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Aberrant DNA methylation and genome instability and mutation in
cancer
Song Li1, Yihan Wang1, Hongbo Liu1, Jingyuan Fu2, Yan Zhang2
1. College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
2. The Northeast Agricultural University, Harbin, 150031, China
[email protected] (YZ)
Abstract
In the process of normal cells transforming into cancer cells with the disruption control
of epigenetic and genetic, they will gradually acquire the cancer Hallmarks. Epigenetic
and genetic influence each other and closely cooperate to promoter oncogenic
transformation in variety ways. It is clear that DNA methylation plays important roles
in generation of mutation of tumor suppressor genes (TSGs) eventually lead to
inactivation such as the probability of C mutation to T of the well-known TSGs p53 is
high due to 5-methylcytosine residues is more prone to spontaneous deamination. The
most common pattern of epigenetic control of tumor suppressor genes inactivation is
hypermethylation of promoter region in cancers and the hypermethylation of CpG
islands can also contribute to the increasing mutation rate of tumor suppressor genes
such as CpG islands hypermethylation appeared to be tightly linked with the V600E
mutation of the BRAF oncogene in colorectal cancer. Global hypomethylation is
closely associated with chromosomal instability, which the methylation status of LINE1 is a marker of global methylation, there is a significant relationship between LINE-1
hypomethylation and DNA copy number variation in the gastrointestinal stromal tumor.
Aberrant DNA methylation is pervasive in cancer, which is similar to genomic
instability and mutation.
Keywords: hypermethylation; hypomethylation; chromosomal instability; mutation;
cancer
Introduction
In the successful disruption of cell proliferation, and angiogenesis, cell death, invasion
and metastasis of the control, the normal cells will gradually turn into cancer
cells(Hanahan and Weinberg 2011). This process of evolution is the need to continue to
accumulate carcinogenic characteristics in the clonal cell line and most importantly
genetic mechanisms such as mutation, copy number variation, insertion, deletion, and
recombination are consistent with the changes in the phenotype of the tumor. For this
reason, cancer is considered to be a genetic disease for a long time(Esteller and Herman
2002; Choi and Lee 2013) . However, the probability of occurrence of these genetic
events is very low, so it is not a particularly effective method for malignant tumors, the
epigenetic control mechanisms provide another option for obtaining stable oncogenic
characteristics. Epigenetic states are flexible and varied in the process of cell
differentiation, but they are important in determining the phenotype of cells. With the
ongoing genetic and epigenetic studies, we know that they will interact with each other
and work together to help the cells acquire cancer Hallmarks.
DNA methylation is a heritable but irreversible epigenetic modification, which has the
potential to change the gene expression and has the profound development and the
genetic influence(Jones and Baylin 2002). Methylation can induce mutation,
methylated cytosine normally occurs the probability of mutation of 10 to 40 times
higher compared with unmethylated(Rideout, Coetzee et al. 1990; Jones and Gonzalgo
1997; Esteller and Herman 2002). Methylation has a prominent contribution to the
generation of biological diversity and the germ-line mutation and to transition mutation
which leads to tumor suppressor gene inactivation. In addition to mutations, tumor
suppressor gene can also inactivated by high methylation level of promoter. The change
of DNA methylation is a common feature of cancer and plays a driver role in the tumor
primary formation process, this view has been confirmed by a lot of studies(2013; Chen,
Che et al. 2015; Kok-Sin, Mokhtar et al. 2015). The roles of 5-methylcytosine in cancer
is specifically manifested in the following three aspects.
Methylation and mutation
Methylation can induce tumor suppressor genes mutation. Methylated and
unmethylated cytosine both undergo spontaneously hydrolytic deamination but the
product is not the same, uracil and thymine respectively. Uracil bases is not inherent in
DNA, compared with guanine thymine mismatch is easier to be repaired (Cooper, Mort
et al. 2010; Song, Cannistraro et al. 2011; Stier and Kiss 2013). The difference products
in deamination can be very good explanation of methylated cytosine relative to
unmethylated cytosine was greater for the contribution of mutations. Therefore, in CpG
dinucleotides the rate of methylated cytosine to thymine mutation probability is about
ten times higher than the human genome other SNV (Hodgkinson and Eyre-Walker
2011). This effect is particularly prominent in highly proliferative tissues because in the
parent strand 5-methylcytosine deamination is occurring in DNA replication before, all
the T will be a replacement with A so it will not be considered a kind of injury and
repair. In human cancers, close to 1/4 TP53 mutation are caused by methylation.
Although CpG dinucleotides in the human genome accounted for only 1% of all the
dinucleotide, CpG dinucleotides occur transition mutations accounted for 25% of 254
point mutation in p53 gene in a study and in another study accounted for 33 percent of
324 p53 mutation. In other relevant p53 mutation research such as in 263 cases of
human lung cancer with 7%, in 119 cases of HCC with 10% and in 180 cases of
colorectal cancer with 41% were found in the dinucleotide CpG transition mutation.
Rideout and coworkers showed that cytosine residues in the p53 gene known to have
undergone somatic mutation were methylated in all normal human tissues analyzed
(Rideout, Coetzee et al. 1990; Fortes, Kuasne et al. 2015).
Effect of cytosine methylation in germ cell lines also have been studied. The results of
a study showed that human genetic diseases of 135 point mutation in 52 were occurred
in CpG dinucleotides (37%). In an analysis of 216 mutations in the coagulation factor
IX gene, giving rise to hemophilia B, 97 mutations were CpG transitions (45%). The
prominent contribution of CpG dinucleotide in mutation was also obvious for germline mutations in tumor suppressor genes. The results of several LiFraumeni syndrome
researches showed that 2 out of 6 germ-line mutations in the P53 gene were CpG
transition mutations (Hensel, Xiang et al. 1991). Three out of eight germ-line mutations
in patients with retinoblastoma were found to be CpG transition mutations (Sasa, Kondo
et al. 1993).
In addition to the above mentioned, we also know that CIMP is associated with gene
mutation. So what does CIMP means? Aberrant DNA methylation of promoter CpG
islands was initially viewed as a stochastic genome event. However, CpG island
hypermethylation was found in many cases of colorectal cancers with an exceptionally
high frequency. Thus, CpG islands hypermethylation possibly attributed to out of
epigenetic control. This phenomenon is considered as “CpG Island Methylator
Phenotype” (CIMP)(Shen and Laird 2013). So far, many studies have shown that CIMP
is closely related to the gene mutation. For example, CIMP appeared to be tightly linked
with the V600E mutation of the BRAF oncogene in colorectal cancer(Weisenberger,
Siegmund et al. 2006), while CIMP was closely related with IDH1 mutation out of
expectation in glioma (Noushmehr, Weisenberger et al. 2010).
To sum up, we can see that DNA methylation can induce gene mutations in many ways,
which can cause diseases and even cancer. In the process of cancer evolution and
progression, the genetic and epigenetic mechanisms should be mutual influence, and
ultimately cooperate with each other to obtain various cancer Hallmarks.
Aberrant methylation and alerting gene expression
In cancer, we can often see the changes in the two DNA methylation patterns:
hypermethylation of promoter of tumor suppressor genes and the global
hypomethylation. And then affect the expression of cancer genes to help cancer cells to
obtain the selective advantage, therefore the DNA methylation pattern changes plays
an important role in the process of malignant tumor formation (Laird 2010).
Hypermethylation of promoter region is an important mechanism for gene silencing.
The promoter region of cancer suppressor genes is typically low methylation in normal
tissues and cells, while is hypermethylation in cancers. The hypermethylation of CpG
island is found in almost all cancers. Many of the cellular pathways are inactivated by
the effects of this epigenetic change: DNA repair (hMLH1, MGMT), cell cycle (p14,
p15, p16), cell apoptosis (DAPK), cell adhesion (CDH1, CDH13), detoxification
(GSTP1)(Choi and Lee 2013) Hypermethylation is not an independent branch of
epigenetic control. It is closely related to other parts, such as methyl-binding proteins,
DNA methyltransferases and histone deacetylase.
In addition to hypermethylation of promoter of tumor suppressor genes, there are a large
number of literature showed that the global and gene specific loss of methylation have
been observed in cancer. There is now an important question that hypermethylation of
promoter region can inhibit the expression of genes, and whether or not the low
methylation of specific pro-growth genes will increase their expression in cancers. A
lot of works focused on DNA hypomethylation in cancer but unfortunately most of
them have not analyzed the relation between the oncogenes expression level and their
promoter region hypomethylation. Because there are a large majority of the cytosine
located in repeated sequences, mainly the transposons. The global hypomethylation
induced by repeated sequences demethylation in cancer has a close relationship with
the mutation and genome instability (Easwaran and Baylin 2013). We will discuss this
issue in detail later.
We can see a great difference in the pattern of methylation in cancer and normal tissues.
Differentially methylated regions (DMRs) play critical roles in development, aging and
diseases. With the development of the two generation sequencing technology, the
resolution of human genome methylation spectrum will be increasingly higher, but the
price of sequencing will decrease very fast. Advances in technology have provided a
great convenience for the study of the difference methylation pattern between cancer
and normal tissues, but it has also brought a huge challenge to the data analysis. As a
result, more and more highly effective and accurate bioinformatics tools and methods
have been developed. For example, CpG_MPs: identification of CpG methylation
patterns of genomic regions from high-throughput bisulfite sequencing data (Su, Yan et
al. 2013); QDMR: a quantitative method for identification of differentially methylated
regions by entropy (Zhang, Liu et al. 2011). With so many people’s efforts, we believe
that more secrets hidden in DNA methylation will slowly be revealed.
DNA methylation and genomic instability
It is worth noting that global hypomethylation is closely related to the genetic instability
mentioned above, which implies that the abnormal methylation status in cancer cells
plays an important role in the process of chromosome deviation.
A lot of studies have confirmed that global DNA hypomethylation can increase the
instability of the chromosome and is very important in cancer. The methylation status
of the long interspersed nuclear element-1 (LINE-1) sequence is a marker of global
methylation. The methylation level of LINE-1 is lower than that of normal mucosa and
is significantly correlated with lymph node metastasis, and the frequency of p53
mutation in esophageal squamous carcinoma cells ((Kawano, Saeki et al. 2014).
Hiroyuki Kawano and coworkers point out that the whole genome hypomethylation
caused by chronic inflammation, which initiate carcinogenesis of esophageal squamous
cell carcinoma through chromosome instability. In addition, another team has been
investigated the relationship between LINE-1 hypomethylation and chromosome
abnormalities in the gastrointestinal stromal tumor (GISTs)(Igarashi, Suzuki et al.
2010). By carrying out an array CGH analysis they wanted to know whether LINE-1
hypomethylation is linked with chromosomal gain or loss. The results showed that
chromosomal abnormalities associated with LINE-1 hypomethylation are often
represented as losses, not gains and suggested a significant relationship between LINE1 hypomethylation and DNA copy number variation in GISTs. Cristian Coarfa’s group
have developed several tools such as Breakout, an algorithm for fast and accurate
detection of structural variants, to investigate the interaction between hypomethylation
and structural genomic variants. They demonstrated some previous findings that
hypomehlation of DNA and binding sites of Suz12 are closely associated with genome
instability in human germline. Their results suggested that structural mutations are not
randomly distributed relative to the epigenome and are affected by the cell-type specific
hypomethylation patterns in both somatic cells and germline.
The veil of hypomethylation affecting human genome stability has been revealed. With
the development of the sequencing technology and analysis methods and tools, the
secrets of interaction and mechanism between epigenome and structural genomic
variation will gradually emerge from the water.
Conclusion
More and more researches confirmed that the mechanism of genetic and epigenetic
influence each other and cooperate to promoter oncogenic transformation in a variety
of ways. The cancer genome and epigenome affect and cooperate with each other to
achieve similar results, such as the inactivation of tumor suppressor genes mentioned
above such as p53, BRAF, IDH1, RB by either mutation or hypermethylation of
promoter regions. On the one hand, global DNA hypomethylation can induce human
genomic instability, which gives a more chance for the mutation of the oncogene, the
methylation status of LINE-1 is closely associated with chromosomal stability. On the
other hand, hypermehtylation can increase the mutation rate of tumor suppressor genes
such as hypermethylation of promoter region produced a favorable condition for
inactivation mutant of the BRAF in the colorectal cancer.
Many questions remind in this field such as altered methylation patterns in cancer cell
genomes: Cause or consequence? There is such a point that DNA methylation is
considered as a consolidating rather than an initiating event in tumor suppressor gene
inactivation. Somatic inactivation of X chromosome in female, where DNA
hypermethylation of promoter CpG islands is after inactivation not before (71, 95, 108).
Another major question is how to investigate the mechanistic basis for well-known
examples of disruption of epigenetic control. Therefore, the identification of epigenetic
drivers must rely more on the analysis of transcriptional consequences and most
importantly functional experimental validation of the effect of epigenetic genes
inactivation on cellular proliferation, immortality, angiogenesis, cell death, invasion
and metastasis affected.
Acknowledgments
Funding for this work provided by the National Natural Science Foundation of China
(grant numbers 31371334, 61403112), the Natural Scientific Research Fund of
Heilongjiang Provincial (grant number ZD2015003).
References
(2013). "Comprehensive molecular characterization of clear cell renal cell carcinoma." Nature 499(7456):
43-49.
Chen, Z., Q. Che, et al. (2015). "Piwil1 causes epigenetic alteration of PTEN gene via upregulation of DNA
methyltransferase in type I endometrial cancer." Biochem Biophys Res Commun.
Choi, J. D. and J. S. Lee (2013). "Interplay between Epigenetics and Genetics in Cancer." Genomics Inform
11(4): 164-173.
Cooper, D. N., M. Mort, et al. (2010). "Methylation-mediated deamination of 5-methylcytosine appears
to give rise to mutations causing human inherited disease in CpNpG trinucleotides, as well as
in CpG dinucleotides." Hum Genomics 4(6): 406-410.
Easwaran, H. and S. B. Baylin (2013). "Epigenetic abnormalities in cancer find a "home on the range"."
Cancer Cell 23(1): 1-3.
Esteller, M. and J. G. Herman (2002). "Cancer as an epigenetic disease: DNA methylation and chromatin
alterations in human tumours." J Pathol 196(1): 1-7.
Fortes, F. P., H. Kuasne, et al. (2015). "DNA methylation patterns of candidate genes regulated by
thymine DNA glycosylase in patients with TP53 germline mutations." Braz J Med Biol Res: 0.
Hanahan, D. and R. A. Weinberg (2011). "Hallmarks of cancer: the next generation." Cell 144(5): 646674.
Hensel, C. H., R. H. Xiang, et al. (1991). "Use of the single strand conformation polymorphism technique
and PCR to detect p53 gene mutations in small cell lung cancer." Oncogene 6(6): 1067-1071.
Hodgkinson, A. and A. Eyre-Walker (2011). "Variation in the mutation rate across mammalian genomes."
Nat Rev Genet 12(11): 756-766.
Igarashi, S., H. Suzuki, et al. (2010). "A novel correlation between LINE-1 hypomethylation and the
malignancy of gastrointestinal stromal tumors." Clin Cancer Res 16(21): 5114-5123.
Jones, P. A. and S. B. Baylin (2002). "The fundamental role of epigenetic events in cancer." Nat Rev Genet
3(6): 415-428.
Jones, P. A. and M. L. Gonzalgo (1997). "Altered DNA methylation and genome instability: a new pathway
to cancer?" Proc Natl Acad Sci U S A 94(6): 2103-2105.
Kawano, H., H. Saeki, et al. (2014). "Chromosomal instability associated with global DNA
hypomethylation is associated with the initiation and progression of esophageal squamous cell
carcinoma." Ann Surg Oncol 21 Suppl 4: S696-702.
Kok-Sin, T., N. M. Mokhtar, et al. (2015). "Identification of diagnostic markers in colorectal cancer via
integrative epigenomics and genomics data." Oncol Rep 34(1): 22-32.
Laird, P. W. (2010). "Principles and challenges of genomewide DNA methylation analysis." Nat Rev Genet
11(3): 191-203.
Noushmehr, H., D. J. Weisenberger, et al. (2010). "Identification of a CpG island methylator phenotype
that defines a distinct subgroup of glioma." Cancer Cell 17(5): 510-522.
Rideout, W. M., 3rd, G. A. Coetzee, et al. (1990). "5-Methylcytosine as an endogenous mutagen in the
human LDL receptor and p53 genes." Science 249(4974): 1288-1290.
Sasa, M., K. Kondo, et al. (1993). "Frequency of spontaneous p53 mutations (CpG site) in breast cancer
in Japan." Breast Cancer Res Treat 27(3): 247-252.
Shen, H. and P. W. Laird (2013). "Interplay between the cancer genome and epigenome." Cell 153(1):
38-55.
Song, Q., V. J. Cannistraro, et al. (2011). "Rotational position of a 5-methylcytosine-containing
cyclobutane pyrimidine dimer in a nucleosome greatly affects its deamination rate." J Biol
Chem 286(8): 6329-6335.
Stier, I. and A. Kiss (2013). "Cytosine-to-uracil deamination by SssI DNA methyltransferase." PLoS One
8(10): e79003.
Su, J., H. Yan, et al. (2013). "CpG_MPs: identification of CpG methylation patterns of genomic regions
from high-throughput bisulfite sequencing data." Nucleic Acids Res 41(1): e4.
Weisenberger, D. J., K. D. Siegmund, et al. (2006). "CpG island methylator phenotype underlies sporadic
microsatellite instability and is tightly associated with BRAF mutation in colorectal cancer." Nat
Genet 38(7): 787-793.
Zhang, Y., H. Liu, et al. (2011). "QDMR: a quantitative method for identification of differentially
methylated regions by entropy." Nucleic Acids Res 39(9): e58.