scholarly journals Modeling DNA Methylation Profiles through a Dynamic Equilibrium between Methylation and Demethylation

Biomolecules ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1271
Author(s):  
Giulia De Riso ◽  
Damiano Francesco Giuseppe Fiorillo ◽  
Annalisa Fierro ◽  
Mariella Cuomo ◽  
Lorenzo Chiariotti ◽  
...  

DNA methylation is a heritable epigenetic mark that plays a key role in regulating gene expression. Mathematical modeling has been extensively applied to unravel the regulatory mechanisms of this process. In this study, we aimed to investigate DNA methylation by performing a high-depth analysis of particular loci, and by subsequent modeling of the experimental results. In particular, we performed an in-deep DNA methylation profiling of two genomic loci surrounding the transcription start site of the D-Aspartate Oxidase and the D-Serine Oxidase genes in different samples (n = 51). We found evidence of cell-to-cell differences in DNA methylation status. However, these cell differences were maintained between different individuals, which indeed showed very similar DNA methylation profiles. Therefore, we hypothesized that the observed pattern of DNA methylation was the result of a dynamic balance between DNA methylation and demethylation, and that this balance was identical between individuals. We hence developed a simple mathematical model to test this hypothesis. Our model reliably captured the characteristics of the experimental data, suggesting that DNA methylation and demethylation work together in determining the methylation state of a locus. Furthermore, our model suggested that the methylation status of neighboring cytosines plays an important role in this balance.

2021 ◽  
Vol 23 (Supplement_6) ◽  
pp. vi120-vi121
Author(s):  
Mircea Tesileanu ◽  
Pim French ◽  
Marc Sanson ◽  
Alba Ariela Brandes ◽  
Wolfgang Wick ◽  
...  

Abstract BACKGROUND Temozolomide efficacy in high-grade glioma is related to MGMTp methylation. We compared the prognostic and predictive effect of MGMTp between DNA methylation profiling (MGMT-STP27 model) and qMS-PCR in IDH1/2mt anaplastic astrocytoma patients. METHODS The 2x2 factorial design phase III CATNON trial randomized 751 adult patients with newly diagnosed 1p/19q non-codeleted anaplastic glioma to 59.4Gy radiotherapy, radiotherapy with concurrent temozolomide, radiotherapy with 12 cycles of adjuvant temozolomide, or radiotherapy with concurrent and adjuvant temozolomide. MGMTp methylation status was assessed with the MGMT-STP27 model using 850k EPIC data, and qMS-PCR. IDH1/2 mutation status was determined with next-generation sequencing. OS was measured from randomization date. RESULTS We identified 444 IDH1/2mt anaplastic astrocytoma patients. MGMTp was methylated in 365/440 patients (83.0%) with MGMT-STP27 data, and 168/361 patients (46.5%) with qMS-PCR data. The agreement between both modalities is 59.9% (Cohen’s Kappa score 0.229). At database lock, 289 patients with MGMT-STP27 data were alive and 236 patients with qMS-PCR data. The median OS of MGMTp methylated glioma patients was 9.1 yrs [95%CI 7.5-not reached] for the MGMT-STP27 model, and not reached [95%CI 9.1-not reached] for qMS-PCR. For MGMTp unmethylated glioma patients, the median OS was 6.9 yrs [95%CI 6.2-not reached] for the MGMT-STP27 model, and 6.8 yrs [95%CI 6.2-9.7] for qMS-PCR. The HR for OS based on MGMTp methylation was 0.88 [95%CI 0.58-1.31] for the MGMT-STP27 model, and 0.72 [95%CI 0.50-1.03]) for qMS-PCR. The HR for OS after radiotherapy with any temozolomide vs radiotherapy alone for the MGMT-STP27 model was 0.53 [95%CI 0.37-0.78] for MGMTp methylated, and 0.54 [95%CI 0.25-1.18] for MGMTp unmethylated glioma patients; and for MS-PCR was 0.34 [95%CI 0.19-0.61] for MGMTp methylated, and 0.53 [95%CI 0.33-0.85] for MGMTp unmethylated glioma patients. CONCLUSION MGMTp methylation, regardless of assay, was neither prognostic nor predictive for outcome to temozolomide in IDH1/2mt anaplastic astrocytoma patients.


2017 ◽  
Vol 35 (15_suppl) ◽  
pp. 11034-11034
Author(s):  
Shengyang Wu ◽  
Benjamin Thomas Cooper ◽  
Fang Bu ◽  
Christopher Bowman ◽  
Keith Killian ◽  
...  

11034 Background: Bone sarcomas present a unique diagnostic challenge because of the considerable morphologic overlap between different entities. The choice of optimal treatment, however, is dependent upon accurate diagnosis. Genome-wide DNA methylation profiling has emerged as a new approach to aid in the diagnosis of brain tumors, with diagnostic accuracy exceeding standard histopathology. In this work we developed and validated a methylation based classifier to differentiate between osteosarcoma, Ewing’s sarcoma, and synovial sarcoma. Methods: DNA methylation status of 482,421 CpG sites in 15 osteosarcoma, 10 Ewing’s sarcoma, and 11 synovial sarcoma samples were measured using the Illumina HumanMethylation450 array. From this training set of 36 samples we developed a random forest classifier using the 400 most differentially methylated CpG sites (FDR q value < 0.001). This classifier was then validated on 10 synovial sarcoma samples from TCGA, 86 osteosarcoma samples from TARGET-OS, and 15 Ewing’s sarcoma from a recently published series (Huertas-Martinez et al., Cancer Letters 2016). Results: Methylation profiling revealed three distinct molecular clusters, each enriched with a single sarcoma subtype. Within the validation cohorts, all samples from TCGA were correctly classified as synovial sarcoma (10/10, sensitivity and specificity 100%). All but one sample from TARGET-OS were classified as osteosarcoma (85/86, sensitivity 98%, specificity 100%) and all but one sample from the Ewing’s sarcoma series was classified as Ewing’s sarcoma (14/15, sensitivity 93%, specificity 100%). The single misclassified osteosarcoma sample was classified as Ewing’s sarcoma, and was later determined to be a misdiagnosed Ewing’s sarcoma based on RNA-Seq demonstrating high EWRS1 and ETV1 expression. An additional clinical sample that was misdiagnosed as a synovial sarcoma by initial histolopathology, was accurately recognized as osteosarcoma by the methylation classifier. Conclusions: Osteosarcoma, Ewing’s sarcoma and synovial sarcoma have distinct epigenetic profiles. Our validated methylation-based classifier can be used to provide an accurate diagnosis when histological and standard techniques are inconclusive.


2019 ◽  
Author(s):  
Sandra Jeudy ◽  
Sofia Rigou ◽  
Jean-Marie Alempic ◽  
Jean-Michel Claverie ◽  
Chantal Abergel ◽  
...  

AbstractDNA methylation is an important epigenetic mark that contributes to various regulations in all domains of life. Prokaryotes use it through Restriction-Modification (R-M) systems as a host-defense mechanism against viruses. The recently discovered giant viruses are widespread dsDNA viruses infecting eukaryotes with gene contents overlapping the cellular world. While they are predicted to encode DNA methyltransferases (MTases), virtually nothing is known about the DNA methylation status of their genomes. Using single-molecule real-time sequencing we studied the complete methylome of a large spectrum of families: the Marseilleviridae, the Pandoraviruses, the Molliviruses, the Mimiviridae along with their associated virophages and transpoviron, the Pithoviruses and the Cedratviruses (of which we report a new strain). Here we show that DNA methylation is widespread in giant viruses although unevenly distributed. We then identified the corresponding viral MTases, all of which are of bacterial origins and subject to intricate gene transfers between bacteria, viruses and their eukaryotic host. If some viral MTases undergo pseudogenization, most are conserved, functional and under purifying selection, suggesting that they increase the viruses’ fitness. While the Marseilleviridae, Pithoviruses and Cedratviruses DNA MTases catalyze N6-methyl-adenine modifications, some MTases of Molliviruses and Pandoraviruses unexpectedly catalyze the formation of N4-methyl-cytosine modifications. In Marseilleviridae, encoded MTases are paired with cognate restriction endonucleases (REases) forming complete R-M systems. Our data suggest that giant viruses MTases could be involved in different kind of virus-virus interactions during coinfections.


2021 ◽  
Vol 23 (Supplement_2) ◽  
pp. ii6-ii7
Author(s):  
C M S Tesileanu ◽  
P J French ◽  
M Sanson ◽  
A A Brandes ◽  
W Wick ◽  
...  

Abstract BACKGROUND Temozolomide (TMZ) efficacy in high-grade glioma is related to O 6-methylguanine DNA methyltransferase promoter (MGMTp) methylation. We compared the prognostic and predictive effect of MGMTp between DNA methylation profiling (the MGMT-STP27 model) and quantitative methylation specific polymerase chain reaction (qMS-PCR) in isocitrate dehydrogenase 1 and 2 (IDH1/2) mutant (mt) anaplastic astrocytoma patients. MATERIAL AND METHODS The 2x2 factorial design phase III CATNON trial randomized 751 adult patients with newly diagnosed 1p/19q non-codeleted anaplastic glioma to 59.4 Gy radiotherapy (RT), RT with concurrent TMZ, RT with 12 cycles of adjuvant TMZ, or RT with concurrent and adjuvant TMZ. MGMTp methylation status was assessed with the MGMT-STP27 model using 850k EPIC data, and qMS-PCR. IDH1/2 mutation status was determined with a next-generation sequencing panel. Overall survival (OS) was measured from date of randomization. RESULTS We identified 444 IDH1/2mt anaplastic astrocytoma patients of which MGMT-STP27 data was available for 440 patients (99.1%), qMS-PCR data for 361 patients (81.3%), and both for 357 patients (80.4%). MGMTp was methylated in 365 patients (83.0%) for the MGMT-STP27 model, and 168 patients (46.5%) for qMS-PCR. The agreement between the MGMT-STP27 model and qMS-PCR is 59.9% with a Cohen’s Kappa score of 0.229. At database lock, 289 patients with MGMT-STP27 data were still alive and 236 patients with qMS-PCR data. The median OS of MGMTp methylated glioma patients was 9.1 yrs [95 % confidence interval (CI) 7.5-not reached] for the MGMT-STP27 model, and not reached [95 % CI 9.1-not reached] for the qMS-PCR data. For MGMTp unmethylated glioma patients, the median OS was 6.9 yrs [95% CI 6.2-not reached] for the MGMT-STP27 model, and 6.8 yrs [95% CI 6.2–9.7] for the qMS-PCR data. The hazard ratio (HR) for OS based on MGMTp methylation was 0.88 [95% CI 0.58–1.31] for the MGMT-STP27 data, and 0.72 [95% CI 0.50–1.03]) for the qMS-PCR data. The HR for OS after RT with any TMZ vs RT alone for the MGMT-STP27 model was 0.53 [95% CI 0.37–0.78] for MGMTp methylated, and 0.54 [95% CI 0.25–1.18] for MGMTp unmethylated glioma patients; and for the MS-PCR data was 0.34 [95% CI 0.19–0.61] for MGMTp methylated, and 0.53 [95% CI 0.33–0.85] for MGMTp unmethylated glioma patients. CONCLUSION MGMTp methylation, regardless of assay, was neither prognostic nor predictive for outcome to temozolomide in IDH1/2mt anaplastic astrocytoma patients.


2012 ◽  
Vol 2012 ◽  
pp. 1-6
Author(s):  
Hiroaki Harada ◽  
Kazuaki Miyamoto ◽  
Yoshinori Yamashita ◽  
Kikuo Nakano ◽  
Kiyomi Taniyama ◽  
...  

In lung cancer, the roles of molecular alterations in blood, sputum, bronchial brushing, and exhaled gas samples, which are relatively easy to obtain, have been evaluated for clinical availability. This study was based on the hypothesis that similar molecular alterations occur in the lung and oral cavity because both are exposed to the same environmental or tobacco-derived carcinogens. Because epigenetic alterations due to exposure to carcinogens are thought to play a major role in the development of lung cancer, the DNA methylation status of 11 genes in the oral epithelium was analyzed in lung cancer patients (n=16) and control individuals without lung cancer (n=32). DNA methylation profiling revealed that GDNF, RARB, and HS3ST2 were methylated more frequently in cancer patients than in the control participants (P=0.0017, 0.0062, and 0.0193, resp.). Combined analysesindicatedthat 6 of 16 cancer patients (37.5%), but only 1 of 32 control individuals (3.1%) showed DNA methylation in 2-3 of these 3 genes (P=0.0015). These combined analyses showed the high specificity and positive predictive value in total and subgroup analyses. Our data suggest that DNA methylation profiling using oral epithelium may help in the identification of individuals with a high risk of lung cancer.


2021 ◽  
Vol 22 (23) ◽  
pp. 12989
Author(s):  
Witold Józef Światowy ◽  
Hanna Drzewiecka ◽  
Michalina Kliber ◽  
Maria Sąsiadek ◽  
Paweł Karpiński ◽  
...  

Physical activity is a strong stimulus influencing the overall physiology of the human body. Exercises lead to biochemical changes in various tissues and exert an impact on gene expression. Exercise-induced changes in gene expression may be mediated by epigenetic modifications, which rearrange the chromatin structure and therefore modulate its accessibility for transcription factors. One of such epigenetic mark is DNA methylation that involves an attachment of a methyl group to the fifth carbon of cytosine residue present in CG dinucleotides (CpG). DNA methylation is catalyzed by a family of DNA methyltransferases. This reversible DNA modification results in the recruitment of proteins containing methyl binding domain and further transcriptional co-repressors leading to the silencing of gene expression. The accumulation of CpG dinucleotides, referred as CpG islands, occurs at the promoter regions in a great majority of human genes. Therefore, changes in DNA methylation profile affect the transcription of multiple genes. A growing body of evidence indicates that exercise training modulates DNA methylation in muscles and adipose tissue. Some of these epigenetic markers were associated with a reduced risk of chronic diseases. This review summarizes the current knowledge about the influence of physical activity on the DNA methylation status in humans.


2016 ◽  
Vol 2016 ◽  
pp. 1-7 ◽  
Author(s):  
Jiufeng Wei ◽  
Guodong Li ◽  
Shuwei Dang ◽  
Yuhui Zhou ◽  
Kai Zeng ◽  
...  

Colorectal carcinoma (CRC) is one of the most prevalent malignant tumors worldwide. Screening and early diagnosis are critical for the clinical management of this disease. DNA methylation changes have been regarded as promising biomarkers for CRC diagnosis. Here, we map DNA methylation profiling on CRC in six CRCs and paired normal samples using a 450 K bead array. Further analysis confirms the methylation status of candidates in two data sets from the Gene Expression Omnibus. Receiver operating characteristic (ROC) curves are calculated to determine the diagnostic performances. We identify 1549 differentially methylated regions (DMRs) showing differences in methylation between CRC and normal tissue. Two genes (ADD2andAKR1B1), related to the DMRs, are selected for further validation. ROC curves show that the areas under the curves ofADD2andAKR1B1are higher than that ofSEPT9, which has been clinically used as a screening biomarker of CRC. Our data suggests that aberrant DNA methylation ofADD2andAKR1B1could be potential screening markers of CRC.


Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1405
Author(s):  
Oussama Badad ◽  
Naoufal Lakhssassi ◽  
Nabil Zaid ◽  
Abdelhalim El Baze ◽  
Younes Zaid ◽  
...  

Secondary metabolites are particularly important to humans due to their pharmaceutical properties. Moreover, secondary metabolites are key compounds in climate change adaptation in long-living trees. Recently, it has been described that the domestication of Olea subspecies had no major selection signature on coding variants and was mainly related to changes in gene expression. In addition, the phenotypic plasticity in Olea subspecies was linked to the activation of transposable elements in the genes neighboring. Here, we investigated the imprint of DNA methylation in the unassigned fraction of the phenotypic plasticity of the Olea subspecies, using methylated DNA immuno-precipitation sequencing (MeDIP-seq) for a high-resolution genome-wide DNA methylation profiling of leaves and fruits during fruit development in wild and cultivated olives from Turkey. Notably, the methylation profiling showed a differential DNA methylation in secondary metabolism responsible for the sensory quality of olive oil. Here, we highlight for the first time the imprint of DNA methylation in modulating the activity of the Linoleate 9S lipoxygenase in the biosynthesis of volatile aromatic compounds. Unprecedently, the current study reveals the methylation status of the olive genome during fruit ripening.


Genome ◽  
2010 ◽  
Vol 53 (11) ◽  
pp. 856-868 ◽  
Author(s):  
Graham J King ◽  
Stephen Amoah ◽  
Smita Kurup

This review addresses the mechanisms by which epigenetic variation modulates plant gene regulation and phenotype. In particular we explore the scope for harnessing such processes within the context of crop genetic improvement. We focus on the role of DNA methylation as an epigenetic mark that contributes to epiallelic diversity and modulation of gene regulation. We outline the prevalence and distribution of epigenetic marks in relation to eukaryote developmental processes, and in particular identify where this may be relevant to crop traits both in terms of specific developmental stages and in relation to physiological responses to environmental change. Recent whole genome surveys have identified specific characteristics of the distribution of DNA methylation within plant genomes. Together with greater understanding of the mode of action of different maintenance and de novo methyltransferases, this provides an opportunity to modulate DNA methylation status at specific loci as an intervention strategy in crop genetic improvement. We discuss alternative approaches that may be suitable for harnessing such induced epiallelic variation. Most of the discussion is associated with Brassica crops, which demonstrate considerable morphological plasticity, segmental chromosomal duplication, and polyploidy.


Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 1560-1560
Author(s):  
Paloma Martin-Acosta ◽  
Dolores Sanchez-Massa ◽  
Cesareo Corbacho ◽  
Carlos Montalban ◽  
Carmen Bellas

Abstract Introduction: Aberrant methylation of the 5′ gene promoter regions is an epigenetic phenomenon that is the one of the major mechanism of inactivation of tumor supressor genes. DNA methylation of the promoter region has been described for several genes in various malignant diseases, and each tumour type may have its own pattern of methylation. To determine the methylation status and expression of cell cycle inhibitors genes (p14, p15, p16), repair genes (MGMT and hMLH1) and the apoptosis regulator gene (DAPKinase) and the possible role of this epigenetic phenomenon in tumour progression of plasma cell disorders, we analyzed the methylation profile of MM, MGUS, and plasmacytomas comparing them with their protein expression. Patients and Methods: A total of 51 cases: 30 MM, 13 MGUS, and 8 plasmacytomas (3 Solitary Bone Plasmacytoma, 5 Extramedullary Plasmacytoma) were included in the study. Bone marrow plasma cells were purified using magnetic microbeads labeled with CD138 in samples with MM and MGUS. Methylation-specific polymerase chain reaction (MSP) for p14, p15, p16, MGMT, hMLH1 and DAPKinase was performed. MSP results were matched to protein expression studies by immunohistochemistry for p15, p16, MGMT and hMLH1. Results: The frequency of aberrant methylation among the MM samples was: 50% for p16, 16.7% for p15, 10% for hMLH1, 23.3% for MGMT, 30% for DAPK. In MGUS samples we found 38.5% for p16, 15.4% for p15, 0% for hMLH1, 7.7% for MGMT and 15.4% for DAPK methylation. The frequency of methylation in plasmacytomas was 62.5% for p16, 25% for p15, 0% for hMLH1, 62.5% for MGMT and 50% for DAPK. p14 was unmethylated in all cases (n=51). The correlation between gene methylation status and protein expression was assessed in 17 MM, 11 MGUS, and 8 plasmacytomas and we found that promoter methylation was strongly associated with gene silencing. All the samples methylated had lost the protein expression. In summary these findings demonstrate that aberrant methylation is an important mechanism of gene silencing in plasma cell disorders: 83.3% of MM, 46.1 of MGUS, and 75% of plasmacytomas have at least one hypermethylated gene (figure 1). We also show, that hypermethylation of p16 is a common phenomenon in plasma cell discrasias while there was no methylation of p14. Although the size of sample is small, we found that hMLH1 hypermethylation was found only in MM, while in plasmacytomas hypermethylation of MGMT and DAPK were frequent events. Moreover in survival studies of MM patients, a trend was observed between simultaneous aberrant methylation of hMLH1 and MGMT and poorer survival, but the number of cases studied limits the statistical analysis and the clinical implications of these results. To better define the clinical impact of methylation markers in plasma cell discrasias, it is therefore necessary to analyze a large number of patient samples. Figure 1. Gene methylation profiling of MM(A), MGUS(B), and plasmacytomas(C) using MSPCR Figure 1. Gene methylation profiling of MM(A), MGUS(B), and plasmacytomas(C) using MSPCR


Sign in / Sign up

Export Citation Format

Share Document