Review Article | Open Access
Epigenetic Biomarkers: Potential Applications in Gastrointestinal Cancers
Genetics and epigenetics coregulate the cancer initiation and progression. Epigenetic mechanisms include DNA methylation, histone modification, chromatin remodeling, and noncoding RNAs. Aberrant epigenetic modifications play a fundamental role in the formation of gastrointestinal cancers. Advances in epigenetics offer a better understanding of the carcinogenesis and provide new insights into the discovery of biomarkers for diagnosis, and prognosis prediction of human cancers. This review aims to overview the epigenetic aberrance and the clinical applications as biomarkers in gastrointestinal cancers mainly gastric cancer and colorectal cancer.
Cancer is one of the major disorders threatening our life. Gastrointestinal cancers mainly, including gastric cancer (GC) and colorectal cancer (CRC), account for a large proportion of human malignancies. They are both aggressive and the common cause of cancer-related deaths with a high disease-specific mortality rate around the world. There have been a great number of studies on the pathogenesis of gastrointestinal cancers. With a long history of chronic inflammation, GC and CRC result from the accumulation of both genetic and epigenetic changes that cause the transformation of normal cells into cancer cells. The classic genetic alterations are the mutations in key tumor suppressor genes or oncogenes, leading to defects of protein functions or deregulation of gene expression. In contrast, epigenetic events could affect gene expression without any changes in DNA sequence.
2. Overview of the Epigenetics
The term epigenetics was coined in 1942 by C. H. Waddington when he was studying the causality between the genotype and the phenotype . Now epigenetics refers to heritable modifications of the genome without any changes in primary DNA sequences . In 1982, Feinberg and Vogelstein first discovered aberrant epigenetic alterations in human colorectal cancer . Epigenetics which focuses on the process transforming genotype into phenotype is corresponding to genetics that refers to the heredity of genotype. Epigenetic alterations, like gene mutations, contribute to the pathogenesis and molecular heterogeneity of cancers. Epigenetics is different from the traditional genetics, mainly in the reversibility and position effect. The epigenetic modifications currently believed to play a role in cancers include DNA methylation, specific histone modifications, chromatin remodeling, and noncoding RNAs.
2.1. DNA Methylation
The best-characterized epigenetic modification is methylation, a covalent addition of a methyl group to cytosines within CG dinucleotides by DNA methyltransferases (DNMTs) . CG dinucleotide sequence, termed as CpG, is the favored substrate for the DNMTs in mammalian cells. The genome CpG islands are regions where the percentage of the CpG dinucleotides is higher. Generally, CpG islands are defined as sequences greater than 200–500 bases in length with greater than 50% GC content and a CpG ratio of greater than 0.6 . CpG islands mainly exist in the promoter region of genes and are inclined to become aberrantly methylated in cancer cells . Methylation of CpG islands with the promoter region is correlated with transcriptional silencing while methylation that occurs in CpG sites outside of promoter regions, termed as gene body methylation, has been associated with transcriptional activation . In the process of tumor formation, demethylation of the entire genome and hypermethylation in the CpG islands of gene promoters occur simultaneously . A wide range of hypomethylation can cause the change of chromatin structure, lower degree of condensed chromatin, and the increase of genome instability, leading to the occurrence of tumor eventually. For instance, microsatellite DNA sequences are easier to mutate when they are hypomethylated, which have been identified in many kinds of tumor models . On the other hand, the silence of important genes such as tumor suppressor genes due to the hypermethylation in the CpG islands of gene promoter also contributes to tumor developments . Methyl-binding proteins (MBPs) that bind with high affinity to methylated DNA can indirectly block the access of transcription factors to the promoter regions . As mentioned above, the methylation state of genes is regulated by DNA methyltransferases (DNMTs). Among them, DNMT1 is responsible for the maintenance of existing DNA methylation while DNMT3a and DNMT3b catalyze DNA methylation in a de novo fashion [12, 13].
2.2. Histone Modification
Another critical epigenetic mechanism refers to the modifications of the histone tails, such as acetylation, methylation, phosphorylation, ubiquitination, and sumoylation [14, 15]. Two subunits of each of the following histone proteins such as H2A, H2B, H3, and H4 form an octamer which is wrapped by DNA to make up a nucleosome, the basic unit of chromatin . Histones are proteins containing a globular domain and a flexible charged NH2 terminus known as the histone tails that are prone to undergo posttranslational modifications. The interaction between DNA and histones alters the accessibility of DNA transcriptions sites to RNA polymerase II or other transcription factors. These posttranslational modifications to histone tails govern the structural state of chromatin and the resulting transcriptional status of genes within particular sites . As a well-studied covalent modification, histone acetylation is controlled by histone acetyltransferases (HATs) that add an acetyl group to lysine residues and histone deacetylases (HDACs) responsible for removing the acetyl group. Generally, HATs can promote the transcription by neutralizing a positive charge to cause the chromatin open and subsequent transactivation of specific genes while HDACs lead to chromatin condensation and transcriptional inactivation of the involved DNA [18, 19]. HDACs can be divided into four catalytic groups, referred to as classes I (HDAC 1–3 and 8), II (HDAC 4–7, 9, and 10), III (Sir-2 related-protein 1–7), and IV (HDAC11) . Deregulation of HADC activity has been strongly implicated in aberrant gene silencing and tumorigenesis, providing a molecular rationale for targeting HDACs activity in the clinical intervention of human cancers . Histone methylation is another important way to regulate histone which usually happens on lysine and arginine residues of histones H3 and H4. The methylated histone could realize fine control of cell functions by means of collecting many kinds of DNA regulatory factors. The methylation of histone tails is regulated by histone methyltransferases (HMTs) and histone demethylases (HDMs). In 2004, Shi et al. first confirmed that LSD1 (histone demethylase SWIRM1) could mediate histone demethylation, changing the viewpoint that histone methylation was irreversible [22, 23]. Lysine residues might present different levels of methylation, mono-, di-, and trimethylation, leading to various states of the genome [24, 25]. Depending on the residue and the level of methylation, the chromatin might be open such as trimethylation at H3K4 and H3K36 or closed such as trimethylation at H3K27, H3K9, and H4K20 and dimethylation at H3K9 . In addition, histone phosphorylation will affect chromatin structure. For instance, ERK-MAPK (mitogen-activated protein kinases) pathway can induce H3 S10 phosphorylation to prompt chromatin condensation essential for the progression of mitosis . Taken together, multiple combinations of histone modifications in specific genomic regions could contribute to a more “open” or “closed” chromatin structure resulting in the activation or the repression of gene expression .
2.3. Chromatin Remodeling
Chromatin remodeling refers to changes of chromatic location and structure and mainly gives rise to the loss of tightened chromatin in nucleosome joint to expose cis-acting elements in the gene promoter and provide the chance of the combination with trans-acting factors . The process of chromatin remodeling is mediated by ATP (adenosine triphosphate) dependent nucleosome remodeling complex and histone covalent modification complex. The former changes the configuration of nucleosome through ATP hydrolysis while the latter catalyzes the covalent modifications on the histone tails. These complexes work in concert with activating chromatin-modifying enzymes that can be categorized into two families, the ISWI family mobilizing nucleosomes along the DNA and the SWI/SNF (SWItch/Sucrose NonFermentable) family that transiently alters the structure of the nucleosome, whereby exposing DNA [30, 31]. Dynamic chromatin remodeling is the basis of many biological processes such as gene transcription, DNA replication, and DNA damage repair. Therefore, the chaos of such biological processes is directly related with the occurrence and development of tumors.
2.4. Noncoding RNAs
The RNA world was expanded by the recent identification of regulatory noncoding RNAs (ncRNAs), challenging the long-standing assumption that RNA is an intermediate between stable genes and versatile proteins. Actually, most of the genome in mammals and other eukaryotes is transcribed in a developmentally regulated manner to produce large amount of noncoding RNAs. Depending on the functional or biochemical features, ncRNAs can be divided into long noncoding RNAs (lncRNAs) that are longer than 200 nucleotides and small regulatory RNAs such as microRNAs (miRNAs), short interfering RNAs (siRNAs), piwi-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs), and other short RNAs.
The most studied class of ncRNAs is miRNAs that are small ncRNAs of approximately 22 nucleotides and responsible for posttranscriptional gene silencing of more than 60% of protein-coding genes by controlling mRNA translation into proteins [32, 33]. miRNAs play their roles through either cleavage of mRNA or translational repression when pairing with the 3′UTR (untranslated region) region of target genes in an incomplete complementary way [34, 35]. miRNAs are involved in the regulation of many important biological processes, such as cell differentiation, proliferation, and apoptosis [36, 37]. The abnormal expression of miRNAs has been linked to cancers and now is being used to classify many human cancers . The first miRNAs were identified as lin-4 and let-7 in 1993. Both miRNAs have important roles in controlling developmental timing, and when they are inactivated, epithelial cells will go through additional cell division instead of normal differentiation . The transcription of genes coding miRNAs is regulated in a similar manner to the transcription of protein-coding genes . For instance, miRNAs dysregulation can occur through DNA hypermethylation, affecting the production of their primary transcript. Most of the miRNAs are generally downregulated in cancers while a few miRNAs, termed as oncomiRNAs, show elevated expression.
3. Epigenetic Biomarkers in Gastric Cancer and Their Applications
3.1. DNA Methylation in GC
Gastric cancer (GC) is the fourth most frequently diagnosed cancer and the second leading cause of cancer-related deaths worldwide . Incidence of gastric cancer is affected by geographic, ethnic, and cultural factors in addition to Helicobacter pylori infection which always influences the mucosa of the stomach and leads to inflammation [42, 43]. Gastric cancer is a highly heterogeneous disease. Therefore, it is necessary to figure out the alterations involved in individual gastric cancer so as to increase the chance to predict prognosis and establish effective treatment options. Gastric adenocarcinoma accounting for 90–95% of gastric cancers has two histological types—intestinal and diffuse types based on microscopic observation and growth patterns. They are widely different in their molecular pathogeneses . Nonetheless, epigenetic alterations play important role in the development of both types of gastric carcinomas.
DNA methylation mapping in cancer genomes shows that the vast majority of cancer types exist in hundreds of genes with high or low methylation and the highest CpG island hypermethylation frequency takes place in gastric cancer [45, 46]. A number of tumor suppressor genes acting in cell cycle, apoptosis, cell adhesion, and invasion are inactivated by hypermethylation such as CDH1 (cadherin 1) and MLH1 (mutL homolog 1). E-cadherin (CDH1) is a cell-to-cell adhesion protein which exists ubiquitously at adherent junctions of epithelial cells. Inactivations of CDH1 include the loss of heterozygosity (LOH) and DNA hypermethylation of the promoter CpG islands. CDH1 is downregulated in sporadic tumors and associated with a poorly differentiated phenotype and a poor clinical outcome [47, 48]. MLH1, involved in repair of mistakes in replication error (RER) of tandem repeat of the short sequences, is hypermethylated exclusively (80%-100%) in the RER phenotype of GC. Interestingly, MLH1 hypermethylation may be an early event which occurs in precursor cells as the corresponding normal mucosa was also similarly hypermethylated [49, 50]. In addition, HOPX (HOP homeobox) had the highest priority with 84% hypermethylated in GC versus 10% in the corresponding normal tissues . Promoter methylation of PCDH10 (protocadherin 10) was detected in 82% of GC samples compared with 37% in the adjacent nontumor tissues . Its methylation was significantly associated with poor survival in patients with early stage of GC. UCHL1 (ubiquitin carboxyl-terminal esterase L1), responsible for maintaining ubiquitin levels by releasing ubiquitin from tandem conjugated ubiquitin monomers, was commonly silenced through promoter methylation in 77% of GC [53, 54]. Due to the promoter hypermethylation, ADAMTS9 (ADAM metallopeptidase with thrombospondin type 1 motif 9), belonging to the ADAMTS family, was silenced in 75% of GC cell lines . Dkk-3 (dickkopf WNT signaling pathway inhibitor 3), an inhibitor of Wnt signaling, was methylated in 68% of primary GC and it was related significantly and independently with poor survival by multivariate Cox regression analysis . The Kaplan-Meier survival curve revealed that GC patients with methylated Dkk-3 had shorter survival compared with its counterparts—median survival 0.76 years and 2.68 years, respectively. Other relevant candidacy of highly relevant methylation (HRMGs) can be found in the review of Yamashita et al. .
Because of the easier availability and detection of methylated DNAs in various body fluids, they can serve as useful noninvasive biomarkers for GC. The detection of specific methylated genes in the blood DNA of GC patients is of potential diagnostic significance, perhaps eventually overriding the value of CEA (carcinoembryonic antigen), a classical tumor marker in the serum. For example, RNF180 (ring finger protein 180) has been shown as a novel preferentially methylated gene in the plasma of GC patients . Promoter methylation of RNF180 was 76% of GC patients with sensitivity 63% and specificity 91%. Overexpression of RNF180 could suppress cell growth and induce apoptosis mediated by upregulating MTSS1 (metastasis suppressor 1), CDKN2A (cyclin-dependent kinase inhibitor 2A), and TIMP3 (TIMP metallopeptidase inhibitor 3). Another preferential methylation in the blood DNA was evident in the genes like SLC19A3 (solute carrier family 19 member 3) , MHL1, APC (adenomatosis polyposis coli), TIMP3, and E-cadherin . When combining the use of four methylation markers including MHL1, APC, TIMP3, and E-cadherin, the sensitivity was 55% and the specificity was 86%. Interestingly, aberrant methylation in CpG islands of cancer is not only associated with tumor suppressor genes . The CpG island of hTERT (telomerase reverse transcriptase), coding the catalytic subunit of telomerase, was hypermethylated more frequently in neoplastic than in nonneoplastic gastric mucosa . Whether the methylation of hTERT could be a potential biomarker for GC remains to be clarified.
3.2. Histone Modifications in GC
HATs such as p300, CBP, and PCAF (p300/CBP associated factor) have prominent roles in oncogenesis by acetylating multiple histone and nonhistone proteins [63, 64]. Loss of heterozygosity of p300 and missense mutations has been confirmed in gastric cancer . PCAF expression was downregulated in gastric cancer tissues and was correlated with gastric wall invasion, tumor size, and node metastasis stage . On the contrary, patients with high-PACF have a significantly better overall survival. Dysregulation of HDACs activity has also been strongly implicated in abnormal gene silencing and tumorigeneses. Except aberrant gene silencing, altered expression of HDACs such as HDAC1 or HDAC2 has also been observed in gastric carcinoma [67, 68]. The class III HDACs play an important role in cell survival via deacetylation of key cell cycle and apoptosis regulatory molecules including p53 and Rb [69–71]. Histone acetylation has been clinically correlated with pathological epigenetic aberrance in cancers. The reduction of p21 has been validated to be caused by hypoacetylation of histone H3 . By contrast, hyperacetylation in H3 of ZNF312b (FEZ family zinc finger 1) promotes the progression of gastric cancer . Reduced histone H4 acetylation was found in some gastric lesions exhibiting intestinal metaplasia and has been shown to correlate with advanced tumor stage, invasion, and lymph node metastasis in gastric patients [74, 75]. All of these suggest levels of histone acetylation may be closely associated with the development and progression of gastric carcinomas, and the loss of acetylation of specific residues could be as epimarkers of tumor cells . Meanwhile, the methylated levels of H3K9 have been confirmed to be relevant with higher stage, lymph node metastasis, recurrence, and worse prognosis partly due to inactivation of some tumor suppressor genes . Overexpression of phosphorylated histone H3 was related with intestinal type, vessel invasion, lymph node metastasis, and even a poor prognosis in gastric adenocarcinoma .
3.3. miRNAs in GC
Among various ncRNAs, miRNAs are well studied. It is estimated that up to 30% of genes in the human genome are regulated by miRNAs . Owing to their smaller size, high stability in human tissues, and crucial translational regulatory function, miRNAs have strong potential as better biomarkers than mRNA and proteins . A direct link between miRNAs and cancer development was first reported in chronic lymphocytic leukemia caused by downregulation of miR-15 and miR-16 .
Many miRNAs have been reported to be deregulated in GC. MiR-129-2 was silenced in GC and restoration of its expression could trigger apoptosis probably through regulating the relative abundance of proapoptotic and antiapoptotic members of Bcl-2 family . Downregulation of miR-218 in GC is implicated in metastasis resulting from the derepression of its target Robol, a transmembrane receptor for Slit, and thereby enhancing Slit/Robol signaling . The high mobility group A2 (HMGA2) can promote the assembly of regulatory protein complexes at transcriptional sites , thus representing as a hallmark of various malignant tumors, including GC. Loss of inhibition by let-7 can contribute to HMGA2 overexpression and enhance transcription in GC tissues . MiR-141, belonging to miR-200 family and reported to inhibit EMT (epithelial-mesenchymal transition) and enhance E-cadherin expression, was implicated reductive obviously in primary GC [86–88]. An additional downregulated miRNA was miR-9 whose target was RAB34 (member RAS oncogene family) . Wan et al. further found miR-9 could inhibit growth by targeting NF-Kb1 (nuclear factor of kappa light polypeptide gene enhancer in B-cells 1) in GC cells . It is also not unusual that miRNAs are overexpressed in GC which is called oncogenic miRNAs. The levels of miR-106a, which belongs to the miR-106b-25 cluster, were significantly higher compared with normal counterparts and also obviously correlated with tumor stage, size, differentiation, and lymphatic and distant metastasis . Therefore, miR-106a might be used as a diagnostic biomarker of GC. Furthermore, two histological subtypes of GC showed different expression pattern of miRNAs. Eight miRNAs such as miR-105 were upregulated in the diffuse type while only four miRNAs such as miR-373 increased in the intestinal type . In clinical practice, these dysregulated miRNAs can be used as different biomarkers in GC for early diagnosis, prognosis, and predictive response to chemotherapy. High levels of miR-17 and miR-106a have been confirmed in a study in which the value of the area under the receiver-operating characteristic curve for combined miR-17/miR-106a assay was 0.741, suggesting miRNAs could be useful biomarkers for early diagnosis of GC . The expression of miR-451 was reduced in GC and related with worse prognosis . By contrast, overexpression of miR-451 leads to reduction of cell proliferation and increase of sensitivity to radiotherapy. These data suggests miR-451 may play a role in suppressing carcinogenesis and could be a target for cancer therapy. There are many miRNAs involved in drug resistance as well. For instance, the overexpression of miR-15b or miR-16 sensitized SGC7901/VCR cells towards Vincristine (VCR) partly via inhibiting Bcl-2 to increase apoptosis . This indicates a potential therapeutic use of miR-15b and miR-16.
In addition to miRNAs in primary and metastatic tumor tissues, cell-free circulating miRNAs can be detected in plasma and serum because these miRNAs are reproducible, consistent, and resistant to RNase [96, 97]. For instance, from a genome-wide miRNA profile approach, miR-378 showed a higher level in serum of GC patients with 87.5% sensitivity and 70.7% specificity . And the differences of miR-378 levels in serum between patients and controls could be detected at early stages of GC. MiR-31 expression is downregulated in GC tissues, and, interestingly, the positive detection rate of the serum miR-31 is much higher than that of the serum CEA (68.29% versus 21.95%). This study indicates that miR-31 may be a novel diagnostic marker for GC .
4. Epigenetic Biomarkers in Colorectal Cancer and Their Applications
4.1. DNA Methylation in CRC
Colorectal cancer (CRC) is also the result of progressive accumulation of genetic and epigenetic alterations in tumor suppressor genes and oncogenes. The former process was first described by Fearon and Vogelstein in a classic adenoma-cancer progression model from which we understand considerably the molecular pathogenesis of CRC . However, the original model provided a relatively limited explanation of molecular alterations. Now, we believe there are different molecular events contributing to the formation of CRC. For example, apart from mutations and other genetic changes, epigenetic silencing of APC through promoter hypermethylation could lead to activation of the Wnt (wingless and integration site growth factor) pathway .
There is also increasing evidence that aberrant DNA methylation is an important hallmark of CRC. The link between DNA methylation and CRC was first observed in 1983 when it was suggested that cancer cells occurred because of hypomethylation of their genomes . Genomic instability and loss of imprinting genes like IGF2 (insulin-like growth factor 2) may be both initiated by DNA hypomethylation [103, 104]. Global hypomethylation may influence tumor progression by making chromosomes more susceptible to breakage and cause disruption of normal gene structure and function, leading to reactivating previously silenced retrotransposons [105–107]. A typical example of global hypomethylation is the LINE-1 repeat sequence. LINE-1 hypomethylation has been shown to independently prognosticate poor CRC survival and predict poor response to 5-FU (5-fluorouracil) chemotherapy [108, 109].
Similar to GC, DNA hypermethylation in CpG islands is also postulated to silence the expression of some important genes in CRC. A subset of CRC has a specific phenotype termed as CIMP (CpG island methylator phenotype) with a high proportion of methylated genes promoters . Almost 30%–40% of proximal CRC and 3%–12% of distal CRC are characterized as CIMP . According to epigenetic and clinical profiles, primary CRC is divided into three distinct subclasses: CIMP1, CIMP2, and CIMP negative. CIPM1 has a good prognosis, whereas CIMP2 is associated with poor prognosis . CIMP status of cancers has been assessed as a predictive marker for 5-FU responsiveness . Due to the DNA hypermethylation, some tumor suppressor genes are silenced such as P16, VHL (von Hippel-Lindau tumor suppressor), and MLH1 in CRC [114, 115]. MLH1, a mismatch repair (MMR) gene, is inactivated by promoter methylation, resulting in high-level MSI in some sporadic CRC and then genetic instability to drive tumor onset [116, 117].
In recent years, several DNA methylation markers have been proposed as useful early biomarkers for CRC detection. The detection of aberrant methylation of vimentin in fecal DNA is obvious in CRC when compared with normal control patients . The sensitivity and specificity of methylated vimentin to detect CRC were 88% and 87%, respectively . In addition, the transcription factor GATA4 (GATA binding protein 4) has been identified as a novel biomarker for the detection of CRC with a sensitivity of 51–71% and a specificity of 84–93% based on distinct study groups . Blood-based tests for CRC detection could have the potential for better compliance. The methylation of SEPT9 (septin 9), encoding a GTPase involved in dysfunctional cytoskeletal organization, was detected in the CRC patients with an overall sensitivity of 90% and specificity of 88% . Meanwhile since this marker is not influenced by patients’ age, sex, and tumor location, STEPT9 is particularly attractive for biomarker applicability.
Traditional methods cannot sufficiently predict the prognosis of single cancer cases. Clinicians may be not able to accurately decide which patients will be at high risk for recurrence and benefit from chemotherapy. Therefore, it is essential to search for novel biomarkers improving prognosis, and then it would support clinicians in the decision of which patients should receive adjuvant treatment. Promoter methylation of CHFR (checkpoint with forkhead and ring finger domains) was found to be associated with survival and was considered to be an independent predictor for tumor recurrence . Moreover, simultaneous DNA methylation of IGFBP3 (insulin-like growth factor binding protein 3) and CD109 (CD109 molecule) was correlated with worse survival for stage II CRC . The questions of which patients should be treated and why some patients respond to therapy whereas others do not need to be solved as adjuvant cancer therapy imposes unnecessary toxicity and a huge financial burden on patients. Hypermethylation of MGMT (O-6-methylguanine-DNA methyltransferase) has been reported in CRC and inactivation of MGMT was shown to sensitize cells to the effects of alkylating agents . Moving forward, MGMT was able to reduce mutagenic and cytotoxic adducts from guanine in DNA . These data lead to a proposal that MGMT can be used as a predictive marker in CRC. Besides the association with longer survival of CRC patients treated with irinotecan, WRN (Werner syndrome, RecQ helicase-like) hypermethylation appears to be related with mucinous differentiation in CRC [126, 127]. All of these possible markers need to be further validated before they are applied for clinical use.
4.2. Histone Modifications in CRC
In addition to alterations in DNA methylation, histone modification patterns also happen in CRC. Despite their various effects, histone modifications have drawn less attention than DNA methylation biomarkers likely due to less predictable transcriptional response and more intensive detection techniques in CRC. The biomarker studies mainly focused on the expression of global histone modifying enzymes. For example, HDAC2 silencing a group of targeting genes has been shown to be independently associated with poor survival in CRC . The most studied histone-associated protein is EZH2 (enhancer of zeste homolog 2), which encodes a H3 methyltransferase to induce polycomb-mediated repression of target genes. EZH2 has shown poor prognostic effects and can promote loss of cellular adhesion and CRC metastasis [129, 130]. Interactions can occur among different histone modification patterns to generate various impacts. Decreased acetylation at H3K9 and increased methylation at H3K9 were associated with silencing of genes such as P16, MLH1, and MGMT. Hypomethylation alone could not reverse silenced genes. Instead augmented histone acetylation with localized hypomethylation allows the turnover of epigenetically silenced genes. After 5-Aza treatment for 10 days, CDO1 (cysteine dioxygenase type 1) was still expressed as it had a localized hypomethylation and an increased histone H3 acetylation .
4.3. miRNAs in CRC
Similarly, CRC-related miRNAs have also garnered considerable attention as potential biomarkers due to their multifaceted functional roles. MiR-143 and miR-145 are the most extensively studied miRNAs in CRC. They were observed to be downregulated in CRC and ectopic expression of them brought about the inhibition of cell proliferation [132, 133]. Subsequently, their targets have been discovered. K-Ras was identified as a target of miR-143. By inhibiting K-Ras translation, it could suppress CRC growth . More than 50% of CRC cases presented reduced miR-342 and reconstitution of miR-342 induced apoptosis, indicating that miR-342 might act as a proapoptotic gene . The inverse relationship between reduced miR-101 and COX-2 (cyclooxygenase-2) overexpression could confer CRC cells with the ability of growth and invasiveness . P53, the most common mutated tumor suppressor genes, can have an impact on miRNA expression . For example, miR-34a was proved to be regulated directly by P53 and contributed to apoptosis and senescence-like phenotypes via downregulation of the EZF (Kruppel-like factor 4) and SIRT1 (sirtuin 1) and upregulation of P53 and P21 [138–140].
There are also many oncogenetic miRNAs in CRC. For example, miR-21 might function as an oncogene due to its overexpression in CRC . It has been demonstrated that increased expression of miR-21 was correlated with lymph node metastasis and poor survival and response to chemotherapy [142, 143]. These studies suggest that miR-21 could act as a biomarker for gastrointestinal cancers. Of course, there are still discrepancies between GC and CRC. In contrast to the findings that miR-31 expression levels were downregulated in GC, its expression was increased in CRC and correlated with tumor pathological staging, higher expression in stage IV tumors than in stage II tumors. This suggests miRNAs alterations may occur at different stages of colorectal tumorigenesis and malignant progression.
Circulating miRNAs can be detected in plasma and serum of CRC patients as well. Huang et al. showed that miR-29a and miR-92a in plasma discriminated CRC from tissues they arise from with 83.0% sensitivity and 84.7% specificity .
5. Conclusion and Perspectives
It is well known that various epigenetic alterations, especially aberrant DNA methylation, histone modifications, and miRNAs, are involved in tumorigenesis. Advances in our understanding of the molecular pathology of gastrointestinal cancers by elucidating the relevance of epigenetic alterations might lead to the identification of potential biomarkers for the diagnosis, prognosis, and drug development of GC cancers. With the development of the next generation genome sequencing as well as single molecular PCR (polymerase chain reaction), it became possible to analyze trace amount of nuclear acids, including circulating cell-free DNA, that will be the next promising epigenetic biomarkers for cancer detection. Although some methylated DNAs and miRNAs were found to valuable as a single biomarker for cancer detection, more potential epigenetic biomarkers will be found after the wide application of new sequencing platforms with high speed, depth, and accuracy. Epigenetic signatures, including a panel of methylated DNAs or miRNAs, will show the potential in the early diagnosis or screening and prognosis or therapy response prediction of GI (gastrointestinal) cancers. In addition, such biomarkers could be more sensitive and specific for cancer detection when combined with well-used biochemical biomarkers.
Conflict of Interests
The authors declare no conflict of interests regarding the publication of this paper.
This work was supported by Key Program in Science and Technology of Zhejiang Province (2012C13014-4) and Department of Health in Zhejiang Province (2010KYA116; WKJ2012-029).
- C. H. Waddington, “The epigenotype. 1942,” International Journal of Epidemiology, vol. 41, no. 1, pp. 10–13, 2012.
- S. L. Berger, T. Kouzarides, R. Shiekhattar, and A. Shilatifard, “An operational definition of epigenetics,” Genes and Development, vol. 23, no. 7, pp. 781–783, 2009.
- A. P. Feinberg and B. Vogelstein, “Hypomethylation distinguishes genes of some human cancers from their normal counterparts,” Nature, vol. 301, no. 5895, pp. 89–92, 1983.
- T. H. Bestor, “The DNA methyltransferases of mammals,” Human Molecular Genetics, vol. 9, no. 16, pp. 2395–2402, 2000.
- M. Gardiner-Garden and M. Frommer, “CpG islands in vertebrate genomes,” Journal of Molecular Biology, vol. 196, no. 2, pp. 261–282, 1987.
- A. Portela and M. Esteller, “Epigenetic modifications and human disease,” Nature Biotechnology, vol. 28, no. 10, pp. 1057–1068, 2010.
- A. Hellman and A. Chess, “Gene body-specific methylation on the active X chromosome,” Science, vol. 315, no. 5815, pp. 1141–1143, 2007.
- C. Stresemann, B. Brueckner, T. Musch, H. Stopper, and F. Lyko, “Functional diversity of DNA methyltransferase inhibitors in human cancer cell lines,” Cancer Research, vol. 66, no. 5, pp. 2794–2800, 2006.
- K. D. Robertson, “DNA methylation and human disease,” Nature Reviews Genetics, vol. 6, no. 8, pp. 597–610, 2005.
- S. A. Belinsky, “Gene-promoter hypermethylation as a biomarker in lung cancer,” Nature Reviews Cancer, vol. 4, no. 9, pp. 707–717, 2004.
- A. Bird, “DNA methylation patterns and epigenetic memory,” Genes and Development, vol. 16, no. 1, pp. 6–21, 2002.
- A. Hermann, H. Gowher, and A. Jeltsch, “Biochemistry and biology of mammalian DNA methyltransferases,” Cellular and Molecular Life Sciences, vol. 61, no. 19-20, pp. 2571–2587, 2004.
- M. Okano, D. W. Bell, D. A. Haber, and E. Li, “DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development,” Cell, vol. 99, no. 3, pp. 247–257, 1999.
- T. Kouzarides, “Chromatin modifications and their function,” Cell, vol. 128, no. 4, pp. 693–705, 2007.
- A. J. Bannister and T. Kouzarides, “Regulation of chromatin by histone modifications,” Cell Research, vol. 21, no. 3, pp. 381–395, 2011.
- M. Bots and R. W. Johnstone, “Rational combinations using HDAC inhibitors,” Clinical Cancer Research, vol. 15, no. 12, pp. 3970–3977, 2009.
- R. Kanwal and S. Gupta, “Epigenetic modifications in cancer,” Clinical Genetics, vol. 81, no. 4, pp. 303–311, 2012.
- X. J. Yang and E. Seto, “HATs and HDACs: from structure, function and regulation to novel strategies for therapy and prevention,” Oncogene, vol. 26, no. 37, pp. 5310–5318, 2007.
- S. Ropero and M. Esteller, “The role of histone deacetylases (HDACs) in human cancer,” Molecular Oncology, vol. 1, no. 1, pp. 19–25, 2007.
- M. A. Glozak and E. Seto, “Histone deacetylases and cancer,” Oncogene, vol. 26, no. 37, pp. 5420–5432, 2007.
- L. Ellis, P. W. Atadja, and R. W. Johnstone, “Epigenetics in cancer: targeting chromatin modifications,” Molecular Cancer Therapeutics, vol. 8, no. 6, pp. 1409–1420, 2009.
- Y. Shi, F. Lan, C. Matson et al., “Histone demethylation mediated by the nuclear amine oxidase homolog LSD1,” Cell, vol. 119, no. 7, pp. 941–953, 2004.
- Y. Sun, Y. Xu, K. Roy, and B. D. Price, “DNA damage-induced acetylation of lysine 3016 of ATM activates ATM kinase activity,” Molecular and Cellular Biology, vol. 27, no. 24, pp. 8502–8509, 2007.
- A. Shilatifard, “Chromatin modifications by methylation and ubiquitination: implications in the regulation of gene expression,” Annual Review of Biochemistry, vol. 75, pp. 243–269, 2006.
- E. J. Richards and S. C. R. Elgin, “Epigenetic codes for heterochromatin formation and silencing: rounding up the usual suspects,” Cell, vol. 108, no. 4, pp. 489–500, 2002.
- F. Lan and Y. Shi, “Epigenetic regulation: methylation of histone and non-histone proteins,” Science in China C, vol. 52, no. 4, pp. 311–322, 2009.
- S. J. Nowak and V. G. Corces, “Phosphorylation of histone H3 correlates with transcriptionally active loci,” Genes and Development, vol. 14, no. 23, pp. 3003–3013, 2000.
- A. Izzo and R. Schneider, “Chatting histone modifications in mammals,” Briefings in functional genomics, vol. 9, no. 5-6, pp. 429–443, 2010.
- M. Masiero, G. Nardo, S. Indraccolo, and E. Favaro, “RNA interference: implications for cancer treatment,” Molecular Aspects of Medicine, vol. 28, no. 1, pp. 143–166, 2007.
- T. Tsukiyama, C. Daniel, J. Tamkun, and C. Wu, “ISWI, a member of the SWI2/SNF2 ATPase family, encodes the 140 kDa subunit of the nucleosome remodeling factor,” Cell, vol. 83, no. 6, pp. 1021–1026, 1995.
- P. D. Varga-Weisz, M. Wilm, E. Bonte, K. Dumas, M. Mann, and P. B. Becker, “Chromatin-remodelling factor CHRAC contains the ATPases ISWI and topoisomerase II,” Nature, vol. 388, no. 6642, pp. 598–602, 1997.
- M. Esteller, “Non-coding RNAs in human disease,” Nature Reviews Genetics, vol. 12, no. 12, pp. 861–874, 2011.
- J. Lu, G. Getz, E. A. Miska et al., “MicroRNA expression profiles classify human cancers,” Nature, vol. 435, no. 7043, pp. 834–838, 2005.
- D. P. Bartel, “MicroRNAs: genomics, biogenesis, mechanism, and function,” Cell, vol. 116, no. 2, pp. 281–297, 2004.
- A. Rouhi, D. L. Mager, R. K. Humphries, and F. Kuchenbauer, “MiRNAs, epigenetics, and cancer,” Mammalian Genome, vol. 19, no. 7-8, pp. 517–525, 2008.
- W. Filipowicz, S. N. Bhattacharyya, and N. Sonenberg, “Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight?” Nature Reviews Genetics, vol. 9, no. 2, pp. 102–114, 2008.
- L. He and G. J. Hannon, “MicroRNAs: small RNAs with a big role in gene regulation,” Nature Reviews Genetics, vol. 5, no. 7, pp. 522–531, 2004.
- M. V. Iorio, C. Piovan, and C. M. Croce, “Interplay between microRNAs and the epigenetic machinery: an intricate network,” Biochimica et Biophysica Acta, vol. 1799, no. 10–12, pp. 694–701, 2010.
- R. C. Lee, R. L. Feinbaum, and V. Ambros, “The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14,” Cell, vol. 75, no. 5, pp. 843–854, 1993.
- P. Lopez-Serra and M. Esteller, “DNA methylation-associated silencing of tumor-suppressor microRNAs in cancer,” Oncogene, vol. 31, no. 13, pp. 1609–1622, 2012.
- D. M. Parkin, F. Bray, J. Ferlay, and P. Pisani, “Global cancer statistics, 2002,” A Cancer Journal for Clinicians, vol. 55, no. 2, pp. 74–108, 2005.
- K. D. Crew and A. I. Neugut, “Epidemiology of gastric cancer,” World Journal of Gastroenterology, vol. 12, no. 3, pp. 354–362, 2006.
- P. Lauren, “The two histological main types of gastric carcinoma: diffuse and so called intestinal-type carcinoma: an attempt at a histo-clinical classification,” Acta pathologica et microbiologica Scandinavica, vol. 64, pp. 31–49, 1965.
- N. Jinawath, Y. Furukawa, S. Hasegawa et al., “Comparison of gene-expression profiles between diffuse- and intestinal-type gastric cancers using a genome-wide cDNA microarray,” Oncogene, vol. 23, no. 40, pp. 6830–6844, 2004.
- S. B. Baylin and P. A. Jones, “A decade of exploring the cancer epigenome-biological and translational implications,” Nature Reviews Cancer, vol. 11, no. 10, pp. 726–734, 2011.
- S. Z. Ding, J. B. Goldberg, and M. Hatakeyama, “Helicobacter pylori infection, oncogenic pathways and epigenetic mechanisms in gastric carcinogenesis,” Future Oncology, vol. 6, no. 5, pp. 851–862, 2010.
- G. Tamura, J. Yin, S. Wang et al., “E-cadherin gene promoter hypermethylation in primary human gastric carcinomas,” Journal of the National Cancer Institute, vol. 92, no. 7, pp. 569–573, 2000.
- F. Graziano, F. Arduini, A. Ruzzo et al., “Prognostic analysis of E-cadherin gene promoter hypermethylation in patients with surgically resected, node-positive, diffuse gastric cancer,” Clinical Cancer Research, vol. 10, no. 8, pp. 2784–2789, 2004.
- G. H. Kang, Y. H. Shim, H. Y. Jung, W. H. Kim, J. Y. Ro, and M. G. Rhyu, “CpG island methylation in premalignant stages of gastric carcinoma,” Cancer Research, vol. 61, no. 7, pp. 2847–2851, 2001.
- T. Waki, G. Tamura, T. Tsuchiya, K. Sato, S. Nishizuka, and T. Motoyama, “Promoter methylation status of E-cadherin, hMLH1, and p16 genes in nonneoplastic gastric epithelia,” American Journal of Pathology, vol. 161, no. 2, pp. 399–403, 2002.
- A. Ooki, K. Yamashita, S. Kikuchi et al., “Potential utility of HOP homeobox gene promoter methylation as a marker of tumor aggressiveness in gastric cancer,” Oncogene, vol. 29, no. 22, pp. 3263–3275, 2010.
- J. O. Boison, C. D. Salisbury, W. Chan, and J. D. MacNeil, “Determination of penicillin G residues in edible animal tissues by liquid chromatography,” Journal of the Association of Official Analytical Chemists, vol. 74, no. 3, pp. 497–501, 1991.
- H. Osaka, Y. L. Wang, K. Takada et al., “Ubiquitin carboxy-terminal hydrolase L1 binds to and stabilizes monoubiquitin in neuron,” Human Molecular Genetics, vol. 12, no. 16, pp. 1945–1958, 2003.
- J. Yu, Q. Tao, K. F. Cheung et al., “Epigenetic identification of ubiquitin carboxyl-terminal hydrolase L1 as a functional tumor suppressor and biomarker for hepatocellular carcinoma and other digestive tumors,” Hepatology, vol. 48, no. 2, pp. 508–518, 2008.
- W. Du, S. Wang, Q. Zhou et al., “ADAMTS9 is a functional tumor suppressor through inhibiting AKT/mTOR pathway and associated with poor survival in gastric cancer,” Oncogene, vol. 32, no. 28, pp. 3319–3328, 2013.
- J. Yu, Q. Tao, Y. Y. Cheng et al., “Promoter methylation of the Wnt/β-catenin signaling antagonist Dkk-3 is associated with poor survival in gastric cancer,” Cancer, vol. 115, no. 1, pp. 49–60, 2009.
- K. Yamashita, S. Sakuramoto, and M. Watanabe, “Genomic and epigenetic profiles of gastric cancer: potential diagnostic and therapeutic applications,” Surgery Today, vol. 41, no. 1, pp. 24–38, 2011.
- K. F. Cheung, C. N. Y. Lam, K. Wu et al., “Characterization of the gene structure, functional significance, and clinical application of RNF180, a novel gene in gastric cancer,” Cancer, vol. 118, no. 4, pp. 947–959, 2012.
- E. K. O. Ng, C. P. H. Leung, V. Y. Shin et al., “Quantitative analysis and diagnostic significance of methylated SLC19A3 DNA in the plasma of breast and gastric cancer patients,” PLoS ONE, vol. 6, no. 7, Article ID e22233, 2011.
- W. K. Leung, K. F. To, E. S. H. Chu et al., “Potential diagnostic and prognostic values of detecting promoter hypermethylation in the serum of patients with gastric cancer,” British Journal of Cancer, vol. 92, no. 12, pp. 2190–2194, 2005.
- A. M. Deaton and A. Bird, “CpG islands and the regulation of transcription,” Genes and Development, vol. 25, no. 10, pp. 1010–1022, 2011.
- C. O. Gigek, M. F. Leal, P. N. O. Silva et al., “HTERT methylation and expression in gastric cancer,” Biomarkers, vol. 14, no. 8, pp. 630–636, 2009.
- M. A. Glozak, N. Sengupta, X. Zhang, and E. Seto, “Acetylation and deacetylation of non-histone proteins,” Gene, vol. 363, no. 1-2, pp. 15–23, 2005.
- P. K. Davis and R. K. Brackmann, “Chromatin remodeling and cancer,” Cancer Biology & Therapy, vol. 2, no. 1, pp. 22–29, 2003.
- N. Koshiishi, J. M. Chong, T. Fukasawa et al., “p300 gene alterations in intestinal and diffuse types of gastric carcinoma,” Gastric Cancer, vol. 7, no. 2, pp. 85–90, 2004.
- M. Z. Ying, J. J. Wang, D. W. Li et al., “The p300/CBP associated factor is frequently downregulated in intestinal-type gastric carcinoma and constitutes a biomarker for clinical outcome,” Cancer Biology and Therapy, vol. 9, no. 4, pp. 312–320, 2010.
- P. Collas, “The state-of-the-art of chromatin immunoprecipitation,” Methods in Molecular Biology, vol. 567, pp. 1–25, 2009.
- J. Song, J. H. Noh, J. H. Lee et al., “Increased expression of histone deacetylase 2 is found in human gastric cancer,” APMIS, vol. 113, no. 4, pp. 264–268, 2005.
- Y. Ye, Y. Xiao, W. Wang et al., “Inhibition of expression of the chromatin remodeling inhibition of expression of the chromatin remodeling gene, SNF2L, selectively leads to DNA damage, growth inhibition, and cancer cell death,” Molecular Cancer Research, vol. 7, no. 12, pp. 1984–1999, 2009.
- C. O. Gigek, L. C. F. Lisboa, M. F. Leal et al., “SMARCA5 methylation and expression in gastric cancer,” Cancer Investigation, vol. 29, no. 2, pp. 162–166, 2011.
- J. H. Lee, M. Y. Song, E. K. Song et al., “Overexpression of SIRT1 protects pancreatic β-cells against cytokine toxicity by suppressing the nuclear factor-κB signaling pathway,” Diabetes, vol. 58, no. 2, pp. 344–351, 2009.
- Y. Mitani, N. Oue, Y. Hamai et al., “Histone H3 acetylation is associated with reduced p21WAFI/CIPI expression by gastric carcinoma,” Journal of Pathology, vol. 205, no. 1, pp. 65–73, 2005.
- I. S. Song, G. H. Ha, J. M. Kim et al., “Human ZNF312b oncogene is regulated by Sp1 binding to its promoter region through DNA demethylation and histone acetylation in gastric cancer,” International Journal of Cancer, vol. 129, no. 9, pp. 2124–2133, 2011.
- S. Ono, N. Oue, H. Kuniyasu et al., “Acetylated histone H4 is reduced in human gastric adenomas and carcinomas,” Journal of Experimental and Clinical Cancer Research, vol. 21, no. 3, pp. 377–382, 2002.
- W. Yasui, N. Oue, S. Ono, Y. Mitani, R. Ito, and H. Nakayama, “Histone acetylation and gastrointestinal carcinogenesis,” Annals of the New York Academy of Sciences, vol. 983, pp. 220–231, 2003.
- M. F. Fraga, E. Ballestar, A. Villar-Garea et al., “Loss of acetylation at Lys16 and trimethylation at Lys20 of histone H4 is a common hallmark of human cancer,” Nature Genetics, vol. 37, no. 4, pp. 391–400, 2005.
- Y. S. Park, M. Y. Jin, Y. J. Kim, J. H. Yook, B. S. Kim, and S. J. Jang, “The global histone modification pattern correlates with cancer recurrence and overall survival in gastric adenocarcinoma,” Annals of Surgical Oncology, vol. 15, no. 7, pp. 1968–1976, 2008.
- H. Takahashi, Y. Murai, K. Tsuneyama et al., “Overexpression of phosphorylated histone H3 is an indicator of poor prognosis in gastric adenocarcinoma patients,” Applied Immunohistochemistry and Molecular Morphology, vol. 14, no. 3, pp. 296–302, 2006.
- R. W. Carthew and E. J. Sontheimer, “Origins and Mechanisms of miRNAs and siRNAs,” Cell, vol. 136, no. 4, pp. 642–655, 2009.
- B. Song and J. Ju, “Impact of miRNAs in gastrointestinal cancer diagnosis and prognosis,” Expert reviews in Molecular Medicine, vol. 12, article e33, 2010.
- G. A. Calin, C. D. Dumitru, M. Shimizu et al., “Frequent deletions and down-regulation of micro-RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia,” Proceedings of the National Academy of Sciences of the United States of America, vol. 99, no. 24, pp. 15524–15529, 2002.
- R. Shen, S. Pan, S. Qi, X. Lin, and S. Cheng, “Epigenetic repression of microRNA-129-2 leads to overexpression of SOX4 in gastric cancer,” Biochemical and Biophysical Research Communications, vol. 394, no. 4, pp. 1047–1052, 2010.
- J. Tie, Y. Pan, L. Zhao et al., “MiR-218 inhibits invasion and metastasis of gastric cancer by targeting the robo1 receptor,” PLoS Genetics, vol. 6, no. 3, Article ID e1000879, 2010.
- K. Pfannkuche, H. Summer, O. Li, J. Hescheler, and P. Dröge, “The high mobility group protein HMGA2: a co-regulator of chromatin structure and pluripotency in stem cells?” Stem Cell Reviews and Reports, vol. 5, no. 3, pp. 224–230, 2009.
- K. Motoyama, H. Inoue, Y. Nakamura, H. Uetake, K. Sugihara, and M. Mori, “Clinical significance of high mobility group A2 in human gastric cancer and its relationship to let-7 MicroRNA family,” Clinical Cancer Research, vol. 14, no. 8, pp. 2334–2340, 2008.
- P. A. Gregory, A. G. Bert, E. L. Paterson et al., “The miR-200 family and miR-205 regulate epithelial to mesenchymal transition by targeting ZEB1 and SIP1,” Nature Cell Biology, vol. 10, no. 5, pp. 593–601, 2008.
- M. Korpal, E. S. Lee, G. Hu, and Y. Kang, “The miR-200 family inhibits epithelial-mesenchymal transition and cancer cell migration by direct targeting of E-cadherin transcriptional repressors ZEB1 and ZEB2,” Journal of Biological Chemistry, vol. 283, no. 22, pp. 14910–14914, 2008.
- Y. Du, Y. Xu, L. Ding et al., “Down-regulation of miR-141 in gastric cancer and its involvement in cell growth,” Journal of Gastroenterology, vol. 44, no. 6, pp. 556–561, 2009.
- H. Luo, H. Zhang, Z. Zhang et al., “Down-regulated miR-9 and miR-433 in human gastric carcinoma,” Journal of Experimental and Clinical Cancer Research, vol. 28, no. 1, article 82, 2009.
- H. Y. Wan, L. M. Guo, T. Liu, M. Liu, X. Li, and H. Tang, “Regulation of the transcription factor NF-κB1 by microRNA-9 in human gastric adenocarcinoma,” Molecular Cancer, vol. 9, article 16, 2010.
- B. Xiao, J. Guo, Y. Miao et al., “Detection of miR-106a in gastric carcinoma and its clinical significance,” Clinica Chimica Acta, vol. 400, no. 1-2, pp. 97–102, 2009.
- T. Ueda, S. Volinia, H. Okumura et al., “Relation between microRNA expression and progression and prognosis of gastric cancer: a microRNA expression analysis,” The Lancet Oncology, vol. 11, no. 2, pp. 136–146, 2010.
- H. Zhou, J. M. Guo, Y. R. Lou et al., “Detection of circulating tumor cells in peripheral blood from patients with gastric cancer using microRNA as a marker,” Journal of Molecular Medicine, vol. 88, no. 7, pp. 709–717, 2010.
- E. Bandres, N. Bitarte, F. Arias et al., “microRNA-451 regulates macrophage migration inhibitory factor production and proliferation of gastrointestinal cancer cells,” Clinical Cancer Research, vol. 15, no. 7, pp. 2281–2290, 2009.
- L. Xia, D. Zhang, R. Du et al., “miR-15b and miR-16 modulate multidrug resistance by targeting BCL2 in human gastric cancer cells,” International Journal of Cancer, vol. 123, no. 2, pp. 372–379, 2008.
- X. Chen, Y. Ba, L. Ma et al., “Characterization of microRNAs in serum: a novel class of biomarkers for diagnosis of cancer and other diseases,” Cell Research, vol. 18, no. 10, pp. 997–1006, 2008.
- A. Keller, P. Leidinger, R. Gislefoss et al., “Stable serum miRNA profiles as potential tool for non-invasive lung cancer diagnosis,” RNA Biology, vol. 8, no. 3, pp. 506–516, 2011.
- H. Liu, L. Zhu, B. Liu et al., “Genome-wide microRNA profiles identify miR-378 as a serum biomarker for early detection of gastric cancer,” Cancer Letters, vol. 316, no. 2, pp. 196–203, 2012.
- Y. Zhang, J. Guo, D. Li et al., “Down-regulation of miR-31 expression in gastric cancer tissues and its clinical significance,” Medical Oncology, vol. 27, no. 3, pp. 685–689, 2010.
- E. R. Fearon and B. Vogelstein, “A genetic model for colorectal tumorigenesis,” Cell, vol. 61, no. 5, pp. 759–767, 1990.
- M. Esteller, A. Sparks, M. Toyota et al., “Analysis of adenomatous polyposis coli promoter hypermethylation in human cancer,” Cancer Research, vol. 60, no. 16, pp. 4366–4371, 2000.
- Ø. Bruserud, C. Stapnes, E. Ersvær, B. T. Gjertsen, and A. Ryningen, “Histone deacetylase inhibitors in cancer treatment: a review of the clinical toxicity and the modulation of gene expression in cancer cells,” Current Pharmaceutical Biotechnology, vol. 8, no. 6, pp. 388–400, 2007.
- P. W. Laird, L. Jackson-Grusby, A. Fazeli et al., “Suppression of intestinal neoplasia by DNA hypomethylation,” Cell, vol. 81, no. 2, pp. 197–205, 1995.
- H. Cui, P. Onyango, S. Brandenburg, Y. Wu, C. L. Hsieh, and A. P. Feinberg, “Loss of imprinting in colorectal cancer linked to hypomethylation of H19 and IGF2,” Cancer Research, vol. 62, no. 22, pp. 6442–6446, 2002.
- J. J. L. Wong, N. J. Hawkins, and R. L. Ward, “Colorectal cancer: a model for epigenetic tumorigenesis,” Gut, vol. 56, no. 1, pp. 140–148, 2007.
- W. Ji, R. Hernandez, X. Y. Zhang et al., “DNA demethylation and pericentromeric rearrangements of chromosome 1,” Mutation Research, vol. 379, no. 1, pp. 33–41, 1997.
- C. M. Suter, D. I. Martin, and R. I. Ward, “Hypomethylation of L1 retrotransposons in colorectal cancer and adjacent normal tissue,” International Journal of Colorectal Disease, vol. 19, no. 2, pp. 95–101, 2004.
- S. Ogino, K. Nosho, G. J. Kirkner et al., “A cohort study of tumoral LINE-1 hypomethylation and prognosis in colon cancer,” Journal of the National Cancer Institute, vol. 100, no. 23, pp. 1734–1738, 2008.
- K. Kawakami, A. Matsunoki, M. Kaneko, K. Saito, G. Watanabe, and T. Minamoto, “Long interspersed nuclear element-1 hypomethylation is a potential biomarker for the prediction of response to oral fluoropyrimidines in microsatellite stable and CpG island methylator phenotype-negative colorectal cancer,” Cancer Science, vol. 102, no. 1, pp. 166–174, 2011.
- W. M. Grady and J. M. Carethers, “Genomic and epigenetic instability in colorectal cancer pathogenesis,” Gastroenterology, vol. 135, no. 4, pp. 1079–1099, 2008.
- L. Migliore, F. Migheli, R. Spisni, and F. Coppedè, “Genetics, cytogenetics, and epigenetics of colorectal cancer,” Journal of Biomedicine and Biotechnology, vol. 2011, Article ID 792362, 19 pages, 2011.
- L. Shen, M. Toyota, Y. Kondo et al., “Integrated genetic and epigenetic analysis identifies three different subclasses of colon cancer,” Proceedings of the National Academy of Sciences of the United States of America, vol. 104, no. 47, pp. 18654–18659, 2007.
- T. Ide, Y. Kitajima, K. Ohtaka, M. Mitsuno, Y. Nakafusa, and K. Miyazaki, “Expression of the hMLH1 gene is a possible predictor for the clinical response to 5-fluorouracil after a surgical resection in colorectal cancer,” Oncology Reports, vol. 19, no. 6, pp. 1571–1576, 2008.
- J. G. Herman, F. Latif, Y. Weng et al., “Silencing of the VHL tumor-suppressor gene by DNA methylation in renal carcinoma,” Proceedings of the National Academy of Sciences of the United States of America, vol. 91, no. 21, pp. 9700–9704, 1994.
- J. M. Cunningham, E. R. Christensen, D. J. Tester et al., “Hypermethylation of the hMLH1 promoter in colon cancer with microsatellite instability,” Cancer Research, vol. 58, no. 15, pp. 3455–3460, 1998.
- M. F. Kane, M. Loda, G. M. Gaida et al., “Methylation of the hMLH1 promoter correlates with lack of expression of hMLH1 in sporadic colon tumors and mismatch repair-defective human tumor cell lines,” Cancer Research, vol. 57, no. 5, pp. 808–811, 1997.
- J. G. Herman, A. Umar, K. Polyak et al., “Incidence and functional consequences of hMLH1 promoter hypermethylation in colorectal carcinoma,” Proceedings of the National Academy of Sciences of the United States of America, vol. 95, no. 12, pp. 6870–6875, 1998.
- W. D. Chen, Z. J. Han, J. Skoletsky et al., “Detection in fecal DNA of colon cancer-specific methylation of the nonexpressed vimentin gene,” Journal of the National Cancer Institute, vol. 97, no. 15, pp. 1124–1132, 2005.
- S. H. Itzkowitz, L. Jandorf, R. Brand et al., “Improved fecal DNA test for colorectal cancer screening,” Clinical Gastroenterology and Hepatology, vol. 5, no. 1, pp. 111–117, 2007.
- D. M. E. I. Hellebrekers, M. H. F. M. Lentjes, S. M. Van Den Bosch et al., “GATA4 and GATA5 are potential tumor suppressors and biomarkers in colorectal cancer,” Clinical Cancer Research, vol. 15, no. 12, pp. 3990–3997, 2009.
- J. D. Warren, W. Xiong, A. M. Bunker et al., “Septin 9 methylated DNA is a sensitive and specific blood test for colorectal cancer,” BMC Medicine, vol. 9, article 133, 2011.
- M. Tanaka, P. Chang, Y. Li et al., “Association of CHFR promoter methylation with disease recurrence in locally advanced colon cancer,” Clinical Cancer Research, vol. 17, no. 13, pp. 4531–4540, 2011.
- J. M. Yi, M. Dhir, L. Van Neste et al., “Genomic and epigenomic integration identifies a prognostic signature in colon cancer,” Clinical Cancer Research, vol. 17, no. 6, pp. 1535–1545, 2011.
- M. Esteller and J. G. Herman, “Generating mutations but providing chemosensitivity: the role of O 6-methylguanine DNA methyltransferase in human cancer,” Oncogene, vol. 23, no. 1, pp. 1–8, 2004.
- F. V. Jacinto and M. Esteller, “MGMT hypermethylation: a prognostic foe, a predictive friend,” DNA Repair, vol. 6, no. 8, pp. 1155–1160, 2007.
- R. Agrelo, W. H. Cheng, F. Setien et al., “Epigenetic inactivation of the premature aging Werner syndrome gene in human cancer,” Proceedings of the National Academy of Sciences of the United States of America, vol. 103, no. 23, pp. 8822–8827, 2006.
- T. Kawasaki, M. Ohnishi, Y. Suemoto et al., “WRN promoter methylation possibly connects mucinous differentiation, microsatellite instability and CpG island methylator phenotype in colorectal cancer,” Modern Pathology, vol. 21, no. 2, pp. 150–158, 2008.
- W. Weichert, A. Röske, S. Niesporek et al., “Class I histone deacetylase expression has independent prognostic impact in human colorectal cancer: specific role of class I histone deacetylases in vitro and in vivo,” Clinical Cancer Research, vol. 14, no. 6, pp. 1669–1677, 2008.
- C. G. Wang, Y. J. Ye, J. Yuan, F. F. Liu, H. Zhang, and S. Wang, “EZH2 and STAT6 expression profiles are correlated with colorectal cancer stage and prognosis,” World Journal of Gastroenterology, vol. 16, no. 19, pp. 2421–2427, 2010.
- C. C. Lee, W. S. Chen, C. C. Chen et al., “TCF12 protein functions as transcriptional repressor of E-cadherin, and its overexpression is correlated with metastasis of colorectal cancer,” Journal of Biological Chemistry, vol. 287, no. 4, pp. 2798–2809, 2012.
- D. Mossman and R. J. Scott, “Long term transcriptional reactivation of epigenetically silenced genes in colorectal cancer cells requires DNA hypomethylation and histone acetylation,” PLoS ONE, vol. 6, no. 8, Article ID e23127, 2011.
- M. Z. Michael, S. M. O'Connor, N. G. Van Holst Pellekaan, G. P. Young, and R. J. James, “Reduced accumulation of specific MicroRNAs in colorectal neoplasia,” Molecular Cancer Research, vol. 1, no. 12, pp. 882–891, 2003.
- Y. Akao, Y. Nakagawa, and T. Naoe, “MicroRNAs 143 and 145 are possible common onco-microRNAs in human cancers,” Oncology Reports, vol. 16, no. 4, pp. 845–850, 2006.
- X. Chen, X. Guo, H. Zhang et al., “Role of miR-143 targeting KRAS in colorectal tumorigenesis,” Oncogene, vol. 28, no. 10, pp. 1385–1392, 2009.
- W. M. Grady, R. K. Parkin, P. S. Mitchell et al., “Epigenetic silencing of the intronic microRNA hsa-miR-342 and its host gene EVL in colorectal cancer,” Oncogene, vol. 27, no. 27, pp. 3880–3888, 2008.
- A. Strillacci, C. Griffoni, P. Sansone et al., “MiR-101 downregulation is involved in cyclooxygenase-2 overexpression in human colon cancer cells,” Experimental Cell Research, vol. 315, no. 8, pp. 1439–1447, 2009.
- Y. Xi, R. Shalgi, O. Fodstad, Y. Pilpel, and J. Ju, “Differentially regulated micro-RNAs and actively translated messenger RNA transcripts by tumor suppressor p53 in colon cancer,” Clinical Cancer Research, vol. 12, no. 7 I, pp. 2014–2024, 2006.
- T. C. Chang, E. A. Wentzel, O. A. Kent et al., “Transactivation of miR-34a by p53 broadly influences gene expression and promotes apoptosis,” Molecular Cell, vol. 26, no. 5, pp. 745–752, 2007.
- H. Tazawa, N. Tsuchiya, M. Izumiya, and H. Nakagama, “Tumor-suppressive miR-34a induces senescence-like growth arrest through modulation of the E2F pathway in human colon cancer cells,” Proceedings of the National Academy of Sciences of the United States of America, vol. 104, no. 39, pp. 15472–15477, 2007.
- M. Yamakuchi, M. Ferlito, and C. J. Lowenstein, “miR-34a repression of SIRT1 regulates apoptosis,” Proceedings of the National Academy of Sciences of the United States of America, vol. 105, no. 36, pp. 13421–13426, 2008.
- E. Bandrés, E. Cubedo, X. Agirre et al., “Identification by Real-time PCR of 13 mature microRNAs differentially expressed in colorectal cancer and non-tumoral tissues,” Molecular Cancer, vol. 5, article 29, 2006.
- O. Slaby, M. Svoboda, P. Fabian et al., “Altered expression of miR-21, miR-31, miR-143 and miR-145 is related to clinicopathologic features of colorectal cancer,” Oncology, vol. 72, no. 5-6, pp. 397–402, 2008.
- I. A. Asangani, S. A. K. Rasheed, D. A. Nikolova et al., “MicroRNA-21 (miR-21) post-transcriptionally downregulates tumor suppressor Pdcd4 and stimulates invasion, intravasation and metastasis in colorectal cancer,” Oncogene, vol. 27, no. 15, pp. 2128–2136, 2008.
- Z. Huang, D. Huang, S. Ni, Z. Peng, W. Sheng, and X. Du, “Plasma microRNAs are promising novel biomarkers for early detection of colorectal cancer,” International Journal of Cancer, vol. 127, no. 1, pp. 118–126, 2010.
Copyright © 2014 Jiaqiu Li et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.