Epigenetic differences arise during the lifetime of monozygotic twins

Unravelling the epigenetic based mechanism in discovery of anticancer phytomedicine: Evidence based studies

Epigenetic mechanisms play a crucial role in the normal development and maintenance of tissue-specific gene expression patterns in mammals. Disruption of these processes can result in changes to gene function and the transformation of cells into a malignant state. Cancer is characterized by widespread alterations in the epigenetic landscape, revealing that it involves not only genetic mutations but also epigenetic abnormalities. Recent progress in the field of cancer epigenetics has demonstrated significant reprogramming of various components of the epigenetic machinery in cancer, such as DNA methylation, modifications to histones, positioning of nucleosomes, and the expression of non-coding RNAs, particularly microRNAs. The ability to reverse epigenetic abnormalities has given rise to the hopeful field of epigenetic therapy, which has shown advancement with the recent approval by the FDA of three drugs targeting epigenetic mechanisms for the treatment of cancer. In the present manuscript, a comprehensive review has been presented about the role of understanding the epigenetic link between cancer and mechanisms by which phytomedicine offers treatment avenues. Further, this review deciphers the significance of natural products in the identification of epigenetic therapeutics, the diversity of their molecular targets, the use of nanotechnology, and the creation of new strategies for overcoming the inherent clinical challenges associated with developing these drug leads.

Precision Health: Applications for Registered Nurses

Precision health care requires the treatment of individuals, families, communities, and populations based on their genomic, biological, behavioral, and environmental characteristics. Nurses are key factors in identifying health risk factors and coordinating treatment plans." to "Nurses are essential healthcare professionals who identify health risk factors and coordinate treatment plans. Genomics-informed nurses can improve patient outcomes by advocating for appropriate care plans or riskprevention strategies at the individual, family, community, and population levels. Social determinants of health and the resulting epigenomic modifications are important factors to integrate into care plans. Genomics-informed nursing care incorporates genetic and genomic knowledge in the nursing process to promote optimal outcomes through precision health care.

Perinatal Exposure to Lead or Diethylhexyl Phthalate in Mice: Sex-Specific Effects on Cardiac DNA Methylation and Gene Expression across Time

BACKGROUND

Global and site-specific changes in DNA methylation and gene expression are associated with cardiovascular development, aging, and disease, but how the transcriptome and epigenome of the heart change across the life course in males vs. females and how chemical exposures early in life influence this programming have not yet been investigated.

OBJECTIVES

We used an established mouse model of developmental exposures to investigate the effects of perinatal exposure to either lead (Pb) or diethylhexyl phthalate (DEHP), two ubiquitous environmental contaminants that are both strongly associated with cardiovascular diseases (CVDs), on DNA methylation and gene expression across the life course in whole hearts.

METHODS

Dams were randomly assigned to receive human physiologically relevant levels of Pb (32  ppm in water), DEHP (25 mg / kg chow), or control water and chow. Exposures started 2 weeks prior to mating and continued until weaning at postnatal day 21 (3 wk of age). Approximately 1 male and 1 female offspring per litter were followed to 3 wk, 5 months, or 10 months of age, at which time whole hearts were collected (n ≥ 5 per sex per exposure). Enhanced reduced representation bisulfite sequencing (ERRBS) was used to assess the cardiac DNA methylome at 3 wk and 10 months, and RNA-Seq was conducted at all three time points. MethylSig and edgeR were used to identify age-related differentially methylated regions (DMRs) and differentially expressed genes (DEGs), respectively, within each sex and exposure group. Cell type deconvolution of bulk RNA-Seq data was conducted using the MuSiC algorithm and publicly available single-cell RNA-Seq data.

RESULTS

Thousands of DMRs and hundreds of DEGs were identified in control, DEHP, and Pb-exposed hearts across time between 3 wk and 10 months of age. A closer look at the genes and pathways showing differential DNA methylation revealed that the majority were unique to each sex and exposure group. Overall, pathways governing development and differentiation changed across time in all conditions. A small number of genes in each group showed significant differences in DNA methylation and gene expression with life stage, including several that were different in toxicant-exposed but not control mice. We also observed subtle but significant differences in the proportion of several cell types that were associated with life stage, sex, or developmental exposure.

DISCUSSION

Together these data suggest that gene expression and DNA methylation programs, as well as cellular composition, may differ across the life course long after cessation of exposure in perinatal Pb- or DEHP-exposed mice compared to controls and highlight potential biomarkers of developmental toxicant exposures; however, additional studies are required for confirmation. Further studies are also needed to investigate how epigenetic and transcriptional differences impact cardiovascular health across the life course, particularly in old age when the risk of cardiovascular diseases is markedly increased. https://doi.org/10.1289/EHP15503.

IQ differences of identical twins reared apart are significantly influenced by educational differences

Over the last century, several large studies have been published exploring IQ differences amongst monozygotic (MZ) twins reared apart (TRA). By and large, this work has reported that MZ TRAs differ in IQ by ~8.0 points and demonstrate and intraclass correlation (ICC) of ~0.75. Unfortunately, this prior research has largely been amalgamated: it averages data from dozens of TRA pairs without accounting for important life experiences, including education (which has demonstrated a causal impact on IQ performance). In this paper, we gathered data from every available TRA case published in the academic literature over the last century that included both individualized IQ and biographical data. This data set (which we believe represents the entirety of the non-amalgamated TRA field) consists of 87 pairs. For our analysis, we split these pairs into three groups: similar, somewhat dissimilar, and very dissimilar schooling. Analyses reveals that schooling differences have a significant impact not only on the absolute IQ difference between TRA pairs (5.8, 12.1, and 15.1 points, respectively), but also the ICC (0.87, 0.80, 0.56, respectively). These findings raise an important question regarding the historic use of ICC as a measure of genetic influence on IQ and other psychological traits. It is recommended the field of TRA studies focus on individual pairs instead of groups and that researchers share individualized data from TRA pairs included in historic aggregate analyses.

Emergence of CpG-cluster blanket methylation in aged tissues: a novel signature of epigenomic aging

Aging is accompanied by widespread DNA methylation changes across the genome. While age-related methylation studies typically focus on individual CpGs, cluster analysis provides more robust data and improved interpretation. We characterized age-associated CpG-cluster methylation changes in mouse spleens, peripheral blood mononuclear cells, and livers. We identified a novel signature termed blanket methylations (BMs), fully methylated CpG clusters absent in young tissues but appearing in aged tissues. BM formation was locus- and cell-dependent, with minimal overlap among tissues. Statistical analysis, heterogeneity assessment, and random modeling demonstrated that BMs arise through nonrandom mechanisms and correlate with accelerated aging. Notably, BMs appeared in chronologically young mice with progeroid or disease-driven aging, including in 4-month-old Zmpste24-/- (lifespan ∼5 months) and 3-month-old Huntington's disease model mice (lifespan ∼4 months). The detection of BMs in purified CD4+ T cells demonstrated that their occurrence is intrinsic to aging cells rather than a result of infiltration from other tissues. Further investigation revealed age-related downregulation of zinc-finger-CxxC-domain genes, including Tet1 and Tet3, which protect CpG islands from methylation. Importantly, TET1 or TET3 depletion induced BM formation, linking their loss to age-associated methylation drift. These findings establish BMs as a robust marker of epigenomic aging, providing insight into age-related methylation changes.

Genetic and environmental contributions to epigenetic aging across adolescence and young adulthood

BACKGROUND

Epigenetic aging estimators commonly track chronological and biological aging, quantifying its accumulation (i.e., epigenetic age acceleration) or speed (i.e., epigenetic aging pace). Their scores reflect a combination of inherent biological programming and the impact of environmental factors, which are suggested to vary at different life stages. The transition from adolescence to adulthood is an important period in this regard, marked by an increasing and, then, stabilizing epigenetic aging variance. Whether this pattern arises from environmental influences or genetic factors is still uncertain. This study delves into understanding the genetic and environmental contributions to variance in epigenetic aging across these developmental stages. Using twin modeling, we analyzed four estimators of epigenetic aging, namely Horvath Acceleration, PedBE Acceleration, GrimAge Acceleration, and DunedinPACE, based on saliva samples collected at two timepoints approximately 2.5 years apart from 976 twins of four birth cohorts (aged about 9.5, 15.5, 21.5, and 27.5 years at first and 12, 18, 24, and 30 years at second measurement occasion).

RESULTS

Half to two-thirds (50-68%) of the differences in epigenetic aging were due to unique environmental factors, indicating the role of life experiences and epigenetic drift, besides measurement error. The remaining variance was explained by genetic (Horvath Acceleration: 24%; GrimAge Acceleration: 32%; DunedinPACE: 47%) and shared environmental factors (Horvath Acceleration: 26%; PedBE Acceleration: 47%). The genetic and shared environmental factors represented the primary sources of stable differences in corresponding epigenetic aging estimators over 2.5 years. Age moderation analyses revealed that the variance due to individually unique environmental sources was smaller in younger than in older cohorts in epigenetic aging estimators trained on chronological age (Horvath Acceleration: 47-49%; PedBE Acceleration: 33-68%). The variance due to genetic contributions, in turn, potentially increased across age groups for epigenetic aging estimators trained in adult samples (Horvath Acceleration: 18-39%; GrimAge Acceleration: 24-43%; DunedinPACE: 42-57%).

CONCLUSIONS

Transition to adulthood is a period of the increasing variance in epigenetic aging. Both environmental and genetic factors contribute to this trend. The degree of environmental and genetic contributions can be partially explained by the design of epigenetic aging estimators.

Root Exudates Mediate the Production of Reactive Oxygen Species in Rhizosphere Soil: Formation Mechanisms and Ecological Effects

Reactive oxygen species (ROS), as redox messengers, play an important role in regulating plant growth, sensing biotic and abiotic stresses, and integrating different environmental signals. As the microenvironment of the interaction between root, soil and microorganism, the rhizosphere is the hotspot of ROS production and action. Root exudates are an important medium for communication between roots and the soil environment, and they have a significant regulatory effect on the production of ROS in the rhizosphere. At the same time, the formation of rhizosphere ROS is determined by the coupling of various biotic and abiotic factors, and it is also affected by environmental stresses such as temperature, humidity, and disease. This review summarizes how root exudates affect plant growth and induce plant defense mechanisms by regulating the generation and distribution of ROS. It also discusses the role of ROS in promoting the decomposition of soil organic matter, nutrient cycling, and pollutant degradation and transformation. In-depth study of the regulation mechanism of root exudates on ROS not only helps to reveal the molecular mechanism of plant adaptation to environmental stress but also provides theoretical support and practical guidance for sustainable agricultural development and ecological environment protection.

Identifying a monozygotic twin brother as a donor of DNA in minimal, mixed forensic stains - A case example

In forensic casework, monozygotic twins have always provided a challenge, as routinely used forensic Short Tandem Repeat (STR) profiles are not able to differentiate between the twin individuals. In this study, we applied a method to discriminate between two monozygotic twin brothers in a sexual assault case that is unique and challenging for several reasons: the use of contact stains as evidence, the stains contain DNA from two persons (victim and one of the brothers), have minimal amounts of DNA, and there are PCR inhibiting factors. Despite these challenging factors, we present a successfully solved case in which whole genome sequencing was applied to identify multiple somatic differences between the two brothers. Validation of the developed methods and the identified differences was performed on material provided by the two siblings, before applying the method on two evidentiary stains. A statistical framework was developed to provide a likelihood calculation for this type of analysis in mixed stains. The results were accepted in court and contributed to the conviction of the case suspect. Here we provide the scientific details in order to encourage the use of this approach in more such cases in the future.

Insights into clinical phenotypes and treatment responses in a Small cohort of Taiwanese patients with SCN1A variants: A Preliminary study

BACKGROUND

SCN1A channelopathy is the most well-known cause for epileptic encephalopathies and contributes to a wide phenotypic spectrum. The variable expressivity is troublesome for the interpretation of clinical significance and prognoses. To investigate the clinical manifestations, medications and outcomes of patients with SCN1A channelopathies, we conducted this observation retrospective study in Taiwan.

METHODS

A cohort consisting of 16 patients (5 males and 11 females) from multiple centers with identified SCN1A variants was investigated and phenotypically relevant factors were recorded. The variants were identified using NGS and confirmed by Sanger sequencing. A panel of 90 epileptic-related genes was used to identify SCN1A variants and to evaluate some of the potential SCN1A modifier genes.

RESULTS

The mean age of seizure onset was 10.4 months. Twelve of the sixteen patients (75%) had different degrees of neurocognitive sequela and psychobehavioral comorbidity in our cohort. Cognitive impairment was noted in all ten patients with Dravet syndrome (DS) and in two of the patients with non-DS phenotypes. A lower response rate to medications was also noted in patients with DS. Notably, a medication-specific tendency towards valproic acid (VPA), clobazam (CLB), and levetiracetam (LEV) was observed, revealing the effective pharmacotherapies for SCN1A-related seizures. An asymptomatic carrier with a reported pathogenic SCN1A variant was reviewed along with her monozygotic twin sister with DS. Nine novel SCN1A mutations are herein reported, eight of which being classified as pathogenic.

CONCLUSION

Our study revealed unfavorable outcomes for patients with SCN1A variants. Some patients with SCN1A channelopathy showed specific responsiveness to the pharmacotherapies previously either recommended or contraindicated for these patients. Our study also expands the genotype and provides valuable prognostic insights in patients with SCN1A channelopathy.

Advancing translational exposomics: bridging genome, exposome and personalized medicine

Understanding the interplay between genetic predisposition and environmental and lifestyle exposures is essential for advancing precision medicine and public health. The exposome, defined as the sum of all environmental exposures an individual encounters throughout their lifetime, complements genomic data by elucidating how external and internal exposure factors influence health outcomes. This treatise highlights the emerging discipline of translational exposomics that integrates exposomics and genomics, offering a comprehensive approach to decipher the complex relationships between environmental and lifestyle exposures, genetic variability, and disease phenotypes. We highlight cutting-edge methodologies, including multi-omics technologies, exposome-wide association studies (EWAS), physiology-based biokinetic modeling, and advanced bioinformatics approaches. These tools enable precise characterization of both the external and the internal exposome, facilitating the identification of biomarkers, exposure-response relationships, and disease prediction and mechanisms. We also consider the importance of addressing socio-economic, demographic, and gender disparities in environmental health research. We emphasize how exposome data can contextualize genomic variation and enhance causal inference, especially in studies of vulnerable populations and complex diseases. By showcasing concrete examples and proposing integrative platforms for translational exposomics, this work underscores the critical need to bridge genomics and exposomics to enable precision prevention, risk stratification, and public health decision-making. This integrative approach offers a new paradigm for understanding health and disease beyond genetics alone.

Photo-refractoriness reflects bet-hedging strategies deployed in unpredictable environments in male Brandt's voles

Day length, also known as photoperiod, is an important reproductive regulatory factor in most seasonal breeders. Brandt's vole, a long-day breeder, exhibits significant differentces in reproductive development depending on the photoperiod of the season of birth, as is seen in other rodent seasonal breeders. However, there is a lack of comprehensive studies on the effects of photoperiod across different seasons. In the present study, we investigated the impact of long (LP) and short photoperiod (SP) on postnatal development in male voles. We measured somatic and testicular parameters from weaning at three postnatal weeks (PNW3) to PNW19, weighed testis mass from birth, and confirmed the status of testicular development by observing the histological features of the seminiferous epithelium. The results showed no difference in testis mass between LP and SP males up to PNW3, with normal initiation of intratubular meiosis and the presence of leptotene/zygotene spermatocytes in both groups. From PNW4 to PNW10, SP males displayed slower growth in both somatic and testicular parameters and showed suppressed development of primary spermatocytes and Leydig cells compared to LP males. After PNW10, both groups experienced photo-refractoriness, characterized by a reversal of gonadal activity. During this stage, SP voles spontaneously initiated gonadal development and resumed the meiotic process, while LP males showed testicular degeneration accompanied by a progressive loss of germ cells ranging from spermatids to primary spermatocytes. Until PNW19, both groups reached similar testis size and mass. Interestingly, this refractoriness was observed in only half of the males in each group, suggesting a bet-hedging survival strategy that allows populations to cope with unpredictable environmental changes, such as fluctuations in temperature and food. These findings highlight the importance of photoperiod as a key environmental factor in influencing sexual maturation in young Brandt's voles, and indicate that the impact of photoperiod in adult voles can be flexible in vole adulthood, varying according to their natural life cycle. This suggests a bet-hedging survival strategy of photo-refractoriness with complex interactions between environmental cues and life history traits.

Different treatment strategies for monozygotic twins with Class II division 1 malocclusion: 10-year follow-up study

BACKGROUND

Early-stage growth modification has been demonstrated effective in treating prepubertal patients with Class II division 1 malocclusion. Since monozygotic twins are genetically identical, environmental factors, including oral habits and treatment strategies, may contribute to different treatment outcomes. To date, few reported comparisons of different treatment strategies in monozygotic twins with Class II division 1 malocclusion exist.

CASE DESCRIPTION

In this case report, we compare the effects of different functional appliances and extraction strategies in a pair of prepubertal monozygotic twins. Different compliance and treatment protocols may have different effects on their early changes in facial profile. Customized treatment plans are necessary for optimal treatment outcomes. Both twins achieved favourable improvements in facial profile, and their long-term stability of functional occlusion was also maintained after a ten-year follow-up.

PRACTICAL IMPLICATIONS

With the outcome of the case, we acknowledged that functional appliance therapy can affect the potentiality of mandibular growth. Individualized protocols should be approached aside from different functional appliances.

Limitations of genomics to predict and treat autism: a disorder born in the womb

Brain development involves the sequential expression of vulnerable biological processes including cell proliferation, programmed cell death, neuronal migration, synapse and functional unit formation. All these processes involve gene and activity-dependent events that can be distorted by many extrinsic and intrinsic environmental factors, including stress, microbiota, inflammatory signals, hormonal signals and epigenetic factors, hence leading to disorders born in the womb that are manifested later in autism spectrum disorders (ASDs) and other neurodevelopmental disorders. Predicting and treating such disorders call for a conceptual framework that includes all aspects of developmental biology. Here, taking the high incidence of ASDs as an example, we first discuss the intrinsic limitations of the genetic approach, notably the widely used twin studies and SNPs. We then review the long list of in utero events that can deviate developmental sequences, leading to persistent aberrant activity generated by immature misplaced and misconnected neuronal ensembles that are the direct cause of ASD. In a clinical perspective, we suggest analysing non-genetic maternity data to enable an early prediction of babies who will develop ASD years later, thereby facilitating early psycho-educative techniques. Subsequently, agents capable of selectively silencing malformed immature networks offer promising therapeutic perspectives. In summary, understanding developmental processes is critical to predicting, understanding and treating ASD, as well as most other disorders that arise in the womb.

Association of blood cadmium levels with epigenetic age acceleration in U.S. adults aged > 50 years

Objectives

DNA methylation (DNAm) is a sensitive biomarker of aging-related processes, and novel epigenetic-based "clocks" can estimate accelerated biological aging. Cadmium (Cd) can alter cellular processes that promote aging and disrupt global methylation patterns. However, few studies have investigated the association between blood Cd and accelerated aging. We aimed to investigate the association between blood Cd and four DNAm-based epigenetic age accelerations in individuals over 50 in the United States, using data from the National Health and Nutrition Examination Survey (NHANES).

Methods

DNAm-epigenetic biomarkers and blood Cd data from the NHANES database (1999-2002) were retrieved for this study. We evaluated four epigenetic ages: HorvathAge, HannumAge, PhenoAge, and GrimAge. Age acceleration was calculated by extracting the residuals from the regression of chronological age on each epigenetic age measure. We used weighted linear regression models and subgroup analyses to investigate the associations between blood Cd levels and these age accelerations, adjusting for potential confounding factors.

Results

Higher blood Cd levels (≥0.5 μg/dl) were significantly associated with increased age acceleration for PhenoAge (β = 1.37, P = 0.017) and GrimAge (β = 1.31, P = 0.003) in adjusted models. A significant association was also observed for HannumAge (β = 0.94, P = 0.016), although this association was not significant for continuous Cd levels (P = 0.111). No significant associations were found for HorvathAge. Subgroup analyses indicated consistent associations across demographic and lifestyle subgroups, with no significant interactions.

Conclusions

In this study, after adjusting for confounders, blood Cd levels were positively associated with PhenoAge acceleration and GrimAge acceleration in people over 50 in the United States. These results may be useful in proposing interventions in environmental exposures to slow the aging process and prevent age-related diseases.

Epigenetic Biomarkers in Temporomandibular Joint Osteoarthritis: An Emerging Target in Treatment

Osteoarthritis (OA) of the temporomandibular joint (TMJ) is a progressive disease characterized by the progressive destruction of the internal surfaces of the joint. Certain epigenetic biomarkers have been detected in TMJ-OA. We summarized the available evidence on the epigenetic biomarkers in TMJ-OA. There is an increase in the expression of non-coding RNAs related to the degradation of the extracellular matrix, chondrocyte apoptosis, and proinflammatory cytokines, while there is a decrease in the expression of those related to COL2A1, as well as the osteogenic and chondrogenic differentiation of mesenchymal stem cells. Certain methylated genes and histone modifications in TMJ-OA were also identified. In the early stage, DNA methylation was significantly decreased; that is, the expression of inflammation-related genes such as TNF and genes associated with extracellular matrix degradation, such as Adamts, were increased. While in the late stage, there was an increase in the expression of genes associated with the TGF-β and MAPK signaling pathway and angiogenesis-related genes. Although research on the role of epigenetic markers in TMJ-OA is still ongoing, the results here contribute to improving the basis for the identification of accurate diagnostic and prognostic markers and the development of new therapeutic molecules for the prevention and management of TMJ-OA. It also represents a significant advancement in elucidating its pathogenesis.

Longitudinal associations of epigenetic aging with cognitive aging in Hispanic/Latino adults from the Hispanic Community Health Study/Study of Latinos

Due to the paucity of longitudinal DNA methylation data (DNAm), especially among Hispanic/Latino adults, the association between changes in epigenetic clocks over time and cognitive aging phenotypes has not been investigated. This longitudinal study included 2671 Hispanic/Latino adults (57 years; 66% women) with blood DNAm data and neurocognitive function assessed at two visits approximately 7 years apart. We evaluated the associations of 5 epigenetic clocks and their between-visit change with multiple measures of cognitive aging that included a global cognitive function score at each visit, between-visit change in global cognitive function score, MCI diagnosis, and presence of significant cognitive decline at visit 2 (V2). There were significant associations between greater acceleration for all clocks and lower global cognitive function at each visit. The strongest associations were observed for GrimAge and DunedinPACE. Similar results were observed for domain-specific cognitive function at each visit and MCI diagnosis at V2. There was a significant association of decline in global cognitive function with increase in age acceleration between the two visits for PhenoAge and GrimAge. Between-visit increase in age acceleration for these two clocks was also associated with a greater risk of MCI diagnosis and presence of significant cognitive decline at V2. Epigenetic aging is associated with lower global and domain-specific cognitive function, greater cognitive decline, and greater risk of MCI in Hispanic/Latino adults. Longitudinal assessment of change in age acceleration for second-generation clocks, GrimAge and PhenoAge may provide additional value in predicting cognitive aging beyond a single time point assessment.

Reactivation of retrotransposable elements is associated with environmental stress and ageing

Retrotransposable elements (RTEs) are interspersed repetitive sequences that represent a large portion of eukaryotic genomes. Ancestral expansions of RTEs directly contributed to the shaping of these genomes and to the evolution of different species, particularly mammals. RTE activity is tightly regulated by different epigenetic mechanisms but this control becomes compromised as cells age and RTEs are reactivated. This dysregulation of RTEs leads to perturbation of cell function and organ and organismal homeostasis, which drives ageing and age-related disease. Environmental stress is associated with both ageing-related characteristics and the epigenetic mechanisms that control RTE activity, with accumulating evidence indicating that RTE reactivation mediates the effects of environmental stressors on ageing onset and progression. A better understanding of how RTEs are reactivated and their subsequent biological roles may help the development of therapies against ageing-related phenotypes and diseases.

Constitutional Epimutations: From Rare Events Toward Major Cancer Risk Factors?

Constitutional epimutations are epigenetic aberrations that arise in normal cells prenatally. Two major forms exist: secondary constitutional epimutations (SCEs), associated with cis-acting genetic aberrations, and primary constitutional epimutations (PCEs), for which no associated genetic aberrations were identified. Some SCEs have been associated with risk of cancer (MLH1 and MSH2 with colon or endometrial cancers, BRCA1 with familial breast and ovarian cancers), although such epimutations are rare, with a total of <100 cases reported. This contrasts recent findings for PCE, where low-level mosaic BRCA1 epimutations are recorded in 5%-10% of healthy females across all age groups, including newborns. BRCA1 PCEs predict an elevated risk of high-grade serous ovarian cancer and triple-negative breast cancer (TNBC) and are estimated to account for about 20% of all TNBCs. A similarly high population frequency is observed for mosaic constitutional epimutations in MGMT, occurring as PCE or SCE, but not in MLH1. Contrasting BRCA1 and MLH1, a potential association with cancer risk for MGMT epimutations is yet unclear. In this review, we provide a summary of findings linking constitutional epimutations to cancer risk with emphasis on PCE. We also highlight challenges in detection of PCE exemplified by low-level mosaic epimutations in BRCA1 and indicate the need for further studies, hypothesizing that improved knowledge about PCE may add significantly to our understanding of cancer risk, carcinogenesis, and potentially development of other diseases as well.

Factors involved in human healthy aging: insights from longevity individuals

The quest to decipher the determinants of human longevity has intensified with the rise in global life expectancy. Long-lived individuals (LLIs), who exceed the average life expectancy while delaying age-related diseases, serve as a unique model for studying human healthy aging and longevity. Longevity is a complex phenotype influenced by both genetic and non-genetic factors. This review paper delves into the genetic, epigenetic, metabolic, immune, and environmental factors underpinning the phenomenon of human longevity, with a particular focus on LLIs, such as centenarians. By integrating findings from human longevity studies, this review highlights a diverse array of factors influencing longevity, ranging from genetic polymorphisms and epigenetic modifications to the impacts of diet and physical activity. As life expectancy grows, understanding these factors is crucial for developing strategies that promote a healthier and longer life.

Prenatal cannabis exposure is associated with alterations in offspring DNA methylation at genes involved in neurodevelopment, across the life course

Prenatal cannabis exposure (PCE) is of increasing concern globally, due to the potential impact on offspring neurodevelopment, and its association with childhood and adolescent brain development and cognitive function. However, there is currently a lack of research addressing the molecular impact of PCE, that may help to clarify the association between PCE and neurodevelopment. To address this knowledge gap, here we present epigenome-wide association study data across multiple time points, examining the effect of PCE and co-exposure with tobacco using two longitudinal studies, the Avon Longitudinal Study of Parents and Children (ALSPAC) and the Christchurch Health and Development Study (CHDS) at birth (0 y), 7 y and 15-17 y (ALSPAC), and ~27 y (CHDS). Our findings reveal genome-wide significant DNA methylation differences in offspring at 0 y, 7 y, 15-17 y, and 27 y associated with PCE alone, and co-exposure with tobacco. Importantly, we identified significantly differentially methylated CpG sites within the genes LZTS2, NPSR1, NT5E, CRIP2, DOCK8, COQ5, and LRP5 that are shared between different time points throughout development in offspring. Notably, functional pathway analysis showed enrichment for differential DNA methylation in neurodevelopment, neurotransmission, and neuronal structure pathways, and this was consistent across all timepoints in both cohorts. Given the increasing volume of epidemiological evidence that suggests a link between PCE and adverse neurodevelopmental outcomes in exposed offspring, this work highlights the need for further investigation into PCE, particularly in larger cohorts.

Differences of tsRNA expression profiles efficiently discriminate monozygotic twins in peripheral blood

Monozygotic twins (MZTs) share nearly identical genomic DNA sequences, making traditional forensic short tandem repeats (STR) genotyping methods ineffective for distinguishing between them. In recent years, the use of epigenetic factors in forensic applications has gained traction. The dynamic epigenetic factors can be influenced by inherited traits or acquired environmental factors. This study analyzed the expression profiles of transfer RNA-derived small RNAs (tsRNAs) in peripheral blood from four pairs of adult MZTs using Panoramic RNA Display by Overcoming RNA Modification Aborted Sequencing (PANDORA-seq). Differentially expressed tsRNAs (DEtsRNAs) were identified and validated using the reverse-transcriptase quantitative polymerase chain reaction (RT-qPCR) and droplet digital PCR (ddPCR) in both adult and newborn MZTs. The study also evaluated the longitudinal temporal stability, resistance to degradation, and suitability of DEtsRNAs for aged bloodstains. A total of 8795 expressed tsRNAs were identified in the four pairs of adult MZTs by PANDORA-seq. After screening with a normalized | log2 (fold change) | > 1 and an adjusted p-value < 0.05, 10, 187, and 1520 DEtsRNAs were shared by 4, 3, and 2 pairs of MZTs. RT-qPCR and ddPCR confirmed the expression of the 10 DEtsRNAs identified by PANDORA-seq. Six candidate tsRNAs (tRNA-Gly-GCC, tRNA-Leu-TAA, tRNA-Lys-CTT, tRNA-Val-AAC_5_end, tRNA-iMet-CAT_5_end, and tsRNA-3023a/b-PheGAA) were identified as effective discrimination markers, even in neonatal MZTs which are largely unaffected by environment factors. Forensic applicability assessment revealed that tRNA-Gly-GCC and tRNA-Leu-TAA remained detectable in the 180-day-series bloodstains, while tRNA-Lys-CTT, tRNA-Val-AAC_5_end, and tRNA-iMet-CAT_5_end were relatively stable after 15 times of freeze-thaw cycles. Additionally, tRNA-Gly-GCC and tRNA-Lys-CTT exhibited long-term stability, with consistent expression over six months. In conclusion, this study demonstrates that differential tsRNAs expression can serve as a novel biomarker for MZT identification in forensic medicine.

The Circulating Methylome in Childhood-Onset Inflammatory Bowel Disease

BACKGROUND

The genetic contribution to inflammatory bowel disease (IBD), encompassing both Crohn's disease (CD) and ulcerative colitis (UC), accounts for around 20% of disease variance, highlighting the need to characterize environmental and epigenetic influences. Recently, considerable progress has been made in characterizing the adult methylome in epigenome-wide association studies.

METHODS

We report detailed analysis of the circulating methylome in 86 patients with childhood-onset CD and UC and 30 controls using the Illumina Infinium Human MethylationEPIC platform.

RESULTS

We derived and validated a 4-probe methylation biomarker (RPS6KA2, VMP1, CFI, and ARHGEF3), with specificity and high diagnostic accuracy for pediatric IBD in UK and North American cohorts (area under the curve: 0.90-0.94). Significant epigenetic age acceleration is present at diagnosis, with the greatest observed in CD patients. Cis-methylation quantitative trait loci (meQTL) analysis identifies genetic determinants underlying epigenetic alterations notably within the HLA 6p22.1-p21.33 region. Passive smoking exposure is associated with the development of UC rather than CD, contrary to previous findings.

CONCLUSIONS

These data provide new insights into epigenetic alterations in IBD and illustrate the reproducibility and translational potential of epigenome-wide association studies in complex diseases.

Current progress and future perspectives in personal identification of monozygotic twins in forensic medicine

The personal identification of monozygotic (MZ) twins is of great importance in forensic medicine. Due to the extreme similarity in genetic between MZ twins, it is challenging to differentiate them using autosomal STR genotyping. Forensic experts are striving to explore available genetic markers that can differentiate between MZ twins. With the advent of next-generation sequence (NGS), an increasing number of genetic markers have been demonstrated to effectively differentiate between MZ twins. Here, we summarized for the relevant studies on MZ twins' differentiation and discussed the limitations of the underlying markers. In details, single-nucleotide variants (SNVs), copy number variation (CNV), mitochondrial DNA (mtDNA), DNA methylation, and non-coding RNA have been demonstrated considerable value. Furthermore, the utilization of proteomics, metabolomics, and microbiomics has shed light on MZ twin differentiation. Additionally, we introduce the methodologies for MZ differentiation based on external morphological variations observed in the human body. Looking to the future, the process of aging may represent a novel avenue for the differentiation of MZ twins.

MGMT epimutations and risk of incident cancer of the colon, glioblastoma multiforme, and diffuse large B cell lymphomas

BACKGROUND

Constitutional BRCA1 epimutations (promoter hypermethylation) are associated with an elevated risk of triple-negative breast cancer and high-grade serous ovarian cancer. While MGMT epimutations are frequent in colon cancer, glioblastoma, and B-cell lymphoma, it remains unknown whether constitutional MGMT epimutations are associated with risk of any of these malignancies.

METHODS

We designed a nested case-control study, assessing potential associations between MGMT epimutations in blood from healthy individuals and subsequent risk of incident cancer. The study cohort was drawn from postmenopausal women, participating in the Women's Health Initiative (WHI) study, who had not been diagnosed with either colon cancer, glioblastoma, or B-cell lymphoma prior to study entry. The protocol included n = 400 women developing incident left-sided and n = 400 women developing right-sided colon cancer, n = 400 women developing diffuse large B-cell lymphomas, all matched on a 1:2 basis with cancer-free controls, and n = 195 women developing incident glioblastoma multiforme, matched on a 1:4 basis. All cancers were confirmed in centralized medical record review. Blood samples, collected at entry, were analyzed for MGMT epimutations by massive parallel sequencing. Associations between MGMT methylation and incident cancers were analyzed by Cox proportional hazards regression.

RESULTS

Analyzing epimutations affecting the key regulatory area of the MGMT promoter, the hazard ratio (HR) was 1.07 (95% CI 0.79-1.45) and 0.80 (0.59-1.08) for right- and left-sided colon cancer, respectively, 1.13 (0.78-1.64) for glioblastoma, and 1.11 (0.83-1.48) for diffuse large B-cell lymphomas. Sensitivity analyses limited to subregions of the MGMT promoter and to individuals with different genotypes of a functional SNP in the MGMT promoter (rs16906252), revealed no significant effect on HR for any of the cancer forms. Neither did we observe any effect of rs16906252 status on HR for any of the cancer forms among individuals methylated or non-methylated at the MGMT promoter.

CONCLUSIONS

Constitutional MGMT promoter methylation in normal tissue is not associated with an increased risk of developing colon cancer, glioblastoma, or B-cell lymphoma.

An Update on Neuroaging on Earth and in Spaceflight

Over 400 articles on the pathophysiology of brain aging, neuroaging, and neurodegeneration were reviewed, with a focus on epigenetic mechanisms and numerous non-coding RNAs. In particular, this review the accent is on microRNAs, the discovery of whose pivotal role in gene regulation was recognized by the 2024 Nobel Prize in Physiology or Medicine. Aging is not a gradual process that can be easily modeled and described. Instead, multiple temporal processes occur during aging, and they can lead to mosaic changes that are not uniform in pace. The rate of change depends on a combination of external and internal factors and can be boosted in accelerated aging. The rate can decrease in decelerated aging due to individual structural and functional reserves created by cognitive, physical training, or pharmacological interventions. Neuroaging can be caused by genetic changes, epigenetic modifications, oxidative stress, inflammation, lifestyle, and environmental factors, which are especially noticeable in space environments where adaptive changes can trigger aging-like processes. Numerous candidate molecular biomarkers specific to neuroaging need to be validated to develop diagnostics and countermeasures.

Epigenomics-guided precision oncology: Chromatin variants in prostate tumor evolution

Prostate cancer is a common malignancy that in 5%-30% leads to treatment-resistant and highly aggressive disease. Metastasis-potential and treatment-resistance is thought to rely on increased plasticity of the cancer cells-a mechanism whereby cancer cells alter their identity to adapt to changing environments or therapeutic pressures to create cellular heterogeneity. To understand the molecular basis of this plasticity, genomic studies have uncovered genetic variants to capture clonal heterogeneity of primary tumors and metastases. As cellular plasticity is largely driven by non-genetic events, complementary studies in cancer epigenomics are now being conducted to identify chromatin variants. These variants, defined as genomic loci in cancer cells that show changes in chromatin state due to the loss or gain of epigenomic marks, inclusive of histone post-translational modifications, DNA methylation and histone variants, are considered the fundamental units of epigenomic heterogeneity. In prostate cancer chromatin variants hold the promise of guiding the new era of precision oncology. In this review, we explore the role of epigenomic heterogeneity in prostate cancer, focusing on how chromatin variants contribute to tumor evolution and therapy resistance. We therefore discuss their impact on cellular plasticity and stochastic events, highlighting the value of single-cell sequencing and liquid biopsy epigenomic assays to uncover new therapeutic targets and biomarkers. Ultimately, this review aims to support a new era of precision oncology, utilizing insights from epigenomics to improve prostate cancer patient outcomes.

The androgen clock is an epigenetic predictor of long-term male hormone exposure

Aging is a complex process characterized by biological decline and a wide range of molecular alterations to cells, including changes to DNA methylation. In this study, we used a male-specific epigenetic marker of aging to build an epigenetic predictor that measures long-term androgen exposure in sheep and mice (median absolute error of 4.3 and 1.4 mo, respectively). We term this predictor the androgen clock and show its "tick" is mediated by the androgen receptor and can be accelerated beyond that in normal male mice by supplementing females with dihydrotestosterone. Conversely, the removal of androgens by castration in sheep completely halted the androgen clock. In addition to potential applications in medicine and agriculture, we predict the androgen clock will prove a useful model to understand the mechanisms and processes of age-associated DNA methylation change because it can be precisely enhanced and halted using small molecule manipulation with few additional effects on the cell.

Characterization of DNA methylation clock algorithms applied to diverse tissue types

BACKGROUND

DNA methylation (DNAm) data from human samples has been leveraged to develop "epigenetic clock" algorithms that predict age and other aging-related phenotypes. Some DNAm clocks were trained using DNAm obtained from blood cells, while other clocks were trained using data from diverse tissue/cell types. To assess how DNAm clocks perform across non-blood tissue types, we applied DNAm algorithms to DNAm data generated from 9 different human tissue types.

METHODS

We generated array-based DNAm measurements for 973 samples from deceased tissue donors from the GTEx (Genotype Tissue Expression) project representing nine distinct tissue types: lung, colon, prostate, ovary, breast, kidney, testis, skeletal muscle, and whole blood. For all samples, we generated DNAm clock estimates for 8 epigenetic clocks and characterized these tissue-specific clock estimates in terms of their distributions, correlations with chronological age, correlations of clock estimates between tissue types, and association with participant characteristics.

RESULTS

For each clock, the mean DNAm age estimate varied substantially across tissue types, and the mean values for the different clocks varied substantially within tissue types. For most clocks, the correlation with chronological age varied across tissue types, with blood often showing the strongest correlation. Each clock showed strong correlation across tissues, with some evidence of some residual correlation after adjusting for chronological age. In lung tissue, smoking generally had a positive association with epigenetic age.

CONCLUSIONS

This work demonstrates how differences in epigenetic aging among tissue types leads to clear differences in DNAm clock characteristics across tissue types. Tissue or cell-type specific epigenetic clocks are needed to optimize predictive performance of DNAm clocks in non-blood tissues and cell types.

Insights to aging prediction with AI based epigenetic clocks

Over the past century, human lifespan has increased remarkably, yet the inevitability of aging persists. The disparity between biological age, which reflects pathological deterioration and disease, and chronological age, indicative of normal aging, has driven prior research focused on identifying mechanisms that could inform interventions to reverse excessive age-related deterioration and reduce morbidity and mortality. DNA methylation has emerged as an important predictor of age, leading to the development of epigenetic clocks that quantify the extent of pathological deterioration beyond what is typically expected for a given age. Machine learning technologies offer promising avenues to enhance our understanding of the biological mechanisms governing aging by further elucidating the gap between biological and chronological ages. This perspective article examines current algorithmic approaches to epigenetic clocks, explores the use of machine learning for age estimation from DNA methylation, and discusses how refining the interpretation of ML methods and tailoring their inferences for specific patient populations and cell types can amplify the utility of these technologies in age prediction. By harnessing insights from machine learning, we are well-positioned to effectively adapt, customize and personalize interventions aimed at aging.

Epigenomic heterogeneity as a source of tumour evolution

In the past decade, remarkable progress in cancer medicine has been achieved by the development of treatments that target DNA sequence variants. However, a purely genetic approach to treatment selection is hampered by the fact that diverse cell states can emerge from the same genotype. In multicellular organisms, cell-state heterogeneity is driven by epigenetic processes that regulate DNA-based functions such as transcription; disruption of these processes is a hallmark of cancer that enables the emergence of defective cell states. Advances in single-cell technologies have unlocked our ability to quantify the epigenomic heterogeneity of tumours and understand its mechanisms, thereby transforming our appreciation of how epigenomic changes drive cancer evolution. This Review explores the idea that epigenomic heterogeneity and plasticity act as a reservoir of cell states and therefore as a source of tumour evolution. Best practices to quantify epigenomic heterogeneity and explore its various causes and consequences are discussed, including epigenomic reprogramming, stochastic changes and lasting memory. The design of new therapeutic approaches to restrict epigenomic heterogeneity, with the long-term objective of limiting cancer development and progression, is also addressed.

Remodeling the Epigenome Through Meditation: Effects on Brain, Body, and Well-being

Epigenetic mechanisms are key processes that constantly reshape genome activity carrying out physiological responses to environmental stimuli. Such mechanisms regulate gene activity without modifying the DNA sequence, providing real-time adaptation to changing environmental conditions. Both favorable and unfavorable lifestyles have been shown to influence body and brain by means of epigenetics, leaving marks on the genome that can either be rapidly reversed or persist in time and even be transmitted trans-generationally. Among virtuous habits, meditation seemingly represents a valuable way of activating inner resources to cope with adverse experiences. While unhealthy habits, stress, and traumatic early-life events may favor the onset of diseases linked to inflammation, neuroinflammation, and neuroendocrine dysregulation, the practice of mindfulness-based techniques was associated with the alleviation of many of the above symptoms, underlying the importance of lifestyles for health and well-being. Meditation influences brain and body systemwide, eliciting structural/morphological changes as well as modulating the levels of circulating factors and the expression of genes linked to the HPA axis and the immune and neuroimmune systems. The current chapter intends to give an overview of pioneering research showing how meditation can promote health through epigenetics, by reshaping the profiles of the three main epigenetic markers, namely DNA methylation, histone modifications, and non-coding RNAs.

Human brain aging is associated with dysregulation of cell type epigenetic identity

Significant links between aging and DNA methylation are emerging from recent studies. On the one hand, DNA methylation undergoes changes with age, a process termed as epigenetic drift. On the other hand, DNA methylation serves as a readily accessible and accurate biomarker for aging. A key missing piece of information, however, is the molecular mechanisms underlying these processes and how they are related, if any. Addressing the limitations of previous research due to the limited number of investigated CpGs and the heterogeneous nature of tissue samples, here, we have examined DNA methylation of over 20 million CpGs across a broad age span in neurons and non-neuronal cells, primarily oligodendrocytes. We show that aging is a primary predictor of DNA methylation variation, surpassing the influence of factors such as sex and schizophrenia diagnosis, among others. On the genome-wide scale, epigenetic drift manifests as significant yet subtle trends that are influenced by the methylation level of individual CpGs. We reveal that CpGs that are highly differentiated between cell types are especially prone to age-associated DNA methylation alterations, leading to the divergence of epigenetic cell type identities as individuals age. On the other hand, CpGs that are included in commonly used epigenetic clocks tend to be those sites that are not highly cell type differentiated. Therefore, dysregulation of epigenetic cell type identities and current DNA epigenetic clocks represent distinct features of age-associated DNA methylation alterations.

Unlocking the epigenetic code: new insights into triple-negative breast cancer

Triple-negative breast cancer (TNBC) is a highly aggressive and clinically challenging subtype of breast cancer, lacking the expression of estrogen receptor (ER), progesterone receptor (PR), and HER2/neu. The absence of these receptors limits therapeutic options necessitating the exploration of novel treatment strategies. Epigenetic modifications, which include DNA methylation, histone modifications, and microRNA (miRNA) regulation, play a pivotal role in TNBC pathogenesis and represent promising therapeutic targets. This review delves into the therapeutic potential of epigenetic interventions in TNBC, with a focus on DNA methylation, histone modifications, and miRNA therapeutics. We examine the role of DNA methylation in gene silencing within TNBC and the development of DNA methylation inhibitors designed to reactivate silenced tumor suppressor genes. Histone modifications, through histone deacetylation and acetylation in particular, are critical in regulating gene expression. We explore the efficacy of histone deacetylase inhibitors (HDACi), which have shown promise in reversing aberrant histone deacetylation patterns, thereby restoring normal gene function, and suppressing tumor growth. Furthermore, the review highlights the dual role of miRNAs in TNBC as both oncogenes and tumor suppressors and discusses the therapeutic potential of miRNA mimics and inhibitors in modulating these regulatory molecules to inhibit cancer progression. By integrating these epigenetic therapies, we propose a multifaceted approach to target the underlying epigenetic mechanisms that drive TNBC progression. The synergistic use of DNA methylation inhibitors, HDACi, and the miRNA-based therapies offers a promising avenue for personalized treatment strategies, aiming to enhance the clinical outcome for patients with TNBC.

DNA Imprinting and Differentially Expressed Genes in Longissimus thoracis Muscle of Bos indicus Submitted to Early Weaning Management

Background/Objectives: Early weaning management followed by energy supplementation can lead to metabolic alterations in the calf that exert long-term effects on the animal's health and performance. It is believed that the main molecular basis underlying these metabolic adaptations are epigenetic mechanisms that regulate, activate, or silence genes at different stages of development and/or in response to different environmental stimuli. However, little is known about postnatal metabolic programming in Bos indicus. Therefore, this study aimed to compare the DNA methylation profile of Nellore animals submitted to conventional and early weaning and to correlate the findings with genes differentially expressed in the Longissimus thoracis skeletal muscle of Bos indicus cattle. Methods: For this, we used Reduced Representation Bisulfite Sequencing (RRBS) and RNA-Sequencing techniques to prospect differentially methylated genes (DMGs). Results: A total of 481 differentially methylated regions were identified, with 52% (250) being hypermethylated and 48% (231) hypomethylated. Functional enrichment analysis of 53 differentially methylated and differentially expressed genes was performed. The main enriched terms and pathways were associated with 3'-5'-cyclic adenosine monophosphate (cAMP) signaling, which presents the upregulated adenylate cyclase 3 (ADCY3) gene and significatively hypomethylated in the promoter region. Alterations in cAMP signaling are involved in numerous processes, many of them related to lipid metabolism. The relative differential expression of key genes of this pathway demonstrates the relationship between cAMP signaling and de novo lipogenesis. Conclusions: These findings suggest an important role of postnatal metabolic programming through DNA methylation mechanisms in determining fat deposition in beef.

The Role of Methylation in Ferroptosis

Methylation modification is a crucial epigenetic alteration encompassing RNA methylation, DNA methylation, and histone methylation. Ferroptosis represents a newly discovered form of programmed cell death (PCD) in 2012, which is characterized by iron-dependent lipid peroxidation. The comprehensive investigation of ferroptosis is therefore imperative for a more profound comprehension of the pathological and pathophysiological mechanisms implicated in a wide array of diseases. Researches show that methylation modifications can exert either promotive or inhibitory effects on cell ferroptosis. Consequently, this review offers a comprehensive overview of the pivotal role played by methylation in ferroptosis, elucidating its associated factors and underlying mechanisms.

The impact of sex on memory during aging and Alzheimer's disease progression: Epigenetic mechanisms

Alzheimer's disease (AD) is a leading cause of dementia, disability, and death in the elderly. While the etiology of AD is unknown, there are several established risk factors for the disease including, aging, female sex, and genetics. However, specific genetic mutations only account for a small percentage (1-5%) of AD cases and the much more common sporadic form of the disease has no causative genetic basis, although certain risk factor genes have been identified. While the genetic code remains static throughout the lifetime, the activation and expression levels of genes change dynamically over time via epigenetics. Recent evidence has emerged linking changes in epigenetics to the pathogenesis of AD, and epigenetic alterations also modulate cognitive changes during physiological aging. Aging is the greatest risk factor for the development of AD and two-thirds of all AD patients are women, who experience an increased rate of symptom progression compared to men of the same age. In humans and other mammalian species, males and females experience aging differently, raising the important question of whether sex differences in epigenetic regulation during aging could provide an explanation for sex differences in neurodegenerative diseases such as AD. This review explores distinct epigenetic changes that impact memory function during aging and AD, with a specific focus on sexually divergent epigenetic alterations (in particular, histone modifications) as a potential mechanistic explanation for sex differences in AD.

Developmental psychopathology as a meta-paradigm: From zero-sum science to epistemological pluralism in theory and research

In a thoughtful commentary in this journal a decade ago, Michael Rutter reviewed 25 years of progress in the field before concluding that developmental psychopathology (DP) initiated a paradigm shift in clinical science. This deduction requires that DP itself be a paradigm. According to Thomas Kuhn, canonical paradigms in the physical sciences serve unifying functions by consolidating scientists' thinking and scholarship around single, closed sets of discipline-defining epistemological assumptions and methods. Paradigm shifts replace these assumptions and methods with a new field-defining framework. In contrast, the social sciences are multiparadigmatic, with thinking and scholarship unified locally around open sets of epistemological assumptions and methods with varying degrees of inter-, intra-, and subdisciplinary reach. DP challenges few if any of these local paradigms. Instead, DP serves an essential pluralizing function, and is therefore better construed as a metaparadigm. Seen in this way, DP holds tremendous untapped potential to move the field from zero-sum thinking and scholarship to positive-sum science and epistemological pluralism. This integrative vision, which furthers Dante Cicchetti's legacy of interdisciplinarity, requires broad commitment among scientists to reject zero-sum scholarship in which portending theories, useful principles, and effective interventions are jettisoned based on confirmation bias, errors in logic, and ideology.

The Effect of Maternal Diet and Lifestyle on the Risk of Childhood Obesity

Background/Objectives: Childhood obesity is a global health problem that affects at least 41 million children under the age of five. Increased BMI in children is associated with serious long-term health consequences, such as type 2 diabetes, cardiovascular disease, and psychological problems, including depression and low self-esteem. Although the etiology of obesity is complex, research suggests that the diet and lifestyle of pregnant women play a key role in shaping metabolic and epigenetic changes that can increase the risk of obesity in their children. Excessive gestational weight gain, unhealthy dietary patterns (including the Western diet), and pregnancy complications (such as gestational diabetes) are some of the modifiable factors that contribute to childhood obesity. The purpose of this narrative review is to summarize the most important and recent information on the impact of the diet and lifestyle of pregnant women on the risk of childhood obesity. Methods: This article is a narrative review that aims to summarize the available literature on the impact of pregnant women's diet and lifestyle on the risk of obesity in their offspring, with a focus on metabolic and epigenetic mechanisms. Results/Conclusions: Current evidence suggests that a pregnant woman's lifestyle and diet can significantly contribute to lowering the risk of obesity in their offspring. However, further high-quality research is needed to understand better the metabolic and epigenetic relationships concerning maternal factors that predispose offspring to obesity.

Epigenetic Study of Cohort of Monozygotic Twins With Hypertrophic Cardiomyopathy Due to MYBPC3 (Cardiac Myosin-Binding Protein C)

BACKGROUND

Hypertrophic cardiomyopathy is an autosomal dominant cardiac disease. The mechanisms that determine its variable expressivity are poorly understood. Epigenetics could play a crucial role in bridging the gap between genotype and phenotype by orchestrating the interplay between the environment and the genome regulation. In this study we aimed to establish a possible correlation between the peripheral blood DNA methylation patterns and left ventricular hypertrophy severity in patients with hypertrophic cardiomyopathy, evaluating the potential impact of lifestyle variables and providing a biological context to the observed changes.

METHODS AND RESULTS

Methylation data were obtained from peripheral blood samples (Infinium MethylationEPIC BeadChip arrays). We employed multiple pair-matched models to extract genomic positions whose methylation correlates with the degree of left ventricular hypertrophy in 3 monozygotic twin pairs carrying the same founder pathogenic variant (MYBPC3 p.Gly263Ter). This model enables the isolation of the environmental influence, beyond age, on DNA methylation changes by removing the genetic background. Our results revealed a more anxious personality among more severely affected individuals. We identified 56 differentially methylated positions that exhibited moderate, proportional changes in methylation associated with left ventricular hypertrophy. These differentially methylated positions were enriched in regions regulated by repressor histone marks and tended to cluster at genes involved in left ventricular hypertrophy development, such as HOXA5, TRPC3, UCN3, or PLSCR2, suggesting that changes in peripheral blood may reflect myocardial alterations.

CONCLUSIONS

We present a unique pair-matched model, based on 3 monozygotic twin pairs carrying the same founder pathogenic variant and different phenotypes. This study provides further evidence of the pivotal role of epigenetics in hypertrophic cardiomyopathy variable expressivity.

Exploring the potential of epigenetic clocks in aging research

The process of aging is a notable risk factor for numerous age-related illnesses. Hence, a reliable technique for evaluating biological age or the pace of aging is crucial for understanding the aging process and its influence on the progression of disease. Epigenetic alterations are recognized as a prominent biomarker of aging, and epigenetic clocks formulated on this basis have been shown to provide precise estimations of chronological age. Extensive research has validated the effectiveness of epigenetic clocks in determining aging rates, identifying risk factors for aging, evaluating the impact of anti-aging interventions, and predicting the emergence of age-related diseases. This review provides a detailed overview of the theoretical principles underlying the development of epigenetic clocks and their utility in aging research. Furthermore, it explores the existing obstacles and possibilities linked to epigenetic clocks and proposes potential avenues for future studies in this field.

Epigenetic regulation of cardiovascular diseases induced by behavioral and environmental risk factors: Mechanistic, diagnostic, and therapeutic insights

Behavioral and environmental risk factors are critical in the development and progression of cardiovascular disease (CVD). Understanding the molecular mechanisms underlying these risk factors will offer valuable insights for targeted preventive and therapeutic strategies. Epigenetic modifications, including DNA methylation, histone modifications, chromatin remodeling, noncoding RNA (ncRNA) expression, and epitranscriptomic modifications, have emerged as key mediators connecting behavioral and environmental risk factors to CVD risk and progression. These epigenetic alterations can profoundly impact on cardiovascular health and susceptibility to CVD by influencing cellular processes, development, and disease risk over an individual's lifetime and potentially across generations. This review examines how behavioral and environmental risk factors affect CVD risk and health outcomes through epigenetic regulation. We review the epigenetic effects of major behavioral risk factors (such as smoking, alcohol consumption, physical inactivity, unhealthy diet, and obesity) and environmental risk factors (including air and noise pollution) in the context of CVD pathogenesis. Additionally, we explore epigenetic biomarkers, considering their role as causal or surrogate indicators, and discuss epigenetic therapeutics targeting the mechanisms through which these risk factors contribute to CVD. We also address future research directions and challenges in leveraging epigenetic insights to reduce the burden of CVD related to behavioral and environmental factors and improve public health outcomes. This review aims to provide a comprehensive understanding of behavioral and environmental epigenetics in CVD and offer valuable strategies for therapeutic intervention.

Retrotransposon SINEs in age-related diseases: Mechanisms and therapeutic implications

Retrotransposons are self-replicating genomic elements that move from one genomic location to another using a "copy-and-paste" method involving RNA intermediaries. One family of retrotransposon that has garnered considerable attention for its association with age-related diseases and anti-aging interventions is the short interspersed nuclear elements (SINEs). This review summarizes current knowledge on the roles of SINEs in aging processes and therapies. To underscore the significant research on the involvement of SINEs in aging-related diseases, we commence by outlining compelling evidence on the classification and mechanism, highlighting implications in age-related phenomena. The intricate relationship between SINEs and diseases such as neurodegenerative disorders, heart failure, high blood pressure, atherosclerosis, type 2 diabetes mellitus, osteoporosis, visual system dysfunctions, and cancer is explored, emphasizing their roles in various age-related diseases. Recent investigations into the anti-aging potential of SINE-targeted treatments are examined, with particular attention to how SINE antisense RNA mitigate age-related alterations at the cellular and molecular levels, offering insights into potential therapeutic targets for age-related pathologies. This review aims to compile the most recent advances on the multifaceted roles of SINE retrotransposons in age-related diseases and anti-aging interventions, providing valuable insights into underlying mechanisms and therapeutic avenues for promoting healthy aging.

Effects of Cohabitation on Neurodevelopmental Outcomes in Rats Discordant for Neonatal Exposure to Sevoflurane

Background

Having a sibling with autism spectrum disorder is a risk factor for autism spectrum disorder. We used a rat model in which the general anesthetic sevoflurane (SEVO) induces autism spectrum disorder-like neurodevelopmental abnormalities to test whether they can be transmitted via cohabitation.

Methods

Male rat pups from several litters were mixed and randomized to 3 new litter types: SEVO-exposed (SEVO), SEVO-unexposed (control), and equal numbers of SEVO-exposed and SEVO-unexposed (MIXED). After weaning, rats in experiment 1 were housed with littermates in SEVO, control, and MIXED (MIXED-exposed and MIXED-unexposed) pairs. In experiment 2, MIXED-exposed and MIXED-unexposed rats were paired with an unfamiliar naïve cagemate. Corticosterone levels, gene expression, central inflammatory markers (experiment 1), and behavior and corticosterone levels (experiment 2) were assessed in adulthood.

Results

In experiment 1, compared with control rats, SEVO rats exhibited abnormalities in the hypothalamic-pituitary-adrenal axis, inflammatory markers, oxytocin, arginine vasopressin, and DNA methylation systems. Almost all these measures in MIXED-exposed and MIXED-unexposed rats were statistically indistinguishable from and similar to those in SEVO or control rats, with most measures in MIXED rats being similar to those in SEVO rats. Experiment 2 showed that pairing with unfamiliar, naïve rats after weaning caused MIXED-unexposed and MIXED-exposed rats' behavior to be no different from that of control and SEVO rats, respectively; however, the 2 groups of MIXED rats also did not differ from each other.

Conclusions

These findings suggest that neurodevelopmental abnormalities can be transmitted to otherwise healthy individuals through interactions during cohabitation; however, subsequent pairing with unfamiliar, naïve cohabitants may weaken this interaction effect.

A new insight of blood vs. buccal DNA methylation in the forensic identification of monozygotic triplets

The case of the monozygotic (MZ) twin as a suspect demonstrates a practical problem in forensic casework. As the MZ twins are genetically identical, they share the same short tandem repeat (STR) profile. Many studies showed that older MZ twins have significant differences in overall content and genomic distribution of methylation between them. However, studies addressing the investigation of epigenetic MZ triplet differentiation in various forensic reference materials are lacking. Here, one triplet set of Egyptian MZ twins was used as an analog to a forensic case. The genome-wide methylation analysis was performed via the new Human Methylation EPIC BeadChip array. Following normalization methods, potential differentially methylated positions (DMPs) were discovered. This resulted in the detection of 24 potential DMPs in reference-type blood DNA and 11 potential DMPs in reference-type buccal DNA. Then, the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analyses were performed to show the associated biological functions. Our findings revealed that the 35 potential DMPs were enriched in 283 significant GO terms. These terms are mainly enriched in the immune system. Overall, this study demonstrates the general feasibility of epigenetic MZ triplet differentiation in the forensic context and highlights that some potential DMPs identified in blood DNA were not informative in buccal DNA. This is due to various reasons, including the tissue specificity of DNA methylation.

Epigenetics as a link between environmental factors and dementia risk

Dementia encompasses a broad spectrum of neuropsychiatric disease states marked by cognitive impairments that interfere with day-to-day functioning. Most dementias are complex phenotypes that result from a genome-environment interplay. Epigenetic regulation has emerged as a candidate mechanism for studying this interplay. In this narrative review, we discuss state-of-the-art evidence on environmental exposures relevant to dementia, including nutrition, physical exercise, psychosocial stress, and environmental toxins, and highlight epigenetic mechanisms that have been reported as a putative link between each exposure and dementia risk. We then discuss the clinical implications and future directions of this line of research. An improved understanding of the epigenetic mechanisms involved in dementia pathogenesis can promote the development of novel biomarkers for predicting outcomes but also targeted therapies to intervene early in the course of the disease.

Hippocampal HDAC5-mediated histone acetylation underlies stress susceptibility in mice exposed to chronic social defeat stress

Chronic stress leads to social avoidance and anhedonia in susceptible individuals, a phenomenon that has been observed in both human and animal models. Nevertheless, the underlying molecular mechanisms underpinning stress susceptibility and resilience remain largely unclear. There is growing evidence that epigenetic histone deacetylase (HDAC) mediated histone acetylation is involved in the modulation of depressive-related behaviors. We hypothesized that histone deacetylase 5 (HDAC5), which is associated with stress-related behaviors and antidepressant response, may play a vital role in the susceptibility to chronic stress. In the current study, we detected the levels of HDAC5 and acetylation of histone 4 (H4) in the hippocampus subsequent to chronic social defeat stress (CSDS) in C57BL/6J mice. We found that CSDS induces a notable increase in HDAC5 expression, concomitant with a reduction in the acetylation of histone H4 at lysine 12 (H4K12) in the hippocampus of susceptible mice. Meanwhile, intrahippocampal infusion of HDAC5 shRNA or HDAC inhibitor suberoylanilide hydroxamic acid (SAHA) both reversed the depression susceptibility in susceptible mice that subjected to CSDS. Furthermore, HDAC5 overexpression was sufficient to induce depression susceptibility following microdefeat stress, accompanied by a significant reduction in H4K12 level within the hippocampus of mice. Additionally, the Morris water maze (MWM) results indicated that neither CSDS nor HDAC5 exerted significant effects on spatial memory function in mice. Taken together, these investigations indicated that HDAC5-modulated histone acetylation is implicated in regulating the depression susceptibility, and may be serve as potential preventive targets for susceptible individuals.

Can social adversity alter the epigenome, trigger oral disease, and affect future generations?

The nature versus nurture debate has intrigued scientific circles for decades. Although extensive research has established a clear relationship between genetics and disease development, recent evidence has highlighted the insufficiency of attributing adverse health outcomes to genetic factors alone. In fact, it has been suggested that environmental influences, such as socioeconomic position (SEP), may play a much larger role in the development of disease than previously thought, with extensive research suggesting that low SEP is associated with adverse health conditions. In relation to oral health, a higher prevalence of caries (tooth decay) exists among those of low SEP. Although little is known about the biological mechanisms underlying this relationship, epigenetic modifications resulting from environmental influences have been suggested to play an important role. This review explores the intersection of health inequalities and epigenetics, the role of early-life social adversity and its long-term epigenetic impacts, and how those living within the lower hierarchies of the socioeconomic pyramid are indeed at higher risk of developing diseases, particularly in relation to oral health. A deeper understanding of these mechanisms could lead to the development of targeted interventions for individuals of low SEP to improve oral health or identify those who are at higher risk of developing oral disease.

Epigenetic effects of cannabis: A systematic scoping review of behavioral and emotional symptoms associated with cannabis use and exocannabinoid exposure

BACKGROUND

Recent research suggests that epigenetic modifications may mediate the behavioral effects of cannabis, influencing exocannabinnoids' long term effects in cognitive function and its role in the emergence of psychotic symptoms.

BASIC PROCEDURES

In this systematic scoping review, we assessed the current evidence of epigenetic effects associated with the use of cannabis or exocannabinoid administration and their relationship with behavioral and emotional symptoms. We searched PubMed, Cochrane CENTRAL, and Web of Science, up to January 2022, using the terms "cannabis" and "epigenetics." The search yielded 178 articles, of which 43 underwent full article revision; 37 articles were included in the review.

MAIN FINDINGS

The gathered evidence included observational cross-sectional studies conducted on human subjects and experimental designs using animal models that conveyed disparity in administration dosage, methods of cannabis use assessment and targeted epigenetic mechanisms. Nine studies performed epigenome-wide analysis with identification of differentially methylated sites; most of these studies found a global hypomethylation, and enrichment in genes related to cellular survival and neurodevelopment. Other studies assessed methylation at specific genes and found that cannabis exposure was associated with reduced methylation at Cg05575921, DNMT1, DRD2, COMT, DLGAP2, Arg1, STAT3, MGMT, and PENK, while hypermethylation was found at DNMT3a/b, NCAM1, and AKT1.

CONCLUSIONS

The review found evidence of an exocannabinoid-induced epigenetic changes that modulate depressive-anxious, psychotic, and addictive behavioural phenotypes. Further studies will require dosage exposure/administration uniformization and a customized pool of genes to assess their suitability as biomarkers for psychiatric diseases.

Next-generation CRISPR technology for genome, epigenome and mitochondrial editing

The application of rapidly growing CRISPR toolboxes and methods has great potential to transform biomedical research. Here, we provide a snapshot of up-to-date CRISPR toolboxes, then critically discuss the promises and hurdles associated with CRISPR-based nuclear genome editing, epigenome editing, and mitochondrial editing. The technical challenges and key solutions to realize epigenome editing in vivo, in vivo base editing and prime editing, mitochondrial editing in complex tissues and animals, and CRISPR-associated transposases and integrases in targeted genomic integration of very large DNA payloads are discussed. Lastly, we discuss the latest situation of the CRISPR/Cas9 clinical trials and provide perspectives on CRISPR-based gene therapy. Apart from technical shortcomings, ethical and societal considerations for CRISPR applications in human therapeutics and research are extensively highlighted.