Do Glioma Cells Rewire Neural Circuits through Epigenetic Changes? DNA Methylation Analysis of Genes Involved in Neuron-Glioma Communication in the Human Frontal Cortex.

Proliferation-Dependent Alterations of the DNA Methylation Landscape Underlie Hematopoietic Stem Cell Aging

Background: Aging is the largest risk factor for breast cancer, with 80% of new cases diagnosed in women over 50y. However, the molecular mechanism underlying age-associated cancer susceptibility is still not well understood. While aging-associated phenotypes in a number of tissues have been correlated with transcriptional and epigenetic changes, few studies have looked at epigenetic regulation at the resolution of individual cell populations. The bilayered epithelia of the mammary gland is composed of an apical layer of secretory luminal epithelial cells (LEP) surrounded by a basal layer of contractile and tumor suppressive myoepithelial cells (MEP). Breast cancer cells of origin are thought to reside mainly in the luminal or supra-basal regions directly adjacent to the apical surfaces of the MEP. Thus, an understanding of how LEP and MEP interact and maintain lineage-specific expression, and how this is dysregulated with age may elucidate a potential mechanism regulating increased breast cancer susceptibility with age. Previously, we showed that loss of lineage fidelity of LEP and MEP is a key feature of aging. Moreover, this loss of lineage fidelity can be imposed by old MEP onto young LEP in a cell non-autonomous manner (Miyano & Sayaman, et al, Aging 2017). Methods: We present a detailed analysis of genome-wide DNA methylation (Infinium Human Methylation 450K) changes at lineage-specific resolution from FACS-sorted MEP and LEP populations isolated from finite lifespan human mammary epithelial cells (HMEC) derived from reduction mammoplasties of younger (<30y) and older women (>55y). Results: In younger epithelia, maintenance of lineage fidelity is associated with lineage-specific differential methylation (DM) of CpG sites at key regulatory regions. We find that loss of lineage fidelity is recapitulated in genome-wide DNA methylation, with loss of DM at canonical proximal regions associated with transcriptional regulation, specifically annotated CpG island groups, enhancer regions, and CTCF binding sites thought to be involved in chromatin remodeling. Strikingly, DM changes with age occur almost exclusively in LEP population, with older LEP acquiring more MEP-like DNA methylation patterns at the dysregulated sites. Aged LEP and MEP also exhibit significant variability in DNA methylation at both hypo- and hypermethylated regions that show little variance in young samples. Furthermore, predictions of physiologic age using Horvath’s clock show MEP to have older physiologic ages than their isogenic LEP counterparts. Titus et al, found that DM regions (DMRs) between early stage breast tumors and normal-adjacent breast samples in The Cancer Genome Atlas (TCGA) are significantly more enriched in the LUMA, LUMB and HER2 than the Basal molecular subtypes (Sci Reports, 2017). We show that CpG sites associated with the luminal-subtype DMRs are lineage specific and that a significant fraction of the epigenetic changes that occur in these early stage breast cancers are already present during aging. Conclusions: The lineage bias of age-specific of DNA methylation changes suggests that epithelial lineages age via different mechanisms. That LEP are significantly more differentially regulated via DNA methylation with age than MEP raises possibilities that DNA methylation affects aging-associated breast cancer risk in a lineage-specific manner. This lineage bias, along with age-specific changes in breast composition, may underlie the differences in incidence rates of breast cancer subtypes with age and the prevalence of ER+ luminal-subtype breast cancers in women post-menopause. We suggest that these epigenetic changes in the luminal lineage may be priming events that make breast cells more vulnerable to further dysregulation that leads to cancer. Citation Format: Rosalyn W. Sayaman, Masaru Miyano, Mark A. LaBarge. Loss of epigenetic lineage fidelity with age primes breast epithelia for malignant transformation [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P4-04-04.

Development of the human pancreas requires the precise temporal control of gene expression via epigenetic mechanisms and the binding of key transcription factors. We quantified genome-wide patterns of DNA methylation in human fetal pancreatic samples from donors aged 6 to 21 post-conception weeks. We found dramatic changes in DNA methylation across pancreas development, with > 21% of sites characterized as developmental differentially methylated positions (dDMPs) including many annotated to genes associated with monogenic diabetes. An analysis of DNA methylation in postnatal pancreas tissue showed that the dramatic temporal changes in DNA methylation occurring in the developing pancreas are largely limited to the prenatal period. Significant differences in DNA methylation were observed between males and females at a number of autosomal sites, with a small proportion of sites showing sex-specific DNA methylation trajectories across pancreas development. Pancreas dDMPs were not distributed equally across the genome and were depleted in regulatory domains characterized by open chromatin and the binding of known pancreatic development transcription factors. Finally, we compared our pancreas dDMPs to previous findings from the human brain, identifying evidence for tissue-specific developmental changes in DNA methylation. This study represents the first systematic exploration of DNA methylation patterns during human fetal pancreas development and confirms the prenatal period as a time of major epigenomic plasticity.

Research on epigenetics has surged in the past two decades as it has become apparent that changes in gene function aside from those related to DNA mutations or natural variations may be integral factors in numerous perplexing health disorders. But much remains unknown about this relatively new field. Of the thousands of epigenetics studies published,1 a few hundred have addressed behavioral and mental health outcomes, but only a fraction of those have dealt with fetal or childhood exposures or outcomes. However, early results in the niche field of behavioral epigenetics suggest such studies could provide insights into behavioral and mental health conditions such as autism spectrum disorders (ASDs), attention deficit/hyperactivity disorder, schizophrenia, bipolar disorder, depression, and anxiety.

DNA methylation, through 5-methyl- and 5-hydroxymethylcytosine (5mC and 5hmC), is considered to be one of the principal interfaces between the genome and our environment, and it helps explain phenotypic variations in human populations. Initial reports of large differences in methylation level in genomic regulatory regions, coupled with clear gene expression data in both imprinted genes and malignant diseases, provided easily dissected molecular mechanisms for switching genes on or off. However, a more subtle process is becoming evident, where small (<10 %) changes to intermediate methylation levels are associated with complex disease phenotypes. This has resulted in two clear methylation paradigms. The latter “subtle change” paradigm is rapidly becoming the epigenetic hallmark of complex disease phenotypes, although we are currently hampered by a lack of data addressing the true biological significance and meaning of these small differences.Our initial expectation of rapidly identifying mechanisms linking environmental exposure to a disease phenotype led to numerous observational/association studies being performed. Although this expectation remains unmet, there is now a growing body of literature on specific genes, suggesting wide ranging transcriptional and translational consequences of such subtle methylation changes. Data from the glucocorticoid receptor (NR3C1) has shown that a complex interplay between DNA methylation, extensive 5′UTR splicing, and microvariability gives rise to the overall level and relative distribution of total and N-terminal protein isoforms generated. Additionally, the presence of multiple AUG translation initiation codons throughout the complete, processed mRNA enables translation variability, hereby enhancing the translational isoforms and the resulting protein isoform diversity, providing a clear link between small changes in DNA methylation and significant changes in protein isoforms and cellular locations. Methylation changes in the NR3C1 CpG island alters the NR3C1 transcription and eventually protein isoforms in the tissues, resulting in subtle but visible physiological variability.This review addresses the current pathophysiological and clinical associations of such characteristically small DNA methylation changes, the ever-growing roles of DNA methylation and the evidence available, particularly from the glucocorticoid receptor of the cascade of events initiated by such subtle methylation changes, as well as addressing the underlying question as to what represents a genuine biologically significant difference in methylation.

S-adenosylmethionine Levels Regulate the Schwann Cell DNA Methylome

Pharmacological inhibition of DNA methylation attenuates pressure overload-induced cardiac hypertrophy in rats

Hypermethylation of the ribosomal DNA coding sequence and disordered transcription factor binding as hallmarks of acute myeloid leukemia

Tobacco smoking is considered the most common reason of death and infertility around the world. This study was designed to assess the impact of tobacco heavy smoking on sperm DNA methylation patterns and to determine whether the transcription level of ALDH3B2, PTGIR, PRICKLE2, and ALS2CR12 genes is different in heavy smokers compared to non-smokers. As a screening study, the 450K array was used to assess the alteration in DNA methylation patterns between heavy smokers (n = 15) and non-smokers (n = 15). Then, four CpGs that have the highest difference in methylation level (cg16338278, cg08408433, cg05799088, and cg07227024) were selected for validation using deep bisulfite sequencing in an independent cohort of heavy smokers (n = 200) and non-smokers (n = 100). A significant variation was found between heavy smokers and non-smokers in the methylation level at all CpGs within the PRICKLE2 and ALS2CR12 gene amplicon (P < 0.001). Similarly, a significant variation was found in the methylation level at nine out of thirteen CpGs within the ALDH3B2 gene amplicon (P < 0.01). Additionally, eighteen CpGs out of the twenty-six within the PTGIR gene amplicon have a significant difference in the methylation level between heavy smokers and non-smokers (P < 0.01). The study showed a significant difference in sperm global DNA methylation, chromatin non-condensation, and DNA fragmentation (P < 0.001) between heavy smokers and non-smokers. A significant decline was shown in the transcription level of ALDH3B2, PTGIR, PRICKLE2, and ALS2CR12 genes (P < 0.001) in heavy smokers. In conclusion, heavy smoking influences DNA methylation at several CpGs, sperm global DNA methylation, and transcription level of the PRICKLE2, ALS2CR12, ALDH3B2, and PTGIR genes, which affects negatively the semen parameters of heavy smokers.

Cardiovascular disease (CVD) is a leading cause of death worldwide, and early detection and prevention are essential to reduce its burden. Although traditional risk factors such as hypertension and lipid levels are standard predictors, they tend to identify the risk of disease at a later date There is an urgent need to develop more accurate, leading-edge biomarkers indicating molecular changes that occur before the onset of clinical symptoms. Epigenetic changes, in particular DNA methylation, provide a promising approach to identify individuals at risk for CVD. Despite advances in understanding the genetic underpinnings of CVD, little is known about how dynamic epigenetic modifications influenced by environmental and lifestyle factors can serve as early predictive biomarkers the risk of the disease. This study aims to address this gap by investigating whether DNA methylation patterns can predict future CVD risk before clinical manifestations. The primary objective of this study was to systematically investigate the association between DNA methylation patterns and CVD risk. Specifically, the study seeks to identify regions where DNA methylation changes are associated with cardiovascular outcomes and investigate the predictive potential of these epigenetic changes for future disease. 1,000 participants aged 30-75 years were followed for 5 to 10 years. Periodic blood samples were collected for DNA methylation analysis by bisulfite sequencing and microarrays. Major CVD risk factors such as adiposity, hypertension and smoking status were also controlled. Comprehensive statistical models were used to assess the association between DNA methylation changes and CVD incidence. Participants who developed CVD showed significant differences in DNA methylation in regions associated with lipid metabolism (e.g., APOA5) and inflammation (e.g., TNF-α) Over time, those who developed heart disease and vascular events revealed progressive hyper methylation of key genes, with 85% sensitivity 78 to predict future CVD risk % and specificity skin. These methylation patterns were discovered years before the appearance of conventional clinical pathology. This study shows that DNA methylation patterns are determinants of acute cardiovascular risk, providing a novel approach for early detection and prevention The findings suggest the inclusion of epigenetic biomarkers in routine risk assessment about may improve the identification of individuals at high risk for CVD It is important to inform individuals at high risk of CVD of the diagnosis and to explore possible interventions that can alter change a occurs in this epigenetic and reduced CVD risk.

Genetic selection is often implicated as the underlying cause of heritable phenotypic differences between hatchery and wild populations of steelhead trout (Oncorhynchus mykiss) that also differ in lifetime fitness. Developmental plasticity, which can also affect fitness, may be mediated by epigenetic mechanisms such as DNA methylation. Our previous study identified significant differences in DNA methylation between adult hatchery- and natural-origin steelhead from the same population that could not be distinguished by DNA sequence variation. In the current study, we tested whether hatchery-rearing conditions can influence patterns of DNA methylation in steelhead with known genetic backgrounds, and assessed the stability of these changes over time. Eyed-embryos from 22 families of Methow River steelhead were split across traditional hatchery tanks or a simulated stream-rearing environment for 8 months, followed by a second year in a common hatchery tank environment. Family assignments were made using a genetic parentage analysis to account for relatedness among individuals. DNA methylation patterns were examined in the liver, a relatively homogeneous organ that regulates metabolic processes and somatic growth, of juveniles at two time points: after eight months of rearing in either a tank or stream environment and after a subsequent year of rearing in a common tank environment. Further, we analyzed DNA methylation in the sperm of mature 2-year-old males from the earlier described treatments to assess the potential of environmentally-induced changes to be passed to offspring. Hepatic DNA methylation changes in response to hatchery versus stream-rearing in yearling fish were substantial, but few persisted after a second year in the tank environment. However, the early rearing environment appeared to affect how fish responded to developmental and environmental signals during the second year since novel DNA methylation differences were identified in the livers of hatchery versus stream-reared fish after a year of common tank rearing. Furthermore, we found profound differences in DNA methylation due to age, irrespective of rearing treatment. This could be due to smoltification associated changes in liver physiology after the second year of rearing. Although few rearing-treatment effects were observed in the sperm methylome, strong family effects were observed. These data suggest limited potential for intergenerational changes, but highlight the importance of understanding the effects of kinship among studied individuals in order to properly analyze and interpret DNA methylation data in natural populations. Our work is the first to study family effects and temporal dynamics of DNA methylation patterns in response to hatchery-rearing.

Persistent organic pollutants : aberrant DNA methylation underlying potential health effects

Persistent Organic Pollutants

Effects of DNA Methylation on Progression to Interstitial Fibrosis and Tubular Atrophy in Renal Allograft Biopsies: A Multi-Omics Approach.

Otosclerosis (OTSC) is a complex bone disorder of the otic capsule, which causes conductive hearing impairment in human adults. The dysregulation of the signaling axis mediated by the receptor activator of nuclear factor-kappa-B (RANK), RANK ligand (RANKL), and osteoprotegerin has been widely attributed to the context of metabolic bone disorders. While genetic associations and epigenetic alterations in the TNFSF11 gene (RANKL) have been well-linked to metabolic bone diseases of the skeleton, particularly osteoporosis, they have never been addressed in OTSC. This study aimed to assess whether the genetic association of rs1021188 polymorphism in the upstream of TNFSF11 and the DNA methylation changes in its promoter CpG-region reveal the susceptibility of OTSC. Peripheral blood DNA samples were collected from unrelated Tunisian-North African subjects for genotyping (109 cases and 120 controls) and for DNA methylation analysis (40 cases and 40 controls). The gender-stratified analysis showed that the TNFSF11 rs1021188 C/T was associated with OTSC in men (p = 0.023), but not in women (p = 0.458). Individuals with CC genotype were more susceptible to OTSC, suggesting an increased risk to disease development. Using publicly available data, the rs1021188 was within a cluster grouping the subpopulations with African ethnicity. Moreover, 26 loci in the TNFSF11 gene were in linkage disequilibrium with rs1021188, revealing relative similarities between different populations. Significant differences in both DNA methylation and unmethylation status were detected with 4.53- and 4.83-fold decreases in the global DNA methylation levels in female and male OTSC groups, respectively. These changes could contribute to an increased risk of OTSC development. Bioinformatic analyses indicated that each of the rs1021188 variations and the DNA methylation changes in the promoter CpG-sites within TNFSF11 may play an important role in its transcription regulation. To our knowledge, this is the first study that investigates an independent effect of the rs1021188 polymorphism and DNA hypomethylation of TNFSF11 promoter in OTSC. Genetic and epigenetic changes in the regulatory regions of TNFSF11 could offer new molecular insights into the understanding of the complexity of OTSC.