saliva showed higher DNA methylation ages (B = 3.77-19.72 years vs BC, p < 0.001), whereas PBMC and BC were comparable (B = -0.06-0.39 years vs BC, p ≥ 0.436). The exception was the next-generation clock DunedinPace showing comparability (p = 0.486). Similar patterns were observed for age acceleration estimates. Altogether, MZ pairs (meta-analytic r = 0.49, 95%CI = 0.32,0.66) and DZ pairs (meta-analytic r = 0.38, 95%CI = 0.25,0.52) were moderately correlated (Spearman), but MZ pairs showed heterogeneity across tissues (p < 0.034): saliva was lower (mean r = 0.33, SD = 0.25) than BC (mean r = 0.64, SD = 0.10) and PBMC (mean r = 0.49, SD = 0.18). Next-generation PCGrimAge and DunedinPace clocks showed consistent zygosity correlations across tissues, while multi-tissue clocks (e.g. ZhangQ) showed comparable MZ-DZ correlations. While saliva-based DNA methylation is not a direct substitute for blood-based DNA methylation, BC and PBMC show comparability; nevertheless, all tissue types may be appropriate for DNA methylation aging studies when compared within tissues.
Birthweight is heritable and strongly associated with epigenetic differences at birth. It is unclear whether a genetic birthweight score is associated with DNA methylation (DNAm) and, if so, whether through direct genetic effects (i.e. child genotype) or indirect genetic effects (i.e. parental genotype, independent of child genotype), which are suspected to be mediated by the prenatal environment (e.g. metabolic factors). We constructed polygenic scores (PGS) for birthweight predisposition in mothers and children using an existing ‘pre-adjusted’ GWAS assessing maternal indirect effects (maternal genotype on offspring birthweight, correcting for offspring genotype) or fetal effects (offspring genotype on offspring birthweight, correcting for maternal genotype) in 2116 families from the Generation R Study. Offspring DNAm levels at 829 birthweight-related sites were then regressed on both maternal and fetal effect PGS. Additionally, we aggregated 829 DNAm sites into a methylation profile score for birthweight (MPS-BW) and tested which pregnancy health factors (n = 13) might mediate genetic effects. We identified six DNAm sites associated with maternal indirect effects and the birthweight MPS revealed indirect genetic associations, as well. Paternal genotype was not associated with offspring DNAm in this study but was limited by lower sample size and lack of GWAS on paternal indirect effects, thus requiring a posteriori disentanglement of direct and indirect effects. Gestational age partly mediated maternal indirect effects on DNAm, but no other mediators were identified. Results did not depend on offspring sex. This study presents first evidence of maternal genetic effects on offspring birthweight being associated with offspring epigenetic patterns at birth.
