DNA Methylation Processes Research Articles

DNA methylation inhibition participates in the anterograde amnesia key mechanism through the suppression of the transcription of genes involved in memory formation in grape snails

The study of the amnesia mechanisms is of both theoretical and practical importance. The mechanisms of anterograde amnesia are the least studied, due to the lack of an experimental model that allows studying this amnesia type molecular and cellular mechanisms. Previously, we found that conditional food aversion memory reconsolidation impairment in snails by NMDA glutamate receptor antagonists led to the amnesia induction, in the late stages of which (>10 days) repeated training did not cause long-term memory formation. In the same animals, long-term memory aversion to a new food type was formed. We characterized this amnesia as specific anterograde amnesia. In the present work we studied the role of epigenetic DNA methylation processes as well as protein and mRNA synthesis in the mechanisms of anterograde amnesia and memory recovery. DNMT methyltransferase inhibitors (iDNMT: zebularine, RG108 (N-Phthalyl-1-tryptophan), and 5-AZA (5-Aza-2'-deoxycytidine)) were used to alter DNA methylation. It was found that in amnesic animals the iDNMT administration before or after shortened repeated training led to the rapid long-term conditional food aversion formation (Ebbinghaus saving effect). This result suggests that amnestic animals retain a latent memory, which is the basis for accelerated memory formation during repeated training. Protein synthesis inhibitors administration (cycloheximide) before or immediately after repeated training or administration of RNA synthesis inhibitor (actinomycin D) after repeated training prevented memory formation under iDNMT action. The earlier protein synthesis inhibitor effect suggests that the proteins required for memory formation are translated from the pre-existing, translationally repressed mRNAs. Thus, we have shown for the first time that the anterograde amnesia key mechanism is DNMT-dependent suppression of the transcription of genes involved in memory mechanisms. Inhibition of DNMT during repeated training reversed these genes expression blockade, opening access to them by transcription factors synthesized during training from the pre-existing mRNAs.

Methylenetetrahydrofolate reductase (MTHFR) 677C>T polymorphisms in breast cancer: A Filipino preliminary case-control study

Single nucleotide polymorphisms (SNP) present in folate metabolic enzymes, such as methylenetetrahydrofolate reductase (MTHFR), affect DNA synthesis and methylation processes that can lead to cancer development. Several studies suggest that MTHFR SNP is associated with breast cancer risk, particularly among Asian populations. Thus, this study determined the association of MTHFR 677C>T SNP with breast cancer risk in selected Filipino population. DNA samples from breast cancer cases (n = 100) and clinically healthy controls (n = 100) were analyzed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). The differences in MTHFR genotype and allele frequencies were evaluated by computing for the odds ratio (OR) with a 95 % confidence interval (CI). The CT genotype (OR: 0.775, 95 % CI: 0.35–1.71, p = 0.53), T allele (OR: 0.703, 95 % CI: 0.34–1.48, p = 0.35), and presence of at least one T allele (ORCT+TT: 0.729, 95 % CI: 0.33–1.60, p = 0.43) were not associated with breast cancer risk. Based on the SNP interaction with other risk factors, no significant difference (p > 0.05) was observed for the tumor characteristics, menarche age, and menopause age. Interestingly, a decreased risk (OR: 0.342, 95 % CI: 0.14–0.84, p = 0.019) was observed for the CC genotype in individuals who consumed dietary fibers. Meanwhile, there was an increased risk for passive smokers with the CC genotype (OR: 6.31, 95 % CI: 2.68–14.9, p < 0.001). Overall, the MTHFR 677C>T was not significantly associated with breast cancer risk in a selected Filipino population. Since this study involved a relatively small number of participants, increasing the number of samples is recommended for a more conclusive test of association of MTHFR 677C>T with breast cancer risk in Filipinos.

DNA methylation dynamics and dysregulation delineated by high-throughput profiling in the mouse

SUMMARYWe have developed a mouse DNA methylation array that contains 296,070 probes representing the diversity of mouse DNA methylation biology. We present a mouse methylation atlas as a rich reference resource of 1,239 DNA samples encompassing distinct tissues, strains, ages, sexes, and pathologies. We describe applications for comparative epigenomics, genomic imprinting, epigenetic inhibitors, patient-derived xenograft assessment, backcross tracing, and epigenetic clocks. We dissect DNA methylation processes associated with differentiation, aging, and tumorigenesis. Notably, we find that tissue-specific methylation signatures localize to binding sites for transcription factors controlling the corresponding tissue development. Age-associated hypermethylation is enriched at regions of Polycomb repression, while hypomethylation is enhanced at regions bound by cohesin complex members. ApcMin/+ polyp-associated hypermethylation affects enhancers regulating intestinal differentiation, while hypomethylation targets AP-1 binding sites. This Infinium Mouse Methylation BeadChip (version MM285) is widely accessible to the research community and will accelerate high-sample-throughput studies in this important model organism.

Abstract 3738: Monitoring chemotherapy response status of colorectal cancer patients using liquid biopsy samples

Abstract Background and aims: The early detection of colorectal cancer (CRC) recurrence and the monitoring of therapeutic response are crucial steps in the determination and modification of treatment strategies. The currently used gold standard tumor markers such as CEA and CA 19-9 and the different imaging techniques have several limitations in many cases. Therefore, we aimed to establish a liquid biopsy-based approach for tracking tumor dynamics in post-operative non-metastatic (n=32) and metastatic (n=23) CRC patients. Methods: Blood samples were collected from each patient before and during chemotherapy, and finally, patients were classified according to disease outcome. Longitudinal investigations of the total amount, global and local (SFRP2 and SDC2 genes) DNA methylation pattern of cell-free DNA (cfDNA) fraction were performed. The plasma concentration of homocysteine was also determined, as it is one of the main components of the DNA methylation process, and its level defines the methylation potential. We examined how the parameters mentioned above were affected depending on the different therapy responses. Results: The average cfDNA amount was significantly higher (p&amp;lt;0.05) in patients with recurrent cancer (30.4±17.6ng) and progressive disease (PD) (44.3±34.5ng) than individuals who achieved remission (REM) (13.2±10.0ng). More than 10% elevation of cfDNA from first to last sample collection was detected in 92% of PD patients, while reduced cfDNA concentration was observed in 67% of the non-metastatic CRC patients with REM. An effective differentiation was detected between patients achieving remission and showing tumor progression based on cfDNA level with 94% sensitivity and 81% specificity. The average global cfDNA methylation was determined by bisulfite pyrosequencing analysis of long interspersed nuclear element-1 (LINE-1), and it was significantly lower (p&amp;lt;0.05) in the PD group compared to people with remission (71.0±6.7% vs. 78.9±2.0%). Methylation level changes between the study beginning and end indicated a decline (75.5±3.4% vs. 68.2±8.4%) in PD; in contrast, we found a reverse change in remission. The mean relative change of homocysteine concentration revealed an opposite trend with the global DNA methylation suggesting a linkage between these parameters, as it showed an increase (+12.5%) in the case of PD and a decrease (-15.8%) in patients with REM. Regarding local DNA methylation, SFRP2 and SDC2 genes revealed higher promoter hypermethylation in the PD set compared to patients with remission. Conclusion: Our study offers the possibility to monitor the therapeutic response during chemotherapy with a minimally-invasive blood-based method that combines the analysis of cfDNA, its global and local DNA methylation pattern, and homocysteine level. Citation Format: Barbara Kinga Bartak, Tamás Fodor, Alexandra Kalmár, Zsófia Brigitta Nagy, Sára Zsigrai, Krisztina Andrea Szigeti, William Kothalawala, Gábor Valcz, Péter Igaz, István Takács, Magdolna Dank, Béla Molnár. Monitoring chemotherapy response status of colorectal cancer patients using liquid biopsy samples [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3738.

Dietary phytochemicals/nutrients as promising protector of breast cancer development: a comprehensive analysis.

Genetic change, particularly epigenetic alteration, is one of the imperative factors for sporadic breast cancer development in the worldwide population of women. The DNA methylation process is essential and natural for human cellular renewal and tissue homeostasis, but its dysregulation contributes to many pathological changes, including breast tumorigenesis. Chemopreventive agents mainly protect the abnormal DNA methylation either by hindering the division of pre-malignant cells or looming the DNA damage, which leads to malignancy. The present review article is about understanding the potential role of dietary phytochemicals in breast cancer prevention. Accordingly, a literature search of the published article until August 2021 has been performed. Further, we have investigated the binding affinity of different phytochemicals isolated from diverse dietary sources against the various oncogenic proteins related to breast cancer initiation to understand the common target(s) in breast cancer prevention mechanisms. Various small phytochemicals, especially dietary phytochemicals including sulforaphane, mahanine, resveratrol, linolenic acid, diallyl sulfide, benzyl/phenethyl isothiocyanate, etc. are being investigated as the chemopreventive agent to manage breast cancer development, and some of them have shown promising outcomes in the cited research. In this present review, we discuss the recent advancement in acceptance of such types of potential dietary phytochemicals as a chemopreventive agent against breast cancer development and their inner lining mechanism. The critical clinical trials and cohort studies have also been considered to understand the progress in contemporary perspectives.

Homocysteine-Induced Disturbances in DNA Methylation Contribute to Development of Stress-Associated Cognitive Decline in Rats.

Chronic stress is generally accepted as the main risk factor in the development of cognitive decline; however, the underlying mechanisms remain unclear. Previous data have demonstrated that the levels of homocysteine (Hcy) are significantly elevated in the plasma of stressed animals, which suggests that Hcy is associated with stress and cognitive decline. To test this hypothesis, we analyzed the cognitive function, plasma concentrations of Hcy, and brain-derived neurotropic factor (BDNF) levels in rats undergoing chronic unpredicted mild stress (CUMS). The results showed that decreased cognitive behavioral performance and decreased BDNF transcription and protein expression were correlated with hyperhomocysteinemia (HHcy) levels in stressed rats. Diet-induced HHcy mimicked the cognitive decline and BDNF downregulation in the same manner as CUMS, while Hcy reduction (by means of vitamin B complex supplements) alleviated the cognitive deficits and BDNF reduction in CUMS rats. Furthermore, we also found that both stress and HHcy disturbed the DNA methylation process in the brain and induced DNA hypermethylation in the BDNF promoter. In contrast, control of Hcy blocked BDNF promoter methylation and upregulated BDNF levels in the brain. These results imply the possibility of a causal role of Hcy in stress-induced cognitive decline. We also used ten-eleven translocation (TET1), an enzyme that induces DNA demethylation, to verify the involvement of Hcy and DNA methylation in the regulation of BDNF expression and the development of stress-related cognitive decline. The data showed that TET1-expressing viral injection into the hippocampus inhibited BDNF promoter methylation and significantly mitigated the cognitive decline in HHcy rats. Taken together, novel evidence from the present study suggests that Hcy is likely involved in chronic stress-induced BDNF reduction and related cognitive deficits. In addition, the negative side-effects of HHcy may be associated with Hcy-induced DNA hypermethylation in the BDNF promoter. The results also suggest the possibility of Hcy as a target for therapy and the potential value of vitamin B intake in preventing stress-induced cognitive decline.

M6A echoes with DNA methylation: Coordinated DNA methylation and gene expression data analysis identified critical m6A genes associated with asthma

Asthma is a chronic inflammatory disease that involves complex gene-environment interactions. Methylation of nucleotides, such as 5-methylcytosine (5mC) in DNA and N6-methyladenosine (m6A) in mRNA, carries important information for gene regulation. Our study screened m6A genes and genes associated with asthma from the Gene Expression Omnibus (GEO) databases GSE63383, GSE119580, GSE38003, GSE34313, GSE13168, and GSE35643. GSE52778, GSE35643, GSE40996, and GSE64744), and DNA methylation data from GSE85568 and GSE146377. We screened out 6 m6A related genes (FTO, IGF2BP2, RBM15, RBMX, WTAP, and YTHDC1) that were significantly dysregulated in asthma or proinflammatory conditions. A correlation study showed a high correlation between m6A genes and gene pairs such as WTAP, IL7R, and TLR2; RBMX, SLC22A4, IL33, TNC, FLG, and IL6R (|r| ≥ 0.8). Following DNA methylation dataset analysis, we proposed several DNA methylation-m6A modification asthma-related gene axes such as cg19032951/cg15153914-IGF2BP2-SMAD3. Interestingly, several target genes, such as SMAD3, possess the ability to participate in DNA methylation processes, which may reciprocally regulate the expression of m6A genes and form a closed-loop regulation axis. Some classic DNA methylation-related genes, such as TET1, UHRF1, and ZBTB4, were also involved. We identified an integrated profile of m6A gene expression in asthma and proposed a novel potential interplay between DNA methylation and m6A modification in asthma pathogenesis. Using the CMAP database, we found that resveratrol may target these dysregulated m6A genes, and therefore may serve as a potential therapeutic agent for asthma.

DNMT3B System Dysregulation Contributes to the Hypomethylated State in Ischaemic Human Hearts.

A controversial understanding of the state of the DNA methylation machinery exists in ischaemic cardiomyopathy (ICM). Moreover, its relationship to other epigenetic alterations is incomplete. Therefore, we carried out an in-depth study of the DNA methylation process in human cardiac tissue. We showed a dysregulation of the DNA methylation machinery accordingly with the genome-wide hypomethylation that we observed: specifically, an overexpression of main genes involved in the elimination of methyl groups (TET1, SMUG1), and underexpression of molecules implicated in the maintenance of methylation (MBD2, UHRF1). By contrast, we found DNMT3B upregulation, a key molecule in the addition of methyl residues in DNA, and an underexpression of miR-133a-3p, an inhibitor of DNMT3B transcription. However, we found many relevant alterations that would counteract the upregulation observed, such as the overexpression of TRAF6, responsible for Dnmt3b degradation. Furthermore, we showed that molecules regulating Dnmts activity were altered; specifically, SAM/SAH ratio reduction. All these results are in concordance with the Dnmts normal function that we show. Our analysis revealed genome-wide hypomethylation along with dysregulation in the mechanisms of addition, elimination and maintenance of methyl groups in the DNA of ICM. We describe relevant alterations in the DNMT3B system, which promote a normal Dnmt3b function despite its upregulation.

Short-Term Hypothermic Holding of Mouse Immature Testicular Tissue Does Not Alter the Expression of DNA Methyltransferases and Global DNA Methylation Level, Post-Organotypic Culture.

IntroductionCryopreservation of immature-testicular-tissue (ITT) prior to gonadotoxic treatment, while experimental, is the only recommended option for fertility preservation in prepubertal boys. The handling and manipulation of ITT prior to banking could influence the functionality, genetic and epigenetic integrity of cells.ObjectivesTo investigate the impact of length of hypothermic holding of mouse ITT on the relative mRNA expression of the DNA methyltransferases (DNMTs) and global DNA methylation, post 14-days of organotypic culture.MethodsITT from 6-day old mice were handled at hypothermic temperature (4 °C) for 6 and 24 h prior to 14-days organotypic culture. Relative mRNA expression of Dnmt1, Dnmt3a, and Dnmt3b along with global DNA methylation was measured from the cultured ITT.ResultsNo significant variation in the expression of Dnmt1, Dnmt3a, and Dnmt3b was observed in relation to varying holding time periods used. Further, global DNA methylation was comparable between 0, 6 and 24 h holding groups.ConclusionsShort-term holding of ITT at 4 °C does not affect the DNA methylation process post organotypic culture. While fully acknowledging the limitations of this approach in the mouse model, the results we presented in this report will be of significant interest to the field.

The study of expression levels of DNA methylation regulators in patients affected with congenital heart defects (CHDs).

Congenial heart defects (CHDs) have multifactorial etiology with complex interplay of genetic and environmental factors. Environmental impact can have epigenetic mechanism of CHD development. Many studies have reported the causal association between CHD and distinct DNA methylation profile which is one of the key epigenetic events, which has vital role in normal embryonic development. The products of DNMT1, DNMT3A, DNMT3B, and MBD2 are important regulators of DNA methylation process. Changes in the expression of these genes are implicated in congenital structural cardiac defects. Hence, in this proof-of-concept study, we have compared the expression levels of these genes in the blood samples of healthy controls and CHD cases while investigating the etiology of CHD. In this study with 48 CHD cases and 47 healthy controls, total RNA was isolated from the whole blood samples using TRI reagent. Quantitative RT PCR (qRT-PCR) was used to analyze the mRNA levels of DNMT1, DNMT3A, DNMT3B, and MBD2. The expression levels have been analyzed by relative quantification. We observed that DNMT3B (fold change=-2.563; p=.0018) and DNMT3A (fold change=-2.169; p=.05) were significantly downregulated in CHD patients, whereas the expression of DNMT1 and MBD2 was not significantly different between cases and controls. Lower expression of de novo methyltransferases, namely, DNMT3B and DNMT3A in CHD cases, may be an important contributor to the mechanism of CHD pathogenesis. Further studies with age-matched controls and analysis of global DNA methylation profile are required to investigate the proposed causal association.

A Broad Survey of Gene Body and Repeat Methylation in Cnidaria Reveals a Complex Evolutionary History.

DNA methylation, an important component of eukaryotic epigenetics, varies in pattern and function across Metazoa. Notably, bilaterian vertebrates and invertebrates differ dramatically in gene body methylation (GbM). Using the frequency of cytosine-phospho-guanines (CpGs), which are lost through mutation when methylated, we report the first broad survey of DNA methylation in Cnidaria, the ancient sister group to Bilateria. We find that: 1) GbM differentially relates to expression categories as it does in most bilaterian invertebrates, but distributions of GbM are less discretely bimodal. 2) Cnidarians generally have lower CpG frequencies on gene bodies than bilaterian invertebrates potentially suggesting a compensatory mechanism to replace CpG lost to mutation in Bilateria that is lacking in Cnidaria. 3) GbM patterns show some consistency within taxonomic groups such as the Scleractinian corals; however, GbM patterns variation across a range of taxonomic ranks in Cnidaria suggests active evolutionary change in GbM within Cnidaria. 4) Some but not all GbM variation is associated with life history change and genome expansion, whereas GbM loss is evident in endoparasitic cnidarians. 5) Cnidarian repetitive elements are less methylated than gene bodies, and methylation of both correlate with genome repeat content. 6) These observations reinforce claims that GbM evolved in stem Metazoa. Thus, this work supports overlap between DNA methylation processes in Cnidaria and Bilateria, provides a framework to compare methylation within and between Cnidaria and Bilateria, and demonstrates the previously unknown rapid evolution of cnidarian methylation.

An Update in Epigenetics in Metabolic-Associated Fatty Liver Disease.

Metabolic-associated fatty liver disease (MAFLD) is characterized by hepatic steatosis accompanied by one of three features: overweight or obesity, T2DM, or lean or normal weight with evidence of metabolic dysregulation. It is distinguished by excessive fat accumulation in hepatocytes, and a decrease in the liver's ability to oxidize fats, the accumulation of ectopic fat, and the activation of proinflammatory pathways. Chronic damage will keep this pathophysiologic cycle active causing progression from hepatic steatosis to cirrhosis and eventually, hepatocarcinoma. Epigenetics affecting gene expression without altering DNA sequence allows us to study MAFLD pathophysiology from a different perspective, in which DNA methylation processes, histone modifications, and miRNAs expression have been closely associated with MAFLD progression. However, these considerations also faced us with the circumstance that modifying those epigenetics patterns might lead to MAFLD regression. Currently, epigenetics is an area of great interest because it could provide new insights in therapeutic targets and non-invasive biomarkers. This review comprises an update on the role of epigenetic patterns, as well as innovative therapeutic targets and biomarkers in MAFLD.

Trisomy 21 and Assisted Reproductive Technologies: A review.

Trisomy 21 is the most common genetic disorder seen among infants, and it causes spontaneous abortions, abnormal neural development and other pathologies associated with newborn development. In newborns with this trisomy, 90-95% have full trisomy, 1.4-1.9% have mosaicism, and 1-4.7% have translocations. The principal cause of trisomy 21 is advanced maternal age, in which recombination errors may occur during fetal development, age-related accumulation of damaged DNA, cohesin degradation producing the premature loss of chromosomes or sister chromatids, and alterations during the spindle formation process. The paternal age has also an effect on trisomy 21, specifically during male aging, when there is higher risk of chromosomal breaking in spermatozoa. Epigenetics is also an important risk factor of trisomy 21 through changes in the DNA methylation process, histone modification and non-coding RNAs. Assisted reproductive technologies (ART) have emerged in recent years as a safe alternative for couples with fertility problems. These techniques, which include controlled ovarian stimulation (COS), in vitro fertilization (IVF), intracytoplasmic sperm injection (ICSI) and vitrification, decrease the incidence of aneuploidy in human preimplantation embryos, and are widely used. The following study aims to review and discuss the available literature on trisomy 21 in the field of assisted human reproduction.

Methylenetetrahydrofolate reductase C677T polymorphism across acute leukemia

Background Methylenetetrahydrofolate reductase (MTHFR) is the key enzyme for folate metabolism and also plays a role in DNA biosynthesis and the epigenetic process of DNA methylation. MTHFR gene polymorphisms, mainly the C677T, have been implicated as risk factors for several types of cancers such as the acute leukemia (AL). Main body of the abstract This study was conducted to examine the extent of the association between MTHFR C677T polymorphism and AL across a comprehensive literature of meta-analysis. Relevant English-language literature was searched and retrieved from PubMed using the terms MTHFR, the C677T polymorphism, and AL. Several parameters have been studied in the assessment of correlation between AL and the MTHFR polymorphism, such as folate intake, ethnicity, age, and sex. Nevertheless, the results are contrasting. Short conclusion Comprehensive analysis of MTHFR C677T in AL may be helpful and provide new insights for a personalized therapy based on the human genotype.

Early life adversity and age acceleration at mid-life and older ages indexed using the next-generation GrimAge and Pace of Aging epigenetic clocks

ObjectiveThis retrospective cross-sectional study was designed to explore whether the experience of childhood adversity was associated with epigenetic age acceleration in mid-life and older ages using the next generation GrimAge and Pace of Aging DNA methylation clocks. MethodThe study involved a sub-sample of 490 individuals aged 50–87 years of age participating in the Irish Longitudinal Study on Aging (TILDA); a large nationally representative prospective cohort study of aging in Ireland. Childhood adversity was ascertained via self-report using 5-items that were deemed to indicate potentially nefarious childhood exposures, including growing up poor, death of a parent, parental substance abuse in the family, childhood physical abuse, and childhood sexual abuse. ResultsOnly childhood poverty was associated with significant epigenetic age acceleration according to the GrimAge and Pace of Aging clocks, hastening biological aging by 2.04 years [CI= 1.07, 3.00; p < 0.001] and 1.16 years [CI= 0.11, 2.21; p = 0.030] respectively. Analysis of the dose-response pattern revealed each additional adversity was associated with 0.69 years of age acceleration [CI= 0.23, 1.15; p = 0.004] according to the GrimAge clock. Mediation analysis suggested that lifetime smoking explains a substantial portion (>50%) of the excess risk of age acceleration amongst those who experienced childhood poverty. ConclusionsThis study adds to the growing body of evidence which implicates early life adversity, particularly deprivation as a potential precipitant of earlier biological aging, and implicates smoking-related changes to DNA methylation processes as a candidate pathway and mechanism through which the social environment gets transduced at a biological level to hasten the aging process.

Influence of Benzo(a)pyrene on Different Epigenetic Processes.

Epigenetic changes constitute one of the processes that is involved in the mechanisms of carcinogenicity. They include dysregulation of DNA methylation processes, disruption of post-translational patterns of histone modifications, and changes in the composition and/or organization of chromatin. Benzo(a)pyrene (BaP) influences DNA methylation and, depending on its concentrations, as well as the type of cell, tissue and organism it causes hypomethylation or hypermethylation. Moreover, the exposure to polyaromatic hydrocarbons (PAHs), including BaP in tobacco smoke results in an altered methylation status of the offsprings. Researches have indicated a potential relationship between toxicity of BaP and deregulation of the biotin homeostasis pathway that plays an important role in the process of carcinogenesis. Animal studies have shown that parental-induced BaP toxicity can be passed on to the F1 generation as studied on marine medaka (Oryzias melastigma), and the underlying mechanism is likely related to a disturbance in the circadian rhythm. In addition, ancestral exposure of fish to BaP may cause intergenerational osteotoxicity in non-exposed F3 offsprings. Epidemiological studies of lung cancer have indicated that exposure to BaP is associated with changes in methylation levels at 15 CpG; therefore, changes in DNA methylation may be considered as potential mediators of BaP-induced lung cancer. The mechanism of epigenetic changes induced by BaP are mainly due to the formation of CpG-BPDE adducts, between metabolite of BaP—BPDE and CpG, which leads to changes in the level of 5-methylcytosine. BaP also acts through inhibition of DNA methyltransferases activity, as well as by increasing histone deacetylases HDACs, i.e., HDAC2 and HDAC3 activity. The aim of this review is to discuss the mechanism of the epigenetic action of BaP on the basis of the latest publications.

Methylation quantitative locus rs3758653 in the DRD4 gene is associated with duration from first heroin exposure to addiction

Opioid addiction is a chronic brain disease with a high heritability. However, the genetic underpinnings remain uncertain. DNA methylation is involved in the adaptive changes in neuroplasticity after prolonged drug use. The dopamine receptor D4 (DRD4) has an essential role in the reward processes associated with addictive drugs. To further elucidate the potential role and mechanism of the DRD4 gene variants in heroin addiction, we detected the methylation level of 46 CpG sites in the promoter region and the genotypes of three SNPs in the DRD4 gene. Correlations between the SNPs and methylation levels of the CpG sites, i.e., the analysis of methylation quantitative trait loci (mQTLs) was conducted. Following the identification of mQTLs that are unique in the heroin addiction group, we performed an association study between the mQTLs and traits of heroin addiction. Our results revealed that there were several correlations of SNPs rs3758653 and rs11246226 with the methylation levels of some CpG sites in the DRD4 gene. Among these SNP-CpG pairs, rs3758653-DRD4_04, rs3758653-DRD4_05, rs3758653-DRD4_13 and rs3758653-DRD4_03 were unique in the heroin addiction group. Moreover, we found that mQTL rs3758653 was associated with duration from first heroin exposure to addiction, and the expression level of the DRD4 gene in human brain regions of the frontal cortex and hippocampus. Our findings suggested that some mQTLs in the genome may be associated with traits of opioid addiction through implicating the processes of DNA methylation and gene expression.

Clinicopathological implications of lncRNAs, immunotherapy and DNA methylation in lung squamous cell carcinoma: a narrative review

ObjectiveTo explore the clinicopathological impact of lncRNAs, immunotherapy, and DNA methylation in lung squamous cell carcinoma (LUSC), emphasizing their exact roles in carcinogenesis and modes of action.BackgroundLUSC is the second most prevalent form, accounting for around 30% of non-small cell lung cancer (NSCLC). To date, molecular-targeted treatments have significantly improved overall survival in lung adenocarcinoma patients but have had little effect on LUSC therapy. As a result, there is an urgent need to discover new treatments for LUSC that are based on existing genomic methods.MethodsIn this review, we summarized and analyzed recent research on the biological activities and processes of lncRNA, immunotherapy, and DNA methylation in the formation of LUSC. The relevant studies were retrieved using a thorough search of Pubmed, Web of Science, Science Direct, Google Scholar, and the university’s online library, among other sources.ConclusionsLncRNAs are the primary components of the mammalian transcriptome and are emerging as master regulators of a number of cellular processes, including the cell cycle, differentiation, apoptosis, and growth, and are implicated in the pathogenesis of a variety of cancers, including LUSC. Understanding their role in LUSC in detail may help develop innovative treatment methods and tactics for LUSC. Meanwhile, immunotherapy has transformed the LUSC treatment and is now considered the new standard of care. To get a better knowledge of LUSC biology, it is critical to develop superior modeling systems. Preclinical models, particularly those that resemble human illness by preserving the tumor immune environment, are essential for studying cancer progression and evaluating novel treatment targets. DNA methylation, similarly, is a component of epigenetic alterations that regulate cellular function and contribute to cancer development. By methylating the promoter regions of tumor suppressor genes, abnormal DNA methylation silences their expression. DNA methylation indicators are critical in the early detection of lung cancer, predicting therapy efficacy, and tracking treatment resistance. As such, this review seeks to explore the clinicopathological impact of lncRNAs, immunotherapy, and DNA methylation in LUSC, emphasizing their exact roles in carcinogenesis and modes of action.

Embryo culture media differentially alter DNA methylating enzymes and global DNA methylation in embryos and oocytes.

The effects of culture media on DNA methylation process, which is one of the epigenetic mechanisms, have not been clearly elucidated although it is known that in vitro culture conditions alter epigenetic mechanisms. This study was designed to address the question: does embryo culture media approach, sequential or single step, differentially affect DNA methylating enzymes and global DNA methylation. Mouse zygotes were cultured either in single step or sequential culture media until the blastocyst stage and in vivo developed blastocyst were utilized as control. Similarly, GV stage oocytes were in vitro matured either in single step or first step of sequential culture media. In vivo matured MII oocytes were used as control. The expression levels and cellular localization of Dnmt1 and 3a enzymes were analyzed by immunofluorescence and western blot analysis while global DNA methylation was evaluated by immunofluorescence. We found that signal intensities of Dnmt1 and Dnmt3a enzymes were significantly low in embryos or oocytes cultured in sequential media compared to single step media and control, which were comparable amongst themself. Similarly, global DNA methylation level in single step media and control groups was comparable but both was higher than the sequential media. This study demonstrated that composition of culture media may differentially affect DNA methylation levels in mouse embryos and oocytes. Since abnormal DNA methylation may cause aberrant oocyte or embryo development, we think that further studies are needed to test human embryos and oocyte, and to explain molecular mechanisms.

Common mechanisms cannot explain time- and dose-dependent DNA methylation changes in earthworms exposed to cadmium

DNA hypermethylation caused by environmental pollutants like cadmium (Cd) has already been demonstrated in many invertebrates, including earthworms. However, the exact epigenetic mechanisms that drive this hypermethylation are largely unknown and even basic DNA methylation and demethylation processes are hardly characterized. Therefore, we used an important bioindicator, the earthworm Lumbricus terrestris, as a model organism to determine time- and dose-dependent effects of Cd on global and gene-specific DNA methylation and its underlying mechanisms. We revealed Cd-induced adenine and cytosine hypermethylation using specific antibodies in dot blots and found that the methylation level of adenine compared to cytosine changed even to a bigger extent. However, the levels of hydroxymethylated cytosine did not differ between treatment groups. General methylation and demethylation components like methyltransferases (DNMT1 and 3), and ten-eleven translocation (TET) genes were confirmed in L. terrestris by quantitative RealTime PCR. However, neither gene expression, nor DNMT and TET enzyme activity showed significant differences in the Cd exposure groups. Using bisulfite conversion and sequencing, gene body methylation (gbm) of metallothionein 2 (MT2), one of the most important detoxification proteins, was characterized. Cd-dependent changes in MT2 gbm could, however, not be correlated to MT2 gene activity evaluated by quantitative RealTime PCR.Future directions as well as missing links are discussed in the present study hinting towards the importance of studying epigenetic marks and mechanistic insights in a broad variety of species to deepen our knowledge on the effects of changing environmental conditions.