Methylation Pattern In Promoter Region Research Articles

Exploring the role of epigenetics in periodontal disease progression: A narrative review

Periodontal disease remains a significant global health concern, characterized by chronic inflammation and destruction of the tooth-supporting structures. While microbial dysbiosis is a well-established factor in its pathogenesis, emerging evidence suggests that epigenetic modifications play a crucial role in the initiation and progression of periodontal disease. This narrative review aims to synthesize current knowledge on the intricate interplay between epigenetics and periodontal disease progression. Epigenetic mechanisms, including DNA methylation, histone modifications, and non-coding RNAs, regulate gene expression patterns without altering the underlying DNA sequence. Dysregulation of these mechanisms can disrupt inflammatory and immune responses, exacerbating periodontal tissue damage. Various studies have highlighted specific epigenetic alterations associated with periodontal disease, such as aberrant DNA methylation patterns in promoter regions of key inflammatory genes and dysregulated microRNA expression profiles implicated in tissue remodeling processes. Moreover, environmental factors, such as smoking, diet, and stress, can modulate epigenetic signatures, further influencing periodontal disease susceptibility and severity. Understanding the epigenetic landscape of periodontal disease offers new avenues for therapeutic interventions and personalized treatment strategies. Targeting epigenetic regulators may provide innovative approaches to mitigate inflammation, promote tissue regeneration, and ultimately improve clinical outcomes in patients with periodontal disease. In conclusion, epigenetics plays a significant role in periodontal disease progression by regulating inflammatory and tissue remodeling pathways. Future research should continue to elucidate the complex epigenetic mechanisms underlying periodontal disease pathogenesis, paving the way for novel therapeutic interventions and personalized management strategies.

The DNA methylation of the interleukin6 as a biomarker for the early detection of colorectal cancer

Objectives: To identify the DNA methylation pattern of the interleukin6 promoter region in colorectal cancer patients and colorectal polys patients that could be a biomarker for early detection of colorectal cancer.
 Methods: For this purpose, we examined the DNA methylation pattern of the promoter region of the IL6 specifically 358 bp (-292 to +67) including 7 CpG sites (-228, -213, -163, -119, +10, +19, +25) in a total of ninety samples with thirty samples each for controls, cancer patients, and colorectal polyps using the bisulfite conversion sequencing method.
 Result: Our results indicate that CpG +25 and CpG -119 can serve as biomarkers for early detection of colon cancer, showing a significant difference in P-values of 0.001 at CpG +25 and 0.004 at CpG-119. The hypomethylation of CpG -119 in cancer groups facilitates the binding of the methyl-sensitive transcription factor Sp1. It enhances the overexpression of IL6 besides hypermethylation of CpG +25 that prevents binding of the methyl-sensitive insulator CTF, unbinding the insulator to the promoter region of the cancer samples makes the promoter region open access to the TFs that enhances overexpression. Furthermore, a remarkable non-recorded SNP at CpG -228 was observed in 98.6% of the enrolled groups.
 Conclusion: In the state of DNA methylation, IL 6 could contribute to the onset of colorectal polyps and colorectal polyps cancer due to a significant level of methylation in CpG +25 and CpG -119.

CTLA4 Methylation and its Expression as a Prognostic Biomarker in Tobacco Users with and without Oral Squamous Cell CarcinomaA Protocol for Cross-sectional Study

Introduction: Oral Squamous Cell Carcinoma (OSCC) is characterised by immunosuppression mediated by evasion of ‘immune checkpoints’ by tumour cells. Cytotoxic T Lymphocyte Associated Protein 4 (CTLA4) is one of the immune checkpoint molecule whose role in oral carcinogenesis remains to be elucidated. Deoxyribonucleic Acid (DNA) methylation of CTLA4 promoter region holds potential as a biomarker for diagnosis and assessment of individuals at risk of developing OSCC. Need for the study: Immunotherapy is an emerging treatment modality in some cancers. Thus, better understanding of role of CTLA4 methylation in OSCC paves a way for newer strategies in immunotherapeutic. Aim: To assess the DNA methylation pattern of promoter region of CTLA4 gene and evaluate its expression in tobacco users with and without OSCC so that it can contribute as biomarker for diagnosis and prognosis of OSCC. Materials and Methods: The proposed longitudinal crosssectional study will be conducted at Sharad Pawar Dental College and Hospital, Maharashtra, India. It will evaluate promoter methylation and protein expression of CTLA4 gene in Smokeless Tobacco (SLT) users. There will be three groups: group A OSCC patients; group B normal individuals with SLT habit without any oral lesion; and group C normal individuals without SLT habit. Formalin Fixed Paraffin Embedded (FFPE) tissue blocks will be prepared from the biopsy obtained from total thirty nine participants. DNA methylation of CTLA4 promoter will be assessed using Methylation-Specific PCR (MS-PCR). In addition, the quantitative expression of CTLA4 will also be assessed using Immunohistochemistry (IHC).

Promoter Hypermethylation Analysis of the Tumor Suppressor Genes RASSF1A and RASSF2A in Iranian Endometrial Carcinoma Patients

Introduction: The endometrial cancer (EC) is the seventh most common malignancies worldwide among females with good prognosis in early stages of the disease. The CpG Island in the promoter region of tumor-suppressor genes are frequently methylated in various types of human cancers. In the present study, we investigated the methylation pattern in promoter region of RASSF1A and RASSF2A genes in Endometrial cancer patients in Iranian women to identify correlations among promoter hypermethylation, disease risk and clinicopathological parameters. Methods: 28 patients and 22 healthy controls were studied. Isolation of genomic DNA from FFPE and peripheral blood was performed and Methylation-Specific PCR (MSP) was applied for analysis of the promoter CpG methylation status of RASSF1A and RASSF2A genes in the studied population. Results: A significant difference was found among the study groups and the presence of promoter CpG hypermethylation status in the RASSF1A (P = 0.0321) and RASSF2A (P = 0.0003) genes. RASSF1A, and RASSF2A gene promoter methylations were present in 53.57% and 42.85% of EC samples when compared to those in the controls with 31.81% and 9.09% respectively. Furthermore, methylation status between tissue and blood samples of RASSF1A, and RASSF2A genes was not significant (P = 0.49 and 0.09 respectively). Our results indicated a corollation between ages, menosososal state and tumor grade with RASSF1A, and RASSF2A promoter methylation. Conclusions: In our study, Hypermethylation of both RASSF1A and RASSF2A genes are important events in carcinogenesis of endometrial cancer. Epigenetic alternations may have diagnostic value for early diagnosis and better clicinal management of susceptibility to endometrial malignancies.

Epigenetic and risk factors of testicular germ cell tumors: a brief review.

Testicular germ cell cancer (TGCT) is the most common malignancy among young adult males, which has become important due to its increased incidence and mortality in the population worldwide. The etiology is multifactorial. Recent studies have shown some associations between the development of isolated TGCT and certain risk factors, such as exposure to endocrine disruptors, cryptorchidism, and family history of cancer, in order to identify the key pieces in carcinogenesis. Some of the most important findings in recent years is the association of different genes, such as c-KIT/KITLG, expression of the miR-371-373 cluster and protein expression as c-KIT and POU5F1 in the development of this neoplasia, and the identification of new molecular markers as TGFBR3 gene, identifying aberrant methylation patterns in promoter regions of several genes, expression of miR-1297 which regulates PTEN and protein expression as DMTR1. In the future, a multidisciplinary research strategy could provide valuable new insights into the etiology of TGCTs, which support clinical diagnosis of TGCT in the next years to increase survival in this kind of patients.

Ineffectiveness of Methylation in Rgulation of VHL, ECAD, and RUNX3 Genes in Erythroid Cells Differentiated by Erythropoietin

Background: Vast variety of intermediate factors including cell cycle regulators, growth factors, transcription factors, and signaling pathways are involved in hematopoietic stem cell (HSC) commitment and differentiation into distinct lineages. VHL, Ecad, and RUNX3 are among these. Epigenetics is currently introduced as a potential mechanism to control the gene regulation. The aim of this study is to reveal the correlation between the expression level and methylation pattern of mentioned genes after in vitro differentiation of cord blood HSCs into erythroid lineage mediated by erythropoietin. M aterials and Methods: After isolation and expansion, the CD34+ cord blood stem cells were divided into two parts. The first part was used to extract the DNA and RNA and the second to differentiate into erythroid lineage. Methylation specific PCR (MSP) and Real-time PCR were used to determine the methylation status and expression levels of the genes, respectively. R es ults: Although the significant upregulation observed for VHL and Ecad genes and a down-regulation for RUNX3 gene after differentiation, no remarkable changes were seen in methylation pattern compared with cord blood HSCs by MSP technique. C onclusion: It is appearing that methylation pattern in promoter region has not an effective role in expression of VHL, Ecad, and RUNX3. Moreover, considering the inability of MSP method to detect subtle differences in methylation level a more sensitive method is needed to distinguish the methylation levels of these genes before and after erythroid differentiation.

RASSF1 and PTEN Promoter Hypermethylation Influences the Outcome in Epithelial Ovarian Cancer

BackgroundTo investigate the methylation pattern in promoter region of RASSF1A and PTEN genes in epithelial ovarian cancer patients in North India. Patients and MethodsFifty patients and 20 healthy controls were studied. Isolation of genomic DNA from peripheral blood and methylation-specific polymerase chain reaction (MSP) were applied for analysis. Results17 of 50 patients (34.0%) were found to be methylated for RASSF1A gene, whereas methylation of the PTEN gene occurred in 8 of 50 cases (16.0%). A statistically significant result was obtained (P = .01) for RASSF1A gene and correlated with the patients' clinicopathologic features. ConclusionHypermethylation of both RASSF1A and PTEN genes in blood DNA from ovarian cancer patients might offer an exposition for early diagnosis of the malignancy.

Expression profile of neurotransmitter receptor and regulatory genes in the prefrontal cortex of spontaneously hypertensive rats: Relevance to neuropsychiatric disorders

The spontaneously hypertensive rat (SHR) strain was shown to be a useful animal model to study several behavioral, pathophysiological and pharmacological aspects of schizophrenia and attention-deficit/hyperactivity disorder. To further understand the genetic underpinnings of this model, our primary goal in this study was to compare the gene expression profile of neurotransmitter receptors and regulators in the prefrontal cortex (PFC) and nucleus accumbens (NAcc) of SHR and Wistar rats (control group). In addition, we investigated DNA methylation pattern of promoter region of the genes differentially expressed. We performed gene expression analysis using a PCRarray technology, which simultaneously measures the expression of 84 genes related to neurotransmission. Four genes were significantly downregulated in the PFC of SHR compared to Wistar rats (Gad2, Chrnb4, Slc5a7, and Qrfpr) and none in nucleus accumbens. Gad2 and Qrfpr have CpG islands in their promoter region. For both, the promoter region was hypomethylated in SHR group, and probably this mechanism is not related with the downregulation of these genes. In summary, we identified genes that are downregulated in the PFC of SHR, and might be related to the behavioral abnormalities exhibited by this strain.

Hypermethylation of estrogen receptor promoter region in adult testis of rats exposed neonatally to bisphenol A

Background Bisphenol A (BPA) is an estrogenic endocrine disruptor commonly used in manufacture of polycarbonate plastics and epoxy resins. Due to its ubiquitous presence in the environment, health concerns are increasing. Earlier studies from our group have shown that neonatal exposure of male rats to BPA affected spermatogenesis leading to impairment in fertility during adulthood. Further we also observed an altered gene expression of ERα and ERβ in adult testis upon BPA exposure. Based on these results, we hypothesized that apart from endocrine action, BPA might mediate perturbations in expression of ERs via epigenetic mechanism. Objectives The present study was undertaken to determine the effect of exposure of neonatal male rats to BPA on DNA methylation profile of estrogen receptor promoter region and on DNA methylation machinery. Methods In order to test this hypothesis, neonatal male rats were subcutaneously injected with 2.4 μg of BPA/day for the first five days of life, i.e., on postnatal days (PND) 1–5, while control group received vehicle (sesame oil). Animals were sacrificed during adulthood (PND-125) and testes were dissected out for analysis. Methylation pattern of promoter region of ERα and ERβ was analyzed in the testis by bisulfite sequencing and expression levels of DNA methyltransferases by quantitative RT-PCR and Western blotting respectively. Results Bisulfite sequencing revealed significant hypermethylation of ERα promoter to varying extents from 40% to 60%, and ERβ promoter region with varying extent from 20% to 65%. Approximately 2-fold increase in Dnmt3a and Dnmt3b expression at transcript and protein level was also observed. Conclusion The experimental evidence demonstrated that the neonatal exposure of rats to BPA led to aberrant DNA methylation in testis, indicating methylation mediated epigenetic changes as one of the possible mechanisms of BPA induced adverse effects on spermatogenesis and fertility.

Evaluation of methylation pattern in promoter region of E-cadherin gene and its relation to tumor grade and stage in breast cancer

The epithelial cadherin gene (CDH1) has been identified as a tumor suppressor gene located within the 16q22.1 region. The CDH1 gene encodes a transmembrane glycoprotein involved in cell to cell adhesion and loss of CDH1 expression contributes to increased proliferation, invasion and metastasis in breast carcinoma. No mutation in CDH1 have been identified in invasive ductal carcinoma (IDC), suggesting that, other inactivation mechanisms are responsible for IDC oncogenesis. In order to analyze the role of promoter methylation in CDH1 gene inactivation in breast cancer, the CpG methylation status of Ecadherin promoter region by bisulfite sequencing PCR (BSP) was investigated. 10 CpG sites [nucleotide (nt) 863, 865, 873, 879, 887, 892, 901, 918, 920 and 940] in the promoter region were screened for methylation. The CDH1 methylation was detected in 94% (47 to 50) of breast tumors which was associated with higher tumor grade (p = 0.035), tumor stage (p = 0.000) and tumor metastasis (p = 0.000). There was also a significant correlation between tumor stage, grade and metastatic status with sites of methylation (p = 0.000). The data indicate that CDH1 promoter methylation might be a potential mechanism for epigenetic silencing of CDH1 in primary breast cancer suggesting a valuable molecular marker for detection of breast cancer progression. Key words: Breast cancer, E-cadherin, methylation pattern, tumor stage, tumor grade.

Dysfunction of endothelial NO system originated from homocysteine-induced aberrant methylation pattern in promoter region of DDAH2 gene

Hyperhomocysteinemia (HHcy)-mediated dysfunction of endothelial NO system is an important mechanism for atherosclerotic pathogenesis. Dimethylarginine dimethylaminohydrolase (DDAH) is the key enzyme for degrading asymmetric dimethylarginine (ADMA), which is an endogenous inhibitor of endothelial nitric oxide (NO) synthase (eNOS). This study was designed to investigate whether the dysfunction of endothelial NO system originates from HHcy-mediated aberrant methylation modification in promotor region of DDAH2 gene. Human umbilical vein endothelial cells (HUVECs) were cultured to the third generation and treated with homocysteine (Hcy) at different concentrations (0, 10, 30, 100, and 300 micromol/L) for 72 hours. The methylation pattern in promoter region CpG island of DDAH2 gene was analyzed by nested methylation-specific PCR (nMSP). The mRNA expression of eNOS gene and DDAH2 gene was detected by semi-quantitative RT-PCR. The activity of DDAH2 and eNOS in cells, and the concentrations of ADMA and NO in culture medium were assayed respectively. Mild increased concentration of Hcy (10 and 30 micromol/L) induced hypomethylation, while high concentration of Hcy (100 and 300 micromol/L) induced hypermethylation in the promoter CpG island of DDAH2 gene. The mRNA expression of DDAH2 increased in mild enhanced concentration of Hcy, and decreased in high concentration of Hcy correspondingly. The inhibition of DDAH2 activity, the increase of ADMA concentration, the reduction of eNOS activity and the decrease of NO production were all consistently relevant to the alteration of Hcy concentration. The increased concentration of Hcy induced aberrant methylation pattern in promotor region of DDAH2 gene and the successive alterations in DDAH/ADMA/NOS/NO pathway, which showed highly relevant and dose-effect relationship. The results suggested that the dysfunction of endothelial NO system induced by HHcy could be partially originated from Hcy-mediated aberrant methylation in DDAH2 gene.

Gene Silencing in the Development of Cancer

To investigate the methylation pattern in promoter region of RASSF1A and PTEN genes in epithelial ovarian cancer patients in North India.Fifty patients and 20 healthy controls were studied. Isolation of genomic DNA from peripheral blood and methylation-specific polymerase chain reaction (MSP) were applied for analysis.17 of 50 patients (34.0%) were found to be methylated for RASSF1A gene, whereas methylation of the PTEN gene occurred in 8 of 50 cases (16.0%). A statistically significant result was obtained (P = .01) for RASSF1A gene and correlated with the patients' clinicopathologic features.Hypermethylation of both RASSF1A and PTEN genes in blood DNA from ovarian cancer patients might offer an exposition for early diagnosis of the malignancy.