# An Overview of DNA Methylation Indicators for the Course of Oral Precancer

Authors: Wenjing Wang; Wei Li; Hongyi Zhang
Journal: Applied Bionics and Biomechanics
 (2022)

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## Abstract

DNA methylation is a physiologically epigenetic alteration that happens when a methyl group is introduced to a CpG dinucleotide in the gene-regulating sequence of DNA. However, the majority of oral cancers have a well-defined precancerous stage; there are few clinical and morphological parameters for detecting and signalling the progression of precancerous to malignant tumours. DNA methylation forms are dynamic and reversible, allowing them to adjust to environmental or therapeutic changes. We did an extensive investigation to compile the data supporting aberrant DNA methylation forms as a possible biomarker for prediction. According to two longitudinal studies, p16 hypermethylation was considerably higher in precancerous lesions that progressed to cancer than in lesions that shrank. Most of the studies examined for this study were tiny cross-sectional research with scant validation and inadequately specified control groups. Existing evidence suggests that DNA methylation sequences can be relevant as a diagnostic biomarker for OPS development; however, sample size and research design restrictions make it difficult to draw definitive conclusions. Strong studies, including extensive epigenome-wide methylation scans of OPS with longitudinal monitoring, are necessary in this study in order to corroborate the recently discovered signals and discover new risk loci and disease progression molecular pathways.


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## Body

## 1. Introduction

Oral cancer (OC) is a significant public health issue across most of Asia, along with some regions of Eastern and Western Europe, the Caribbean, Melanesia, and Latin America [1–4]. While high-prevalence areas in Asia (Bangladesh, Sri Lanka, Pakistan, India, and Taiwan–China) account for more than a 3rd (37.5 percent) of the overall worldwide affliction [1], recent time indicates an increase in incidence in the United States and portions of Europe, notably the United Kingdom (UK) [5–7]. Each year, more than millions of new cases are recorded in the more developed parts of the world [8], with a higher prevalence among young people [6, 9].OC grows sequentially via a sequence of histo-pathological alterations (dysplastic, hyperplastic, normal, and cancer in situ) before progressing to invasive ailment [10–12]. Oral precancer (OPC) may be quickly diagnosed visually in the mouth cavity, and the oral cavity is conveniently reachable for biopsy and cytology verification [13]. While early identification dramatically lowers tumor precise illness and death [14], mouth malignancies are often identified eventually, compromising 5-year existence regardless of advancements in therapy [5]. This is especially true for nations in high-prevalence areas [15, 16]. For individuals with oral cancer, particularly in the last stages of the disorder, surgery is the backbone of therapy for OC patients. External beam radiation treatment and brachytherapy are the gold standard for usage as adjuvant treatment in postoperative cases of individuals suffering from late OC. They have both been utilised effectively as the major treatment option for people with earlier start of OC. Although there is limited evidence regarding the better prognosis when chemo is used to treat people with OC, there is a growing concept toward the usage of chemotherapy in conjunction with radiation treatment, surgery, as well as those suffering from advanced, recurring, or metastatic neck and head tumor [17].OPC is a medically diverse term that refers to a number of abnormalities (erythroplakia, leukoplakia, and palatal tumours in reverse tobacco users) and circumstances (actinic keratosis, submucous fibrosis, and discoid lupus erythematosus lichen planus) that are categorized as potentially malignant disorders (PMDs) [18]. Over a span of 0.5–16 years, precancerous injuries with dysplasia had a 12.3 percent risk of malignant development [12]. The present “wait and watch” method of monitoring cancer growth is determined by clinical feature conundrum surrounding the diagnosis, verification, and initial therapy of OPC [12]. Both excessive and insufficient therapy has a significant role in patient illness [10, 12]. In this situation, at which clinicopathological research studies are extremely unpredictable in identifying precancerous lesions at risk for development as well as a sequence of epigenetic and genetic modifications signal development of the disease, identifying molecular biomarkers of disease development can be extremely beneficial in the initial identification of easily reversible abnormalities, resulting in better diagnostic and therapeutic consequences [10, 12, 19].DNA methylation is a physiologically epigenetic alteration that happens when a methyl group is introduced to a CpG dinucleotide in the gene-regulating sequence of DNA [20–22]. Abnormal (more or less) methylation inhibits cell division’s physiological integrity [23], and is hypothesised to be a mechanism through which ecological risk factors, including cigarette smoking, alcohol consumption, and food consumption, impact ailment risk [24–26]. Increased-methylation of enhencer areas (CpG islands) results in the silence of genes implicated in primary tumour suppression, including those engaged in the processes of DNA renovation, cell cycle control, and apoptosis [27]. When a CpG dinucleotide included in the overall DNA arrangement is hypomethylated, oncogenes, for instance cell cycle signalling genes, are activated [27]. DNA methylation forms are dynamic and reversible, allowing them to adjust to environmental or therapeutic changes [28]. Figure 1 shows the interest in methylation of DNA biomarker in tumor diagnosis. If dynamic behaviour is connected with cancer growth and progression, it may be especially beneficial when precise sensing is necessary, as is the case with primary detection of OPC that may advance or retreat in a period [27]. Time patterns indicating a rise or reduction in aberrant methylation may aid in predicting the pace as well as the possibility of malignant change and the reversal of ailment status. Due to its possible initial diagnostic significance in OPC development, abnormal DNA methylation is a promising alternative for biomarker development [29].Figure 1
DNA methylation biomarker in cancer diagnosis. Diagram illustrating the preneoplastic cells followed by the screening, early detection, and diagnosis of tumor for the insertion of biomarkers based on DNA methylation. Reproduced with permission from [30].We reviewed relevant literature on DNA methylation forms in precancerous mouth abrasions to better understand the possible utility of abnormal methylation of DNA as a prognostic tool for the development of the ailment and to identify information voids in the literature to lead upcoming research. We searched various databases, including PubMed and Web of Sciences using the keywords “DNA methylation” and “oral cancer.” This review is aimed at giving an overview of DNA methylation indicators for the course of oral precancer. Moreover, we also provide an overview of other crucial cancer and methylation indicators to provide a comparative analysis of oral cancer.


### 1.1. Methylation in Oral Squamous Cell Cancer

OC is currently the 6th most often diagnosed tumor in men globally, both in terms of the number of reported cases and fatalities [31]. Since 2003, OC has become the 4th highest major cause of mortality in Taiwan among males. In 2010, the average age of males dying of oral tumor was 56 years, the youngest age of decease among the top ten malignancies in men. Furthermore, mouth tumor has been the main cause of mortality and incidence in Taiwanese men since 2005 having age of 25–44 years [32].Mouth squamous cell carcinoma (OSCC) accounts for more than 90percent of oral malignancies [3]. While early identification and treatment of OSCC have a favourable prognosis, persons with stage IV tumor have a five-year survival rate of only 30% [33]. Despite the ease with which the oral cavity may be examined clinically, OSCC is often identified at an advanced stage owing to the patient’s unawareness of any significant issues [34]. The invention of a simple instrument for early detection of OSCC will enhance not only patient survival, but also minimise related medical costs. This highlights the critical need to identify biomarkers for primary identification of OSCC. In the majority of countries, the key risk elements for OSCC are alcohol consumption and cigarette smoking, and specific indicators for OSCC associated with these lifestyle features have been observed; on the other hand, in Taiwan, the primary risk factor for OSCC is betel-quid chewing, and the OSCC biomarkers associated with betel-quid depletion might be somewhat changed from those associated other with adverse outcomes [35].Epigenetic alterations, such as histone and methylation of DNA variations, are accountable for changed expression gene forms associated with distinct phenotypes. While DNA methylation is required for proper mammalian development, abnormal sequence of methylation are associated with various distinguishing related disorders, for example, numerous kinds of human cancer. The study of tumor-suppressor gene promoter methylation in the context of mouth epithelial dysplasia looks relevant, considering the comparatively high frequency of this epigenetic alteration in OSCC [36]. Initial epigenetic modifications may incline cells to develop more genetic defects, allowing the neoplastic process to proceed. Thus, identifying gene methylation as a sensitive marker for OSCC exposure may be possible.The application of modern technologies, for instance next-generation sequencing and DNA microarray analysis, has expanded the scope of DNA methylation research apart from a few potential genes. The literature describes various procedures for determining the presence of methylation promoter, such as pyrosequencing methylation assay, PCR methylation-specific (MSP), assay for bisulfite sequencing, microarray-based methylation analysis, and combined bisulfite restriction analysis; the MSP procedure accounted for the overwhelming bulk of available research. Reviews of the literature [37, 38] 10-12 have shown a broad range of claimed accuracy and precision for this approach, ranging from 30% to 90%.


## 1.1. Methylation in Oral Squamous Cell Cancer

OC is currently the 6th most often diagnosed tumor in men globally, both in terms of the number of reported cases and fatalities [31]. Since 2003, OC has become the 4th highest major cause of mortality in Taiwan among males. In 2010, the average age of males dying of oral tumor was 56 years, the youngest age of decease among the top ten malignancies in men. Furthermore, mouth tumor has been the main cause of mortality and incidence in Taiwanese men since 2005 having age of 25–44 years [32].Mouth squamous cell carcinoma (OSCC) accounts for more than 90percent of oral malignancies [3]. While early identification and treatment of OSCC have a favourable prognosis, persons with stage IV tumor have a five-year survival rate of only 30% [33]. Despite the ease with which the oral cavity may be examined clinically, OSCC is often identified at an advanced stage owing to the patient’s unawareness of any significant issues [34]. The invention of a simple instrument for early detection of OSCC will enhance not only patient survival, but also minimise related medical costs. This highlights the critical need to identify biomarkers for primary identification of OSCC. In the majority of countries, the key risk elements for OSCC are alcohol consumption and cigarette smoking, and specific indicators for OSCC associated with these lifestyle features have been observed; on the other hand, in Taiwan, the primary risk factor for OSCC is betel-quid chewing, and the OSCC biomarkers associated with betel-quid depletion might be somewhat changed from those associated other with adverse outcomes [35].Epigenetic alterations, such as histone and methylation of DNA variations, are accountable for changed expression gene forms associated with distinct phenotypes. While DNA methylation is required for proper mammalian development, abnormal sequence of methylation are associated with various distinguishing related disorders, for example, numerous kinds of human cancer. The study of tumor-suppressor gene promoter methylation in the context of mouth epithelial dysplasia looks relevant, considering the comparatively high frequency of this epigenetic alteration in OSCC [36]. Initial epigenetic modifications may incline cells to develop more genetic defects, allowing the neoplastic process to proceed. Thus, identifying gene methylation as a sensitive marker for OSCC exposure may be possible.The application of modern technologies, for instance next-generation sequencing and DNA microarray analysis, has expanded the scope of DNA methylation research apart from a few potential genes. The literature describes various procedures for determining the presence of methylation promoter, such as pyrosequencing methylation assay, PCR methylation-specific (MSP), assay for bisulfite sequencing, microarray-based methylation analysis, and combined bisulfite restriction analysis; the MSP procedure accounted for the overwhelming bulk of available research. Reviews of the literature [37, 38] 10-12 have shown a broad range of claimed accuracy and precision for this approach, ranging from 30% to 90%.


## 2. Methylation of Genes in Squamous Cell Carcinoma

Despite chemotherapy and radiation treatment advancements, neck and head squamous cell carcinoma (HNSCC) has a high mortality rate. This is mostly owing to the disease’s high severity heterogeneity at the genetic and morphologic levels. A present limitation in HNSCC prediction and therapy is a dearth of methodologies capable of appropriately addressing the disease’s complexity and variety.Historically, cancer’s molecular pathophysiology has been unraveled one gene at a time. Numerous novel high-throughput analytical approaches for analysing messenger RNA, DNA, and proteins inside a cell have enabled a more thorough molecular characterisation of the genome tumor. Complete high-throughput techniques which have recently been developed in HNSCC have emphasised the role of epigenetic and genetic events, often cooccurring [39] in the formation and development of the disease.Epigenetic methods include histone and DNA changes, which causes genes to be suppressed in a genetic manner without compromising their gene encoding. CpG island hypermethylation inside booster zone is a critical mechanism for gene transcriptional silencing. In methylation of HNSCC, RARB, MGMT, and p16 indicated primary actions, through methylation rates being comparable in cell lines and actual tumours [40].Abnormal methylation of DNA forms in HNSCC have been used as very sensitive diagnostic, risk assessment, and detection indicators. The activator hypermethylation sequences of GSTP1, MGMT, p16, and DAPK have been employed as molecular identifiers for identifying tumor cells in DNA serum, and over half of the individuals with HNSCC and methylated tumours had similar epigenetic abnormalities in the matched serum [41]. After bisulfite treatment, the number of previous data on HNSCC epigenetics comes from MSP chain reaction.16 MSP’s achievement has been thought to be due to its enhanced sensitivity; on the other hand, methylation investigation high-throughput microarrays [39] and multicandidate gene methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) applications usually depend on a carefully selected variety of genes, evaluated one at a time [42].


## 3. Methylation of DNA in Other Cancers

Upregulation of DNMT has been linked to the aetiology of lung cancer. Increased DNMT levels of cancer in the lung may result from overexpression of transcriptional activators, depletion of microRNAs that control DNMTs, and/or defective DNMT proteasomal breakdown by hsp90 [43–45]. Clinical data indicate that overexpression of DNMT1 is related with worse survival in patients with surgically excised lung cancer [46, 47]. In addition to these results, distinct TSGs are make quiet in lung cancer through promoter hypermethylation [43]. Numerous TSGs have a role in proper cellular function, including DNA repair (MGMT), regulation of the cell cycle (p16), caspase-8, apoptosis (DAPK, Wnt signalling regulation (APC)), cell adhesion and invasion (tissue blocker of metalloproteinase-3 and E-cadherin, H-cadherin), and invasion suppression (TIMP-3, CDH13). For instance, Brock et al. [44] identified a correlation between methylation of p16, cdk2A, RASSF1A, APC, and CDH13 with reappearance after resection surgery of phase I NSCLC independent of gender, stage, histology, or a history of smoking. In the same way, new research discovered that methylation of p16 and accompanying reduction of p16 appearance were associated with poorer existence after initial phase NSCLC resection [45]. Simultaneously, IGFBP-3 methylation is linked with cisplatin resistance in NSCLC [48].Apart from its importance as a predictive and predictive indicator, methylation DNA has been identified as a target for treatment by suppressing of the DNMT enzyme. 5-Azacitidine and decitabine are the 02 major DNMT blockers that have been widely investigated in health center [49]. When 5-azacitidine is phosphorylated, it is assimilated into RNA and DNA, proceeded by covalent attachment of DNMTs to the DNA, causing in proteasomal breakdown and a reduction in global methylation of DNA. When these drugs are employed at greater dosages, the DNA impairment and decreased DNA creation caused by DNA-DNMT dimers are accountable for their direct toxicity of cells. In contrast to decitabine, 5′-azacitidine is not integrated into RNA and is hence exclusively selective for DNA [50, 51]. These medicines’ hypomethylating possessions are best accomplished at minor dosages and with a longer duration of administration [52]. Both drugs have revealed anticancer efficacy in preclinical animals by demethylating and repressing various TSGs, as well as p16 [53]. Regrettably, their usage as a single treatment has shown poor efficacy in lung cancer clinical studies [54].In a stage I/II clinical study, fifteen individuals with incurable progressive NSCLC received a high dosage of decitabine (200–660 mg/m2) delivered as an 8-hour constant infusion. While no observable reaction was seen, 04 individuals maintained steady illness for more than six months, and 03 individuals survived for at least 01 year and 03 months, with 01 patient living for 06 year and 09 months. Only one patient finished more than one cycle due to haematological toxicities, which may have reduced therapy success [55, 56]. One more dosage-escalation phase I study, done on thirty-five individuals with solid tumors, 22 of them suffered from lung cancer, examined decitabine given at a lower dose and delivered continuously for 72 hours. There was no objective response seen, despite the fact that 03 patients having squamous cell lung carcinoma were in stable condition. Fascinatingly, pharmacodynamic tests demonstrated that one-third of patients had elevated MAGE-3, p16, and NY-ESO-1 expression [57]. Additional study will be conducted to determine the optimal sequence, dose, duration of therapy, and conjunction with other anticancer treatments, in addition to identify clinically meaningful predictive and pharmacodynamic response indicators.


## 4. Conclusion

The initial molecular alterations in oral carcinogenesis are epigenetic abnormalities, like as abnormal DNA CpG methylation patterns that mute cancer inhibitor genes and/or trigger oncogenes [58–60]. These arrangements of methylation are associated with an individual’s genetic outline along with ecological risk contact (e.g., cigarettes, food, and alcohol) [61], and they occur throughout the carcinogenesis process, including the first phases prior to any morphological alterations [62, 63]. Hence, DNA methylation forms distinguish themselves as promising primary diagnostic sign. These methylation alterations occur slowly and can be reversible in response to environmental variables, risk factor elimination, or early therapeutic intervention, making them attractive targets for involvement in the illness process (pharmacogenomics) [59].We review the literature of the DNA methylation and OPC (n=21 studies after eliminations) to ascertain the present state of the proof and to evaluate the diagnostic value of methylation DNA as indicator for mouth tumor development. Except for one study that assessed the epigenome-wide methylation outline, almost every research analysed CpG stations in tumour suppressor gene promoter regions. Only three research investigated longitudinal patterns of methylation; the other studies described cross-sectional methylation profiles.Assessment of the data found that a small number of genes intricate in the control of the cell cycle (p14, p16), apoptosis (DAPK), and DNA restoration (MGMT) have been repeatedly described in three or more investigations and verified via epigenome-wide methylation study. These loci seem to be favorable candidates for more assessment. Longitudinal investigations have shown that dysplastic lesions that progressed to malignancy had a greater level of hypermethylation (p16) than lesions that retreated [64, 65], suggesting potential dynamic changes in methylation patterns during disease development. Hypermethylation of p16 was seen more often in dysplastic phases of pretumor than in nondysplastic phases (hyperplastic/hyperkeratotic or nondysplastic OPC) [66]. Notably, hypermethylation of p16 has been found to be a possible indicator for recurrence-free subsistence in mouth and oro-pharyngeal malignancies [23]. Other loci, for instance, mi-RNA genes, E-cadherin (an adhesion molecule), and a variety of additional DNA restoration genes that have been examined in mouth malignancies, are being assessed in OPC [67–69].While locus-specific methylation analysis methods are typically used to quantify promoter hypermethylation, high-density arrays enable the measurement of aberrant (hypo and hyper) methylation at single locations throughout the genome in a consistent and reproducible way [70]. The epigenome-wide methylation study of OPC discovered 03 new loci (TRHDE, ZNF454, and KCNAB3) already unknown in any tumor site, as well as validating the MGMT, p16, and DAPK loci. The new locations’ functional relevance is unknown [71].Aberrant methylation may be a biomarker for directing patient-associated treatment choices [18], particularly in cancer locations for instance the mouth cavity, colon [13], and cervix [72, 73], where a precancer phase has been identified and is being treated. Because of the individual differences in the pathological and anatomical features of the development of disease related to colon tumor [73], and differences in the pathophysiological forms and numerous contagious strains of the human papilloma virus that cause cervical tumor [74], identifying methylation indicators for these locations is more challenging than for oral cancer [10].Although our evaluation identified some potential ideas for further investigation, several studies had restrictions in specimen size, research design, and/or presenting quantitative data. Maximum earlier research has lacked information on sociodemographic and lifestyle risk variables. The sampling methodology was substantially nonuniform, particularly with regard to the selection of control samples. 1/3 of the investigations did not disclose control information or did not design their trials with controls in mind. Control experiments vary significantly in their approach to control selection. While matched control sample taken from the same person could be useful for trying to adjust for possible confounders [75] connected with unattached specimens, including such use of tobacco/betel quid [76], this method does not contribute to the “cancerization of the field” that is frequently perceived in patients with OPC [18]. Except for one longitudinal research in which repeated samples were gathered from 38 afflicted individuals (total n=284), all other investigations used modest sample sizes and hence lacked the power for significant elucidation. Many hypermethylated sites were published only once, with no attempt to validate them. At last, most available research uses a cross-sectional design, which is incapable of assessing temporality, making causal inference problematic. Due to these constraints, no significant inference can yet be made for any of the markers found so far.On the other side, the majority of available research employed authenticated bisulfite alteration and MS-PCR procedure to determine methylation of DNA position in conjunction with appropriate quality control methods. Moreover, a large number of investigations analysed methylation in biopsy-confirmed tissue samples. Particularly, two research investigations [77, 78] show that saliva may be a viable medium for noninvasive investigating methylation indicators; however, Liu et al. [78] found that saliva (2.8%) has a decreased DAPK methylation efficiency than tissue (19.5%) or blood (19.5%) (98.8 percent) (Twenty-nine percent). Methylation patterns vary by tissue [18], and one tissue’s methylation pattern can be different from that of another [17]. Because methylation is the source of distinction expression gene, tissue-specific specimens can show precise epigenetic methylation sequences associated with disease pathways [22]. Methylation analysis may also be performed on whole blood and saliva. The nontarget agent would be a whole blood since it contains various cells with varying methylation forms [24]. Instead, saliva may include food detritus, leftover cells, and bacteria [63]. However, other investigations have revealed favourable findings using whole blood [24] and saliva specimens to detect extremely exact salivary biomarkers for example KIF1A and EDNRB [63]. Associations between tissue and blood sample data have also been established (R=0.49, p 0.001) [78]. Cytisine residues in DNA are methylated when they present in the CG dinucleotide shape. Moreover, methylation of CpG islands is the attachment of a methyl group to the 5 positions of cytosine in the promoter zone of genes, thereby inhibiting transcription DNA (Figure 2) [79].Figure 2
(a) Cytisine residues in DNA are methylated when they present in CG dinucleotide shape. (b) Methylation of CpG islands is the attachment of a methyl group to the 5 position of cytosine in the promoter zone of genes, thereby inhibiting transcription DNA. Reproduced with permission from [79].
(a)(b)While the existing data is unclear, we detected some reliability in relation of loci [77, 80, 81] and along with proof for dynamic variations throughout illness development [65]. Several investigations have also found concurrent dysregulated mRNA/protein appearance in abnormally methylated dysplastic mouth premalignant lesions [66]. According to investigations analysing methylation forms associated with genetic changes, for instance, obliterations [82], abnormal methylation may be the first molecular change signalling illness initiation and development. These findings show that methylation forms may be useful as a diagnostic biomarker for mouth precancerous lesions. Large-scale epigenetic modification methylation investigations of OPC with adequate replication are needed in the future, and follow-up data to imprisonment dynamic changes in the methylation profile might aid in identifying robust loci defining disease development and guiding primary detection during important windows. It is critical to emphasise the importance of a suitable study proposal, proper control definitions, devotion to quality control and writing commendations, and assortment of relevant sociodemographic, lifestyle risk factor, clinical, and histopathological data to help the growth of clinically relevant markers.



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