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Abstract
Epigenetic and genetic alterations contribute to cancer initiation and progression. Epigenetics refers to the study of heritable changes in gene expression without alterations in DNA sequences. Epigenetic changes are reversible and include key processes of DNA methylation, chromatin modifications, nucleosome positioning, and alterations in noncoding RNA profiles. Disruptions in epigenetic processes can lead to altered gene function and cellular neoplastic transformation. Epigenetic modifications precede genetic changes and usually occur at an early stage in neoplastic development. Recent technological advances offer a better understanding of the underlying epigenetic alterations during carcinogenesis and provide insight into the discovery of putative epigenetic biomarkers for detection, prognosis, risk assessment, and disease monitoring. In this chapter we provide information on various epigenetic mechanisms and their role in carcinogenesis, in particular, epigenetic modifications causing genetic changes and the potential clinical impact of epigenetic research in the future.
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Affiliation(s)
- Rajnee Kanwal
- Department of Urology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
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Jin L, Wang W, Hu D, Lü J. A new insight into the 5-carboxycytosine and 5-formylcytosine under typical bisulfite conditions: a deamination mechanism study. Phys Chem Chem Phys 2014; 16:3573-85. [PMID: 24413472 DOI: 10.1039/c3cp54266a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
5-Methylcytosine (5-MeCyt) can be converted to 5-hydroxymethylcytosine (5-hmCyt) in mammalian DNA by the ten-eleven translocation enzymes. The conventional bisulfite sequencing cannot discriminate 5-hmCyt from 5-MeCyt, whereas the oxidation products of 5-hmCyt, 5-carboxycytosine (5-caCyt) and 5-formylcytosine (5-fCyt) enable them to be identified in bisulfite sequencing. This mechanism likely involves the decarboxylation of 5-caCyt and deformylation of 5-fCyt to cytosine (Cyt) before deamination. Another possibility could be a direct bisulfite-induced deamination reaction followed by decarboxylation and deformylation. Here the HSO3(-)-induced direct hydrolytic deamination of 5-caCytN3(+)-SO3(-) (paths A and B) and 5-O(+)fCytN3(+)-SO3(-) (paths C and D) has been explored at the MP2/6-311++G(3df,3pd)//B3LYP/6-311++G(d,p) level. The activation free energy (ΔG(s≠) = 54.16 kJ mol(-1)) of the direct hydrolytic deamination of 5-caCytN3(+)-SO3(-) path A is much lower than the ΔG(s≠) of CytN3(+)-SO3(-) (100.91 kJ mol(-1)) under bisulfite conditions, implying that 5-caCyt may firstly involve a process of deamination. Meanwhile, the ΔG(s≠) (103.84 kJ mol(-1)) of the HSO3(-)-induced direct hydrolytic deamination of 5-O(+)fCytN3(+)-SO3(-) path C is in close proximity to our previous theoretical data for CytN3(+)-SO3(-), indicating that the deamination of 5-fCyt is also likely to occur in the presence of bisulfite. Meanwhile, the HSO3(-)-induced direct hydrolytic deamination of 5-caCytN3(+)-SO3(-) path A and 5-O(+)fCytN3(+)-SO3(-) path C is represented and has been further explored in the presence of one and two water molecules. The results show that both in the gas and aqueous phases, the participation of one and two water molecules makes the HSO3(-)-induced direct hydrolytic deamination of 5-caCytN3(+)-SO3(-) path A unfavorable, whereas the contribution of one and two water molecules facilitates the HSO3(-)-induced direct hydrolytic deamination of 5-O(+)fCytN3(+)-SO3(-) path C.
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Affiliation(s)
- Lingxia Jin
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China.
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Jin L, Wang L, Zhang C, Wang W, Min S, Hu D. Is the contribution of cis and trans protonated 5-methylcytosine-SO3(-) isomers equal in the conversion to thymine-SO3(-) under bisulfite conditions? A theoretical perspective. Phys Chem Chem Phys 2014; 16:16264-77. [PMID: 24974803 DOI: 10.1039/c4cp00387j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cytosine (Cyt) can be converted to 5-methylcytosine (5-MeCyt) in CpG sequences of DNA. Conventional bisulfite sequencing can discriminate Cyt from 5-MeCyt, however inappropriate conversion of 5-MeCyt to thymine and a failure to convert Cyt to uracil always occur when Cyt and 5-MeCyt are treated with bisulfite, which would lead to erroneous estimates of DNA methylation densities. Here, the direct hydrolytic deamination of cis (paths A-C) and trans (paths A'-C') 5-MeCytN3(+)-SO3(-) isomers with bisulfite have been explored at the MP2/6-311++G(3df,3pd)//B3LYP/6-311++G(d,p) level. The activation free energies (ΔG(s-a≠)) of the cis and trans 5-MeCytN3(+)-SO3(-) isomers' paths exhibit no obvious differences, implying both isomers may make an equal contribution to the hydrolytic deamination of 5-MeCyt under bisulfite conditions. It is greatly expected that these results could aid experimental scientists to explore new methods to avoid the formation of the deaminated reactants (5-MeCytN3(+)-SO3(-)). Meanwhile, the HSO3(-)-induced direct hydrolytic deamination of cis and trans 5-MeCytN3(+)-SO3(-) isomers is represented by paths A and A', respectively, and has been further explored in the presence of two water molecules. It was found that the contribution of two water molecules renders the HSO3(-)-induced direct hydrolytic deamination of cis and trans 5-MeCytN3(+)-SO3(-) isomers by paths A and A' favourable. In addition, the ΔG(s-a≠) values (85.74-85.34 kJ mol(-1)) of the rate-limiting steps of the two water-mediated paths A and A' are very close to that of the theoretical value for CytN3(+)-SO3(-) (88.18 kJ mol(-1)), implying that the free barrier gap between Cyt and 5-MeCyt is very small under bisulfite conditions. This further suggests that bisulfite sequencing technology may be easily influenced by the external environment.
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Affiliation(s)
- Lingxia Jin
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China.
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Halim MA, Almatarneh MH, Poirier RA. Mechanistic Study of the Deamidation Reaction of Glutamine: A Computational Approach. J Phys Chem B 2014; 118:2316-30. [DOI: 10.1021/jp4107266] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Mohammad A. Halim
- Department
of Chemistry, Memorial University, St. John’s, NL, Canada A1B 3X7
| | | | - Raymond A. Poirier
- Department
of Chemistry, Memorial University, St. John’s, NL, Canada A1B 3X7
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Yu Y, Liu K, Zhao H, Song D. Mechanism of the deamination reaction of isoguanine: a theoretical investigation. J Phys Chem A 2013; 117:5715-25. [PMID: 23789717 DOI: 10.1021/jp4031738] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mechanisms of the deamination reactions of isoguanine with H2O, OH(-), and OH(-)/H2O and of protonated isoguanine (isoGH(+)) with H2O have been investigated by theoretical calculations. Eight pathways, paths A-H, have been explored and the thermodynamic properties (ΔE, ΔH, and ΔG), activation energies, enthalpies, and Gibbs energies of activation were calculated for each reaction investigated. Compared with the deamination reaction of isoguanine or protonated isoguanine (isoGH(+)) with water, the deamination reaction of isoguanine with OH(-) shows a lower Gibbs energy of activation at the rate-determining step, indicating that the deamination reaction of isoguanine is favorably to take place for the deprotonated form isoG(-) with water. With the assistance of an extra water, the reaction of isoguanine with OH(-)/H2O, pathways F and H, are found to be the most feasible pathways in aqueous solution due to their lowest Gibbs energy of activation of 174.7 and 172.6 kJ mol(-1), respectively, at the B3LYP/6-311++G(d,p) level of theory.
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Affiliation(s)
- Youqing Yu
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
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CHEN ZEQIN, XUE YING. MECHANISMS FOR THE DECOMPOSITION OF HYDROXYL-RADICAL-INDUCED CYTOSINE HYDROPEROXIDES: A COMPUTATIONAL STUDY. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2013. [DOI: 10.1142/s0219633613500272] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Hydroxyl-radical-induced damage to cytosine leads to a multitude of base modifications, which contribute to the natural processes of aging, mutagenesis and carcinogenesis. The stable products resulting from the main hydroxyl-radical-induced cytosine hydroperoxide, 5-hydroxy-6-hydroperoxyl-5,6-dihydrocytosine (5-OH-6-OOH-DHC), have been mapped out in the present work for the first time using ab initio calculations. Optimized geometries of all stationary structures in the gas phase were determined at the MP2 and B3LYP using the 6-31G(d) basis set and at the B3LYP/6-311++G(d,p) levels of theory. Energies were also determined at the G3MP2 level of theory. Meanwhile, full optimization of all stationary points were also performed in aqueous solution at the B3LYP/CPCM/6-31G(d) level of theory to evaluate the solvent effect. Three distinct possible pathways, pathways A–C, were evaluated. For pathway C, four channels, channels D–G, were characterized in turn. In each pathway, both the direct and the water-mediated processes were considered. The calculated results clearly manifest that (i) pathway C is kinetically favored over pathways A and B and is the most energetically feasible decomposition process of 5-OH-6-OOH-DHC; (ii) for pathway C, channels D, E and G are energetically feasible mechanisms and 6,7-dihydroxy-[1,3,5]triazepane-2,4-dione, 1-carbamoyl-2-oxo-4,5-dihydroxyimidazolidine, and biuret therefore are predicted to be the kinetically favored decomposition products of 5-OH-6-OOH-DHC; (iii) channel G may be kinetically favored over channels D and E and have the highest possibility to occur; (iv) the thermal decomposition of 5-OH-6-OOH-DHC can be significantly promoted by the presence of one explicit water molecule. Apart from characterizing the experimental products well, the main striking result of the present DFT computational study is the identification of a new theoretical optimum decomposition product, i.e. 6,7-dihydroxy-[1,3,5]triazepane-2,4-dione. The data and insights presented here have elucidated the chemical properties of 5-OH-6-OOH-DHC in free radical reactions and should facilitate to assess their mutagenic features.
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Affiliation(s)
- ZE-QIN CHEN
- College of Chemistry and Chemical Engineering, Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, China West Normal University, Nanchong 637002, People's Republic of China
| | - YING XUE
- College of Chemistry, Key Laboratory of Green Chemistry and Technology in Ministry of Education, Sichuan University, Chengdu 610064, People's Republic of China
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Suspène R, Aynaud MM, Vartanian JP, Wain-Hobson S. Efficient deamination of 5-methylcytidine and 5-substituted cytidine residues in DNA by human APOBEC3A cytidine deaminase. PLoS One 2013; 8:e63461. [PMID: 23840298 PMCID: PMC3688686 DOI: 10.1371/journal.pone.0063461] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Accepted: 04/03/2013] [Indexed: 11/18/2022] Open
Abstract
Deamination of 5-methylcytidine (5MeC) in DNA results in a G:T mismatch unlike cytidine (C) deamination which gives rise to a G:U pair. Deamination of C was generally considered to arise spontaneously. It is now clear that human APOBEC3A (A3A), a polynucleotide cytidine deaminase (PCD) with specificity for single stranded DNA, can extensively deaminate human nuclear DNA. It is shown here that A3A among all human PCDs can deaminate 5-methylcytidine in a variety of single stranded DNA substrates both in vitro and in transfected cells almost as efficiently as cytidine itself. This ability of A3A to accommodate 5-methyl moiety extends to other small and physiologically relevant substituted cytidine bases such as 5-hydroxy and 5-bromocytidine. As 5MeCpG deamination hotspots characterize many genes associated with cancer it is plausible that A3A is a major player in the onset of cancer.
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Affiliation(s)
| | | | | | - Simon Wain-Hobson
- Molecular Retrovirology Unit, Institut Pasteur, Paris, France
- * E-mail:
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Jin L, Wang W, Hu D, Lü J. The conversion of protonated cytosine-SO3− to uracil-SO3−: Insights into the novel induced hydrolytic deamination through bisulfite catalysis. Phys Chem Chem Phys 2013; 15:9034-42. [DOI: 10.1039/c3cp51275d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Abstract
Cancer initiation and progression is controlled by both genetic and epigenetic events. The complexity of carcinogenesis cannot be accounted for by genetic alterations alone but also involves epigenetic changes. Epigenetics refers to the study of mechanisms that alter gene expression without altering the primary DNA sequence. Epigenetic mechanisms are heritable and reversible, and include changes in DNA methylation, histone modifications and small noncoding microRNAs (miRNA). Disruption of epigenetic processes can lead to altered gene function and malignant cellular transformation. Aberrant epigenetic modifications probably occur at a very early stage in neoplastic development, and they are widely described as essential players in cancer progression. Recent advances in epigenetics offer a better understanding of the underlying mechanism(s) of carcinogenesis and provide insight into the discovery of putative cancer biomarkers for early detection, disease monitoring, prognosis, and risk assessment. In this review, we summarize the current literature on epigenetic changes causing genetic alterations that are thought to contribute to cancer, and discuss the potential impact of epigenetics future research.
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Affiliation(s)
- R Kanwal
- Department of Urology, Case Western Reserve University, Case Comprehensive Cancer Center, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
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Abstract
Cancer initiation and progression is controlled by both genetic and epigenetic events. The complexity of carcinogenesis cannot be accounted for by genetic alterations alone but also involves epigenetic changes. Epigenetics refers to the study of mechanisms that alter gene expression without altering the primary DNA sequence. Epigenetic mechanisms are heritable and reversible, and include changes in DNA methylation, histone modifications and small noncoding microRNAs (miRNA). Disruption of epigenetic processes can lead to altered gene function and malignant cellular transformation. Aberrant epigenetic modifications probably occur at a very early stage in neoplastic development, and they are widely described as essential players in cancer progression. Recent advances in epigenetics offer a better understanding of the underlying mechanism(s) of carcinogenesis and provide insight into the discovery of putative cancer biomarkers for early detection, disease monitoring, prognosis, and risk assessment. In this review, we summarize the current literature on epigenetic changes causing genetic alterations that are thought to contribute to cancer, and discuss the potential impact of epigenetics future research.
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Affiliation(s)
- R Kanwal
- Department of Urology, Case Western Reserve University, Case Comprehensive Cancer Center, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
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