DNA methylation and hydroxymethylation patterns in acute myeloid leukemia patients with mutations in DNMT3A and IDH1/2 and their combinations

Šestáková, Šárka; Krejčík, Zdeněk; Folta, Adam; Cerovská, Ela; Šálek, Cyril; Merkerová, Michaela Dostálová; Pecherková, Pavla; Ráčil, Zdeněk; Mayer, Jiřı́; Cetkovský, Petr; Remešová, Hana

doi:10.3233/cbm-182176

Cited by 7 publications

(5 citation statements)

References 15 publications

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“…The three analyzed CpGs with different levels of methylation were selected based on healthy donors’ data from Infinium MethylationEPIC BeadChip (Illumina, San Diego, CA, USA) acquired in our previous work [40]. Characteristic of chosen loci is summarized in Table 7.…”

Section: Methodsmentioning

confidence: 99%

DNA Methylation Validation Methods: a Coherent Review with Practical Comparison

2019

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Here, we present a practical overview of four commonly used validation methods for DNA methylation assessment: methylation specific restriction endonucleases (MSRE) analysis, pyrosequencing, methylation specific high-resolution DNA melting (MS-HRM) and quantitative methylation specific polymerase chain reaction (qMSP). Using these methods, we measured DNA methylation levels of three loci in human genome among which one was highly methylated, one intermediately methylated and one unmethylated. We compared the methods in terms of primer design demands, methods’ feasibility, accuracy, time and money consumption, and usability for clinical diagnostics. Pyrosequencing and MS-HRM proved to be the most convenient methods. Using pyrosequencing, it is possible to analyze every CpG in a chosen region. The price of the instrument may represent the main limitation of this methodology. MS-HRM is a simple PCR-based method. The measurement was quick, cheap and very accurate. MSRE analysis is based on a methylation specific digestion of DNA. It does not require a bisulfite conversion of DNA as the other methods. MSRE analysis was very easy to perform, however, it was not suitable for intermediately methylated regions and it was also quite expensive. qMSP is a qPCR-based method that uses primers designed specifically for methylated and unmethylated alleles of a chosen region. This was the least accurate method and also the primer design and optimization of PCR conditions were highly demanding.

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Section: Methodsmentioning

confidence: 99%

DNA Methylation Validation Methods: a Coherent Review with Practical Comparison

2019

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“…Both of these substitutions are described for the first time not only in spinal cord astrocytomas, but also in CNS tumors in general. We were able to find only two publications where the first mutation (R82K) was described in patients with acute myeloid leukemia [ 11 ] and primary skin melanoma [ 12 ]. We did not find data on the second mutation (I76T).…”

Section: Resultsmentioning

confidence: 99%

Rare Cases of IDH1 Mutations in Spinal Cord Astrocytomas

et al. 2020

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A low occurrence rate of spinal cord gliomas (4.3% of primary and glial CNS tumors) and the associated difficulties in building statistically significant cohorts of patients considerably slow down the development of effective approaches to the treatment of spinal cord tumors compared to brain tumors. Despite our extensiveknowledge regardingIDHmutations in intracranial tumors, mutations of this gene in spinal cord astrocytomas remain poorly understood. In thisstudy, we report on five cases of identified mutations in theIDH1gene in spinal cord astrocytoma cells, two of which are unique, as they have never been previously described in CNS gliomas.

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“…GZMB encodes the preprotein secreted by NK cell and CTLs, which is related to the apoptosis of target cells ( 29 ). Hypermethylation of the enhancer upstream of GZMB might contribute to an inferior overall survival of AML ( 30 ). The mutation in these genes might cause obstacles to the elimination of abnormal cells.…”

Section: Discussionmentioning

confidence: 99%

Development and Validation of a Novel Prognostic Model for Acute Myeloid Leukemia Based on Immune-Related Genes

Ding

Jin

et al. 2021

Front. Immunol.

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The prognosis of acute myeloid leukemia (AML) is closely related to immune response changes. Further exploration of the pathobiology of AML focusing on immune-related genes would contribute to the development of more advanced evaluation and treatment strategies. In this study, we established a novel immune-17 signature based on transcriptome data from The Cancer Genome Atlas (TCGA) and The Genotype-Tissue Expression (GTEx) databases. We found that immune biology processes and transcriptional dysregulations are critical factors in the development of AML through enrichment analyses. We also formulated a prognostic model to predict the overall survival of AML patients by using LASSO (Least Absolute Shrinkage and Selection Operator) regression analysis. Furthermore, we incorporated the immune-17 signature to improve the prognostic accuracy of the ELN2017 risk stratification system. We concluded that the immune-17 signature represents a novel useful model for evaluating AML survival outcomes and may be implemented to optimize treatment selection in the next future.

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DNA methylation and hydroxymethylation patterns in acute myeloid leukemia patients with mutations in DNMT3A and IDH1/2 and their combinations

Cited by 7 publications

References 15 publications

DNA Methylation Validation Methods: a Coherent Review with Practical Comparison

DNA Methylation Validation Methods: a Coherent Review with Practical Comparison

Rare Cases of IDH1 Mutations in Spinal Cord Astrocytomas

Development and Validation of a Novel Prognostic Model for Acute Myeloid Leukemia Based on Immune-Related Genes

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