Specific gene hypomethylation and cancer: new insights into coding region feature trends.
Ontology highlight
ABSTRACT:
SUBMITTER: Daura-Oller E
PROVIDER: S-EPMC2720671 | biostudies-literature | 2009 Apr
REPOSITORIES: biostudies-literature
Publications
Specific gene hypomethylation and cancer: new insights into coding region feature trends.
Daura-Oller Elias E Cabre Maria M Montero Miguel A MA Paternain Jose L JL Romeu Antoni A
Bioinformation 20090421 8
Giving coding region structural features a role in the hypomethylation of specific genes, the occurrence of G+C content, CpG islands, repeat and retrotransposable elements in demethylated genes related to cancer has been evaluated. A comparative analysis among different cancer types has also been performed. In this work, the inter-cancer coding region features comparative analysis carried out, show insights into what structural trends/patterns are present in the studied cancers. ...[more]
Similar Datasets
Project description:Long non-coding RNAs (lncRNAs) have gained widespread interest in the past decade owing to their enormous amount and surprising functions implicated in a variety of biological processes. Some lncRNAs exert function as enhancers, i.e., activating gene transcription by serving as the cis-regulatory molecules. Furthermore, recent studies have demonstrated that many enhancer elements can be transcribed and produce RNA molecules, which are termed as enhancer RNAs (eRNAs). The eRNAs are not merely the by-product of the enhancer transcription. In fact, many of them directly exert or regulate enhancer activity in gene activation through diverse mechanisms. Here, we provide an overview of enhancer activity, transcription of enhancer itself, characteristics of eRNAs, as well as their roles in regulating enhancer activity and gene expression.
| S-EPMC5487526 | biostudies-other
Project description:Interest in the biological roles of long noncoding RNAs (lncRNAs) has resulted in growing numbers of studies that produce large sets of candidate genes, for example, differentially expressed between two conditions. For sets of protein-coding genes, ontology and pathway analyses are powerful tools for generating new insights from statistical enrichment of gene features. Here we present the LnCompare web server, an equivalent resource for studying the properties of lncRNA gene sets. The Gene Set Feature Comparison mode tests for enrichment amongst a panel of quantitative and categorical features, spanning gene structure, evolutionary conservation, expression, subcellular localization, repetitive sequences and disease association. Moreover, in Similar Gene Identification mode, users may identify other lncRNAs by similarity across a defined range of features. Comprehensive results may be downloaded in tabular and graphical formats, in addition to the entire feature resource. LnCompare will empower researchers to extract useful hypotheses and candidates from lncRNA gene sets.
| S-EPMC6602513 | biostudies-literature
Project description:Infrequent and rare genetic variants in the human population vastly outnumber common ones. Although they may contribute significantly to the genetic basis of a disease, these seldom-encountered variants may also be miss-identified as pathogenic if no correct references are available. Somatic and germline TP53 variants are associated with multiple neoplastic diseases, and thus have come to serve as a paradigm for genetic analyses in this setting. We searched 14 independent, globally distributed datasets and recovered TP53 SNPs from 202,767 cancer-free individuals. In our analyses, 19 new missense TP53 SNPs, including five novel variants specific to the Asian population, were recurrently identified in multiple datasets. Using a combination of in silico, functional, structural, and genetic approaches, we showed that none of these variants displayed loss of function compared to the normal TP53 gene. In addition, classification using ACMG criteria suggested that they are all benign. Considered together, our data reveal that the TP53 coding region shows far more polymorphism than previously thought and present high ethnic diversity. They furthermore underline the importance of correctly assessing novel variants in all variant-calling pipelines associated with genetic diagnoses for cancer.
| S-EPMC8166836 | biostudies-literature
Project description:In the human placenta, DNA hypomethylation permits the expression of retrotransposon-derived genes that are normally silenced by methylation in somatic tissues. We previously identified hypomethylation of a retrotransposon-derived transcript of the voltage-gated potassium channel gene KCNH5 that is expressed only in human placenta. However, an RNA sequence from this placental-specific transcript has been reported in melanoma. This study examined the promoter methylation and expression of the retrotransposon-derived KCNH5 transcript in 25 melanoma cell lines to determine whether the acquisition of 'placental' epigenetic marks is a feature of melanoma. Methylation and gene expression analysis revealed hypomethylation of this retrotransposon in melanoma cell lines, particularly in those samples that express the placental KCNH5 transcript. Therefore we propose that hypomethylation of the placental-specific KCNH5 promoter is frequently associated with KCNH5 expression in melanoma cells. Our findings show that melanoma can develop hypomethylation of a retrotransposon-derived gene; a characteristic notably shared with the normal placenta.
| S-EPMC3997481 | biostudies-literature
Project description:ObjectiveEarly-onset colorectal cancer (CRC) represents a clinically distinct form of CRC that is often associated with a poor prognosis. Methylation levels of genomic repeats such as LINE-1 elements have been recognized as independent factors for increased cancer-related mortality. The methylation status of LINE-1 elements in early-onset CRC has not been analyzed previously.DesignWe analyzed 343 CRC tissues and 32 normal colonic mucosa samples, including 2 independent cohorts of CRC diagnosed ? 50 years old (n=188), a group of sporadic CRC >50 years (MSS n=89; MSI n=46), and a group of Lynch syndrome CRCs (n=20). Tumor mismatch repair protein expression, microsatellite instability status, LINE-1 and MLH1 methylation, somatic BRAF V600E mutation, and germline MUTYH mutations were evaluated.ResultsMean LINE-1 methylation levels (± SD) in the five study groups were early-onset CRC, 56.6% (8.6); sporadic MSI, 67.1% (5.5); sporadic MSS, 65.1% (6.3); Lynch syndrome, 66.3% (4.5) and normal mucosa, 76.5% (1.5). Early-onset CRC had significantly lower LINE-1 methylation than any other group (p<0.0001). Compared to patients with <65% LINE-1 methylation in tumors, those with ? 65% LINE-1 methylation had significantly better overall survival (p=0.026, log rank test).ConclusionsLINE-1 hypomethylation constitutes a potentially important feature of early-onset CRC, and suggests a distinct molecular subtype. Further studies are needed to assess the potential of LINE-1 methylation status as a prognostic biomarker for young people with CRC.
| S-EPMC3458035 | biostudies-literature
Project description:BackgroundThe Mediterranean subpopulation of fin whale Balaenoptera physalus (Linnaeus, 1758) has recently been listed as Vulnerable by the IUCN Red List of threatened species. The species is also listed as species in need of strict protection under the Habitat Directive and is one of the indicators for the assessment of Good Environmental Status under the MSFD. Reference values on population abundance and trends are needed in order to set the threshold values and to assess the conservation status of the population.MethodsYearly summer monitoring using ferries as platform of opportunity was performed since 2008 within the framework of the FLT Med Network. Data were collected along several fixed transects crossing the Western Mediterranean basin and the Adriatic and Ionian region. Species presence, expressed by density recorded along the sampled transects, was inspected for assessing interannual variability together with group size. Generalized Additive Models were used to describe density trends over a 11 years' period (2008-2018). A spatial multi-scale approach was used to highlight intra-basin differences in species presence and distribution during the years.ResultsSummer presence of fin whales in the western Mediterranean area showed a strong interannual variability, characterized by the alternance of rich and poor years. Small and large groups of fin whales were sighted only during rich years, confirming the favorable feeding condition influencing species presence. Trends highlighted by the GAM can be summarized as positive from 2008 to 2013, and slightly negative from 2014 to 2018. The sub-areas analysis showed a similar pattern, but with a more stable trend during the second period in the Pelagos Sanctuary sub-area, and a negative one in the other two sub-areas. Our findings further confirm the need for an integrated approach foreseeing both, large scale surveys and yearly monitoring at different spatial scales to correct and interpret the basin wide abundance estimates, and to correlate spatial and temporal trends with the ecological and anthropogenic drivers.
| S-EPMC7745674 | biostudies-literature
Project description:Human PDHA2 is a testis-specific gene that codes for the E(1)? subunit of Pyruvate Dehydrogenase Complex (PDC), a crucial enzyme system in cell energy metabolism. Since activation of the PDHA2 gene in somatic cells could be a new therapeutic approach for PDC deficiency, we aimed to identify the regulatory mechanisms underlying the human PDHA2 gene expression. Functional deletion studies revealed that the -122 to -6 promoter region is indispensable for basal expression of this TATA-less promoter, and suggested a role of an epigenetic program in the control of PDHA2 gene expression. Indeed, treatment of SH-SY5Y cells with the hypomethylating agent 5-Aza-2'-deoxycytidine (DAC) promoted the reactivation of the PDHA2 gene, by inducing the recruitment of the RNA polymerase II to the proximal promoter region and the consequent increase in PDHA2 mRNA levels. Bisulfite sequencing analysis revealed that DAC treatment induced a significant demethylation of the CpG island II (nucleotides +197 to +460) in PDHA2 coding region, while the promoter region remained highly methylated. Taken together with our previous results that show an in vivo correlation between PDHA2 expression and the demethylation of the CpG island II in testis germ cells, the present results show that internal methylation of the PDHA2 gene plays a part in its repression in somatic cells. In conclusion, our data support the novel finding that methylation of the PDHA2 coding region can inhibit gene transcription. This represents a key mechanism for absence of PDHA2 expression in somatic cells and a target for PDC therapy.
| S-EPMC3365900 | biostudies-literature
Project description:Background and objectives: Papillary thyroid carcinoma is the most frequent variety of all malignant endocrine tumors. It represents a heterogeneous malignancy with various clinical outcomes, emphasizing the need to identify powerful biomarkers with clinical relevance. Materials and Methods: Available gene expression data (level 3) for thyroid cancers were downloaded from the Cancer Genome Atlas (TCGA), followed by bioinformatic analyses performed on the data set. Results: Based on gene expression analysis, we were able to identify common and specific gene signatures for the three main types of papillary thyroid carcinoma (classical, follicular variant, and tall-cell). The survival rate was not significantly different among the main subtypes, but we were able to identify a biological adhesion signature with impact in patient prognostic. Conclusions: Taken together, the gene expression signature and particular adhesion signature, along with ITGA10 and MSLN in particular, could be used as a prognostic tool with important clinical relevance.
| S-EPMC6723230 | biostudies-literature
Project description:We have previously reported that the connective tissue stroma of human colon carcinoma contains elevated amounts of decorin, a small proteoglycan involved in the regulation of matrix formation and cell proliferation. These biochemical changes were correlated with increased mRNA levels and general hypomethylation of the decorin gene in human colon cancer DNA. In this report we use a quantitative polymerase chain reaction method coupled with digestion of the DNA template by methylation-sensitive restriction endonucleases to investigate in detail the location of hypomethylated sites in decorin gene. We demonstrate that a specific site in the 3' region of the gene, encompassing codons 360-361, is specifically hypomethylated in both colon carcinoma and benign polyp. In contrast, three HpaII sites, clustered in the 5' untranslated region, show full methylation in normal and neoplastic DNA. The lack of such changes in ulcerative colitis DNA suggests that chronic inflammation alone is not sufficient to alter cytosine methylation in the decorin gene. These results suggest the possibility that the 3' region of the decorin-coding sequence may be involved in the control of decorin gene expression.
| S-EPMC1151091 | biostudies-other
Project description:PurposeThe objective of this study was to conduct a systematic review and meta-analysis to evaluate the cancer risks among firefighters in the time course and from different geographical areas.MethodA PubMed search was performed to identify cohort studies about cancer risk and firefighting presented with standardized incidence ratios (SIRs) or standardized mortality ratios (SMRs). Using random-effect models, meta-relative risk estimates (mSIRs, mSMRs) and 95% confidence intervals (CI) were assessed. Cohort studies with employment starting before 1950 were classified as "old", studies starting between 1950 and 1970 as "medium", and later studies as "new".ResultsThe general cancer risk of firefighters was similar to the general population, but mSMR decreased over time (new studies: mSMR = 0.81, 95% CI 0.70-0.92). We observed an increase of mSIR for melanoma of the skin and prostate cancer as well as a decrease of mSIR for stomach cancer with later employment onset. For those cancer sites, we did not observe a secular trend of mSMRs. Regional differences between relative cancer risks were particularly observed for bladder cancer.ConclusionsAmong other things, innovative firefighting techniques and better personal protective equipment have provided a safer and healthier working environment for firefighters over time leading to a reduction of overall cancer incidence and mortality ratios. Increased general preventive medical checkups and possible additional screenings for firefighters might have led to more findings of malignant melanoma of the skin and prostate cancer in the recent past.
| S-EPMC7452930 | biostudies-literature