Hydroxymethylation and tumors: can 5-hydroxymethylation be used as a marker for tumor diagnosis and treatment?

Xu, Tianmin; Gao, Hao-Yue

doi:10.1186/s40246-020-00265-5

Cited by 39 publications

(49 citation statements)

References 112 publications

(117 reference statements)

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“…Besides, while 5mc is believed to have a repressive effect, 5hmc got permissive ramifications on the gene expression [107] . Also, since enhancers, promoters, and other regulatory elements are found to be enriched with 5hmc, it is also expected to be in more correlation with cellular gene expression [108] . 5hmc has recently been linked to many biological processes and disorders, including brain development, malignant melanoma, breast cancer, bladder cancer, and non-small cell lung cancer [108] , [109] , [110] .…”

Section: Computational Difficulties In Cfdna Methylation Data Analysismentioning

confidence: 99%

“…Also, since enhancers, promoters, and other regulatory elements are found to be enriched with 5hmc, it is also expected to be in more correlation with cellular gene expression [108] . 5hmc has recently been linked to many biological processes and disorders, including brain development, malignant melanoma, breast cancer, bladder cancer, and non-small cell lung cancer [108] , [109] , [110] . Although, in comparison to extensive cfDNA research on 5mc, 5hmc has yet to be thoroughly investigated in the realm of cancer diagnosis.…”

Section: Computational Difficulties In Cfdna Methylation Data Analysismentioning

confidence: 99%

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Computational challenges in detection of cancer using cell-free DNA methylation

Sharma

Verma

Kumar

et al. 2022

Computational and Structural Biotechnology Journal

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Cell-free DNA(cfDNA) methylation profiling is considered promising and potentially reliable for liquid biopsy to study progress of diseases and develop reliable and consistent diagnostic and prognostic biomarkers. There are several different mechanisms responsible for the release of cfDNA in blood plasma, and henceforth it can provide information regarding dynamic changes in the human body. Due to the fragmented nature, low concentration of cfDNA, and high background noise, there are several challenges in its analysis for regular use in diagnosis of cancer. Such challenges in the analysis of the methylation profile of cfDNA are further aggravated due to heterogeneity, biomarker sensitivity, platform biases, and batch effects. This review delineates the origin of cfDNA methylation, its profiling, and associated computational problems in analysis for diagnosis. Here we also contemplate upon the multi-marker approach to handle the scenario of cancer heterogeneity and explore the utility of markers for 5hmC based cfDNA methylation pattern. Further, we provide a critical overview of deconvolution and machine learning methods for cfDNA methylation analysis. Our review of current methods reveals the potential for further improvement in analysis strategies for detecting early cancer using cfDNA methylation.

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Section: Computational Difficulties In Cfdna Methylation Data Analysismentioning

confidence: 99%

Section: Computational Difficulties In Cfdna Methylation Data Analysismentioning

confidence: 99%

Computational challenges in detection of cancer using cell-free DNA methylation

Sharma

Verma

Kumar

et al. 2022

Computational and Structural Biotechnology Journal

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“…Demethylation changes are gene-specific, they occur dynamically under various conditions, and there is both a loss and an increase in the level of 5-mC [ 104 ]. It is believed that the 5-mC content in the genome depends primarily on the activity of TET, which may be influenced not only by mutations in the encoding genes, but also by cofactors such as iron ions and α-KG and co-substrates like ascorbate and molecular oxygen ( Figure 3 ) as TET enzymes are α-KG, oxygen- and iron-dependent dioxygenases [ 68 , 69 ].…”

Section: Role Of Tet Enzymes In Uf Developmentmentioning

confidence: 99%

Epigenetic Regulation in Uterine Fibroids—The Role of Ten-Eleven Translocation Enzymes and Their Potential Therapeutic Application

Włodarczyk

Nowicka

Ciebiera

et al. 2022

IJMS

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Uterine fibroids (UFs) are monoclonal, benign tumors that contain abnormal smooth muscle cells and the accumulation of extracellular matrix (ECM). Although benign, UFs are a major source of gynecologic and reproductive dysfunction, ranging from menorrhagia and pelvic pain to infertility, recurrent miscarriage, and preterm labor. Many risk factors are involved in the pathogenesis of UFs via genetic and epigenetic mechanisms. The latter involving DNA methylation and demethylation reactions provide specific DNA methylation patterns that regulate gene expression. Active DNA demethylation reactions mediated by ten-eleven translocation proteins (TETs) and elevated levels of 5-hydroxymethylcytosine have been suggested to be involved in UF formation. This review paper summarizes the main findings regarding the function of TET enzymes and their activity dysregulation that may trigger the development of UFs. Understanding the role that epigenetics plays in the pathogenesis of UFs may possibly lead to a new type of pharmacological fertility-sparing treatment method.

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“…Some data further suggest that it is not only a demethylation intermediate but also an epigenetic mark on its own [ 54 ]. It has also been proposed that 5hmC may serve as biomarker of cancer risk [ 55 ], diagnosis, and treatment (reviewed in [ 56 ]).…”

Section: Methylation and Demethylation Of Dnamentioning

confidence: 99%

Genomic Uracil and Aberrant Profile of Demethylation Intermediates in Epigenetics and Hematologic Malignancies

Oliński

Slupphaug

Foksiński

et al. 2021

IJMS

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DNA of all living cells undergoes continuous structural and chemical alterations resulting from fundamental cellular metabolic processes and reactivity of normal cellular metabolites and constituents. Examples include enzymatically oxidized bases, aberrantly methylated bases, and deaminated bases, the latter largely uracil from deaminated cytosine. In addition, the non-canonical DNA base uracil may result from misincorporated dUMP. Furthermore, uracil generated by deamination of cytosine in DNA is not always damage as it is also an intermediate in normal somatic hypermutation (SHM) and class shift recombination (CSR) at the Ig locus of B-cells in adaptive immunity. Many of the modifications alter base-pairing properties and may thus cause replicative and transcriptional mutagenesis. The best known and most studied epigenetic mark in DNA is 5-methylcytosine (5mC), generated by a methyltransferase that uses SAM as methyl donor, usually in CpG contexts. Oxidation products of 5mC are now thought to be intermediates in active demethylation as well as epigenetic marks in their own rights. The aim of this review is to describe the endogenous processes that surround the generation and removal of the most common types of DNA nucleobase modifications, namely, uracil and certain epigenetic modifications, together with their role in the development of hematological malignances. We also discuss what dictates whether the presence of an altered nucleobase is defined as damage or a natural modification.

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Hydroxymethylation and tumors: can 5-hydroxymethylation be used as a marker for tumor diagnosis and treatment?

Cited by 39 publications

References 112 publications

Computational challenges in detection of cancer using cell-free DNA methylation

Computational challenges in detection of cancer using cell-free DNA methylation

Epigenetic Regulation in Uterine Fibroids—The Role of Ten-Eleven Translocation Enzymes and Their Potential Therapeutic Application

Genomic Uracil and Aberrant Profile of Demethylation Intermediates in Epigenetics and Hematologic Malignancies

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