No abstract available.
CpG Islands* ; Methylation*

In forensic science practice, age is an important individual information, and one of the indicators to be considered first to depict features of the suspect. Recently, DNA methylation has become a research hotspot in age estimation because of its hig accuracy and stability. New progress has been made in specificity of DNA methylation sites, age estimation in multiple tissues, DNA methylation age estimation of minors, sensitivity of age estimation, forensic practical applications, etc. At the same time, several studies also established more accurate statistical modeling methods, eliminated differences between different detection platforms, found appropriate number of sites in models and analyzed the influence of environment and diseases. This review summarizes these to provide references.
CpG Islands ; DNA Methylation ; Forensic Genetics ; Humans

Colorectal cancer (CRC) has been assumed for many years to be a homogenous condition with the vast majority developing within preexisting-adenomas. However, over the last two-decades, it has become clear that CRC evolves through multiple pathways at the genetic and the epigenetic level. Each of these processes is associated with a unique genetic or epigenetic signature identifiable in the tumor cells. The pathway may be defined on the basis of three molecular features: 1) chromosomal instability (CIN), 2) microsatellite instability (MSI), and 3) CpG island methylator phenotype (CIMP). Those molecular pathways are determined at an early evolutionary stage and are fully established within early cancer. Recently, five subgroups were outlined by using morphological findings and associated molecular changes: type 1 (CIN-stable/ MSI-H/CIMP-H), type 2 (CIN-stable/MSI-L or MSS/ CIMP-H), type 3 (CIN-unstable/MSI-L or MSS/CIMP-L), type 4 (CIN-instable/MSS/CIMP-neg), and type 5 (CIN- stable/MSI-H/CIMP-neg). This approach to the classification of CRC should accelerate understanding of causation and will have an impact on clinical management in the areas of both prevention and treatment.
Chromosomal Instability ; Colorectal Neoplasms ; CpG Islands ; Epigenomics ; Microsatellite Instability ; Phenotype

CpG is the pair of nucleotides C and G, appearing successively, in this order, along one DNA strand. It is known that due to biochemical considerations CpG is relatively rare in most DNA sequences. However, in particular subsequences, which are a few hundred to a few thousand nucleotides long, the couple CpG is more frequent. These subsequences, called CpG islands, are known to appear in biologically more significant parts of the genome. The ability to identify CpG islands along a chromosome will therefore help us spot its more significant regions of interest, such as the promoters or 'start' regions of many genes. In this respect, I developed the CpG islands search tool, CpG Islands Detector, which was implemented in JAVA to be run on any platform. The window-based graphical user interface of CpG Islands Detector may facilitate the end user to employ this tool to pinpoint CpG islands in a genomic DNA sequence. In addition, this tool can be used to highlight potential genes in genomic sequences since CpG islands are very often found in the 5' regions of vertebrate genes.
Base Sequence ; CpG Islands ; DNA ; Genome ; Indonesia ; Nucleotides ; Vertebrates

Sinonasal mucosal melanoma (SMM) is an aggressive and rare type of melanoma. Although the classic RAS-RAF-MEK pathway is thought to be the main pathway involved in melanoma pathogenesis, genetic alterations in the phosphatidylinositol 3-kinase-AKT pathway, including PTEN-regulated signaling, are also thought to contribute. So far, data regarding altered PTEN expression and epigenetic mechanism of PTEN silencing in development of SMM is extremely limited. Herein we report on a case of SMM with liver and bone metastases with an epigenetic alteration of PTEN. Results of mutation analysis for BRAF, NRAS, HRAS, KRAS, PIK3CA, c-Kit, and PTEN were negative; however, methylation of PTEN CpG islands was observed. Our case not only supports PTEN as a major tumor suppressor involved in melanoma tumorigenesis, but also a potential epigenetic mechanism of PTEN silencing in development of SMM.
Carcinogenesis ; CpG Islands ; Epigenomics ; Liver ; Melanoma* ; Methylation* ; Neoplasm Metastasis ; Phosphatidylinositols

Sinonasal mucosal melanoma (SMM) is an aggressive and rare type of melanoma. Although the classic RAS-RAF-MEK pathway is thought to be the main pathway involved in melanoma pathogenesis, genetic alterations in the phosphatidylinositol 3-kinase-AKT pathway, including PTEN-regulated signaling, are also thought to contribute. So far, data regarding altered PTEN expression and epigenetic mechanism of PTEN silencing in development of SMM is extremely limited. Herein we report on a case of SMM with liver and bone metastases with an epigenetic alteration of PTEN. Results of mutation analysis for BRAF, NRAS, HRAS, KRAS, PIK3CA, c-Kit, and PTEN were negative; however, methylation of PTEN CpG islands was observed. Our case not only supports PTEN as a major tumor suppressor involved in melanoma tumorigenesis, but also a potential epigenetic mechanism of PTEN silencing in development of SMM.
Carcinogenesis ; CpG Islands ; Epigenomics ; Liver ; Melanoma* ; Methylation* ; Neoplasm Metastasis ; Phosphatidylinositols

With the improvement of DNA methylation detection techniques, studies on age-related methylation sites have found more age-specific ones across tissues, which improves the sensitivity and accuracy of age estimation. In addition, the establishment of various statistical models also provides a new direction for the age estimation of tissues from different sources. This review summarizes the related studies of age estimation based on DNA methylation from the aspects of detection technology, age-related cytosine phosphate guanine site and model selection in recent years.
DNA Methylation ; Forensic Genetics/methods* ; CpG Islands ; Forensic Medicine

Diverse somatic mutations have been reported to serve as cancer drivers. Recently, it has also been reported that epigenetic regulation is closely related to cancer development. However, the effect of epigenetic changes on cancer is still elusive. In this study, we analyzed DNA methylation data on colon cancer taken from The Caner Genome Atlas. We found that several promoters were significantly hypermethylated in colon cancer patients. Through clustering analysis of differentially methylated DNA regions, we were able to define subgroups of patients and observed clinical features associated with each subgroup. In addition, we analyzed the functional ontology of aberrantly methylated genes and identified the G-protein-coupled receptor signaling pathway as one of the major pathways affected epigenetically. In conclusion, our analysis shows the possibility of characterizing the clinical features of colon cancer subgroups based on DNA methylation patterns and provides lists of important genes and pathways possibly involved in colon cancer development.
Classification* ; Colon* ; Colonic Neoplasms* ; CpG Islands ; DNA ; DNA Methylation ; Epigenomics ; Genome ; Humans ; Methylation*

PURPOSE: DNA methylation is a major epigenetic mechanism for modification of genetic expression without a change in the DNA sequence. MBD2 (methyl-CpG-binding domain 2 protein) belongs to a family of enzymes concerning of DNA demethylation and suppresses the hypermethylation of the CpG island and DNA transcription. In this study, we investigated the change of MBD2 expression in the blood and tissue of colorectal cancer patients and compared the two expression levels. METHODS: The 68 patients included in this study were patients with colorectal cancer who had undergone surgery at our hospital, and 50 other patients with no malignant disease were recruited from normal populations. Total RNA samples were isolated from whole blood samples and cancer tissues of specimens using a TRI REAGENT BD kit. MBD 2 expression was measured by real-time quantitative reverse transcription-polymerase chain reaction assays. RESULTS: The mean age was older in the case group than in the control group. The mean expression level of MBD2 in blood was not different between the two groups. In the case group, the tissue MBD2 expression was lower than the blood MBD2 expression under all conditions, and that difference was statistically significant (P<0.01). The expression of MBD2 in cancer tissue showed a negative correlation with that in the blood of cancer patients, correlation coefficient of R=0.073, but that result was not statistically significant (P=0.611). CONCLUSIONS: The blood MBD2 expression was statistically the same in the cancer and the control groups. In the cancer group, blood MBD2 expression was significantly higher than tissue MBD2 expression. The reverse correlation between blood MBD2 expression and tissue MBD2 expression in cancer patients suggests that MBD2 may affect the mechanism of carcinogenesis.
Base Sequence ; Colorectal Neoplasms ; CpG Islands ; DNA ; DNA Methylation ; Epigenomics ; Humans ; RNA

OBJECTIVE: Hypermethylation of p16, a tumor suppressor gene, has been frequently detected in a variety of cancer cells and is known to represent the level of p16 transcription. In human meningiomas, genetic alterations of p16 have shown to be infrequent. The purpose of this study is to investigate the role of p16 associated with the progression of meningiomas. METHODS: Sixty-eight meningiomas(randomly sampled 29 benign, 16 atypical and 23 malignant formalin-fixed, paraffin-embedded tissues) were analyzed. We examined the molecular mechanism of inactivation of p16 in these benign, atypical and malignant meningiomas by detecting the methylation status of p16 using methylation-specific polymerase chain reaction. RESULTS: One out of 29(3.4%) revealed hypermethylation of p16 in benign meningiomas. Atypical and malignant meningiomas showed hypermethylation of p16 in 2 out of 16 cases(12.5%) and in 5 out of 23 cases(21.7%), respectively. Immunohistochemical analysis of methylation-positive tumors demonstrated that tumor cells had reduced immunoreactivity compared to normal lymphocytes. CONCLUSIONS: Our results suggest that inactivation of p16 gene plays a role in the pathogenesis of meningioma and hypermethylation is one of the processes for gene inactivation.
CpG Islands* ; Gene Silencing ; Genes, p16 ; Genes, Tumor Suppressor ; Humans ; Lymphocytes ; Meningioma* ; Methylation* ; Polymerase Chain Reaction