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Kumari S, Mishra S, Anand N, Hadi R, Rastogi M, Husain N. Circulating free DNA integrity index and promoter methylation of tumor suppressor gene P16, DAPK and RASSF1A as a biomarker for oropharyngeal squamous cell carcinoma. Pathol Res Pract 2023; 246:154489. [PMID: 37150134 DOI: 10.1016/j.prp.2023.154489] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 04/21/2023] [Accepted: 04/24/2023] [Indexed: 05/09/2023]
Abstract
Circulating free DNA (cfDNA) is in use for the non-invasive diagnosis of tumors. Methylation of tumor suppressor genes (TSGs) is an early event in carcinogenesis and may serve as tumor biomarker. We have investigated cfDNA integrity and methylation of tumor suppressor genes P16, DAPK and RASSF1A in serum cfDNA of oropharyngeal squamous cell carcinoma (OPSCC) comparing paired serum and tumor tissue samples to evaluate their diagnostic use. Prospective case-control study, paired serum and tissue samples from 56 OPSCC, and 15 normal controls (NC). Sybr green Quantitate real time PCR was used for cfDNA quantification through amplification ALU 115 and 247 fragments. Promoter methylation of was analyzed in paired samples using methylation specific PCR. There was significantly high cfDNA integrity in OPSCC compared to normal control (p = < 0.0001). The cfDNA integrity values were significantly higher and associated with nodal status (p = 0.016). The AUC for cfDNA integrity was 0.967. The P16, DAPK and RASSF1 promoters were significantly hypermethylated in serum of OPSCC compared to NC with high concordance in tissue (up to 96.55 %). The gene promoter methylation of P16 was associated with smoking (p = 0.030), RASSF1A with stage (p = 0.011). The combination of ALU115 with cfDNA integrity and combination of gene methylation increases diagnostic sensitivity. In followup samples the cfDNA change was not different. Liquid biopsy approach including cfDNA integrity, methylation profiling in cfDNA, in combination or separately can assist in the diagnosis of OPSCC along with radio diagnostic scan. Serum changes represent changes in tissue with very high concordance.
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Affiliation(s)
- Swati Kumari
- Department of Pathology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Vibhuti Khand, Gomti Nagar, Lucknow, U.P. 226010, India
| | - Sridhar Mishra
- Department of Pathology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Vibhuti Khand, Gomti Nagar, Lucknow, U.P. 226010, India
| | - Nidhi Anand
- Department of Pathology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Vibhuti Khand, Gomti Nagar, Lucknow, U.P. 226010, India
| | - Rahat Hadi
- Department of Radiation Oncology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Vibhuti Khand, Gomti Nagar, Lucknow, U.P. 226010, India
| | - Madhup Rastogi
- Department of Radiation Oncology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Vibhuti Khand, Gomti Nagar, Lucknow, U.P. 226010, India
| | - Nuzhat Husain
- Department of Pathology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Vibhuti Khand, Gomti Nagar, Lucknow, U.P. 226010, India.
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Antra, Parashar P, Hungyo H, Jain A, Ahmad S, Tandon V. Unraveling molecular mechanisms of Head and neck cancer. Crit Rev Oncol Hematol 2022; 178:103778. [PMID: 35932993 DOI: 10.1016/j.critrevonc.2022.103778] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 03/02/2022] [Accepted: 08/01/2022] [Indexed: 12/24/2022] Open
Abstract
Malignancies that develop from mucosal epithelium of the upper aerodigestive tract are known as head and neck squamous cell carcinomas (HNSCC). Heterogeneity, late stage diagnosis and high recurrence rate are big hurdles in head and neck treatment regimen. Presently, the biomarkers available for diagnosis and prognosis of HNSCC are based on smoking as the major risk habit. This review shed light on the differential environment of HNSCC in smokeless tobacco consuming Indian patients. Frequent mutation in genes involved in DNA repair pathway (p53), cell proliferation (PIK3CA, HRAS) and cell death (CASP8, FADD) are common in western population. On the contrary, the genes involved in metastasis (MMPs, YAP1), lymphocyte proliferation (TNFRSF4, CD80), cell-cell adhesion (DCC, EDNRB), miRNA processing (DROSHA) and inflammatory responses (TLR9, IL-9) are mutated in Indian HNSCC patients. Gene ontology enrichment analysis highlighted that responses to chemical stimulus, immune pathways and stress pathways are highly enriched in Indian patients.
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Affiliation(s)
- Antra
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067
| | - Palak Parashar
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067
| | - Hungharla Hungyo
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067
| | - Anuja Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067
| | - Shandar Ahmad
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067
| | - Vibha Tandon
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067.
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3
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Lu X, Li G, Liu S, Wang H, Zhang Z, Chen B. Bioinformatics Analysis of KIF1A Expression and Gene Regulation Network in Ovarian Carcinoma. Int J Gen Med 2021; 14:3707-3717. [PMID: 34321916 PMCID: PMC8312510 DOI: 10.2147/ijgm.s323591] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 07/14/2021] [Indexed: 12/24/2022] Open
Abstract
Background The study aims to analyze the expression levels of kinesin family member 1A (KIF1A) in ovarian cancer (OC) and explore its clinical significance in the development of OC and its potential regulatory network. Methods The Cancer Genome Atlas (TCGA) OC data was used to examine the expression differences between OC and normal tissue and explore the correlation with tumor stage. The relationship between KIF1A expression and prognosis was analyzed using Oncomine and Kaplan–Meier plotter tools. The co-expression network of KIF1A in TCGA OC was analyzed based on the application of cBioPortal, GO cluster, and KEGG analyses were performed based on the co-expression network. Immune-infiltration analysis were used to analyze the significant involvement of KIF1A in function. Results KIF1A was highly elevated in OC tissues and KIF1A expression was significantly correlated with the FIGO stage (P=0.015) and age (P=0.020). High KIF1A expression of OC predicted the poor prognosis including overall survival (OS) (HR: 1.27; 95% CI: 1.11–1.45; P=0.00046) and post-progression survival (PFS) (HR: 1.18; 95% CI: 1.03–1.35; P=0.015). GO and KEGG analysis showed KIF1A had a potential role in the biological process of ATP-dependent chromatin remodeling, transcription, DNA-templated cytolysis, positive regulation of T cell proliferation, positive regulation of transcription, DNA-templated via cell adhesion molecules (CAMs), primary immunodeficiency, oxidative phosphorylation, NF-kappa B signaling pathway, pathways in cancer and Wnt signaling pathway, and immune infiltrating cells. Conclusion KIF1A was highly expressed and correlated with poor survival and immune infiltration in OC, and it may be a prognostic biomarker in OC.
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Affiliation(s)
- Xiaoyuan Lu
- Department of Gynecology, The affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, Jiangsu, People's Republic of China
| | - Guilin Li
- Department of Gynecology, Maternal and Child Health Care Hospital affiliated to Xuzhou Medical University, Xuzhou, 221000, Jiangsu, People's Republic of China
| | - Sicong Liu
- Graduate School, Xuzhou Medical University, Xuzhou, 221000, Jiangsu, People's Republic of China
| | - Haihong Wang
- Department of Gynecology, The affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, Jiangsu, People's Republic of China
| | - Zhengzheng Zhang
- Department of Gynecology, The affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, Jiangsu, People's Republic of China
| | - Buze Chen
- Department of Gynecology, The affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, Jiangsu, People's Republic of China.,Xuzhou Medical University, Xuzhou, 221000, Jiangsu, People's Republic of China
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4
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Flausino CS, Daniel FI, Modolo F. DNA methylation in oral squamous cell carcinoma: from its role in carcinogenesis to potential inhibitor drugs. Crit Rev Oncol Hematol 2021; 164:103399. [PMID: 34147646 DOI: 10.1016/j.critrevonc.2021.103399] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 06/02/2021] [Accepted: 06/04/2021] [Indexed: 02/06/2023] Open
Abstract
DNA methylation is one of epigenetic changes most frequently studied nowadays, together with its relationship with oral carcinogenesis. A group of enzymes is responsible for methylation process, known as DNA methyltransferases (DNMT). Although essential during embryogenesis, DNA methylation pattern alterations, including global hypomethylation or gene promoter hypermethylation, can be respectively associated with chromosomal instability and tumor suppressor gene silencing. Higher expression of DNA methyltransferases is a common finding in oral cancer and may contribute to inactivation of important tumor suppressor genes, influencing development, progression, metastasis, and prognosis of the tumor. To control these alterations, inhibitor drugs have been developed as a way to regulate DNMT overexpression, and they are intended to be associated with ongoing chemo- and radiotherapy in oral cancer treatments. In this article, we aimed to highlight the current knowledge about DNA methylation in oral cancer, including main hyper/hypomethylated genes, DNMT expression and its inhibitor treatments.
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Affiliation(s)
| | - Filipe Ivan Daniel
- Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil.
| | - Filipe Modolo
- Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
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Hier J, Vachon O, Bernstein A, Ibrahim I, Mlynarek A, Hier M, Alaoui-Jamali MA, Maschietto M, da Silva SD. Portrait of DNA methylated genes predictive of poor prognosis in head and neck cancer and the implication for targeted therapy. Sci Rep 2021; 11:10012. [PMID: 33976322 PMCID: PMC8113272 DOI: 10.1038/s41598-021-89476-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 04/23/2021] [Indexed: 12/31/2022] Open
Abstract
In addition to chronic infection with human papilloma virus (HPV) and exposure to environmental carcinogens, genetic and epigenetic factors act as major risk factors for head and neck cancer (HNC) development and progression. Here, we conducted a systematic review in order to assess whether DNA hypermethylated genes are predictive of high risk of developing HNC and/or impact on survival and outcomes in non-HPV/non-tobacco/non-alcohol associated HNC. We identified 85 studies covering 32,187 subjects where the relationship between DNA methylation, risk factors and survival outcomes were addressed. Changes in DNA hypermethylation were identified for 120 genes. Interactome analysis revealed enrichment in complex regulatory pathways that coordinate cell cycle progression (CCNA1, SFN, ATM, GADD45A, CDK2NA, TP53, RB1 and RASSF1). However, not all these genes showed significant statistical association with alcohol consumption, tobacco and/or HPV infection in the multivariate analysis. Genes with the most robust HNC risk association included TIMP3, DCC, DAPK, CDH1, CCNA1, MGMT, P16, MINT31, CD44, RARβ. From these candidates, we further validated CD44 at translational level in an independent cohort of 100 patients with tongue cancer followed-up beyond 10 years. CD44 expression was associated with high-risk of tumor recurrence and metastasis (P = 0.01) in HPV-cases. In summary, genes regulated by methylation play a modulatory function in HNC susceptibility and it represent a critical therapeutic target to manage patients with advanced disease.
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Affiliation(s)
- Jessica Hier
- Department of Otolaryngology-Head and Neck Surgery, Lady Davis Institute for Medical Research and Segal Cancer Centre, Sir Mortimer B. Davis-Jewish General Hospital, McGill University, 3755 Côte Ste-Catherine Road, Montreal, QC, H3T 1E2, Canada
| | - Olivia Vachon
- Department of Otolaryngology-Head and Neck Surgery, Lady Davis Institute for Medical Research and Segal Cancer Centre, Sir Mortimer B. Davis-Jewish General Hospital, McGill University, 3755 Côte Ste-Catherine Road, Montreal, QC, H3T 1E2, Canada
| | - Allison Bernstein
- Department of Otolaryngology-Head and Neck Surgery, Lady Davis Institute for Medical Research and Segal Cancer Centre, Sir Mortimer B. Davis-Jewish General Hospital, McGill University, 3755 Côte Ste-Catherine Road, Montreal, QC, H3T 1E2, Canada
| | - Iman Ibrahim
- Department of Otolaryngology-Head and Neck Surgery, Lady Davis Institute for Medical Research and Segal Cancer Centre, Sir Mortimer B. Davis-Jewish General Hospital, McGill University, 3755 Côte Ste-Catherine Road, Montreal, QC, H3T 1E2, Canada
| | - Alex Mlynarek
- Department of Otolaryngology-Head and Neck Surgery, Lady Davis Institute for Medical Research and Segal Cancer Centre, Sir Mortimer B. Davis-Jewish General Hospital, McGill University, 3755 Côte Ste-Catherine Road, Montreal, QC, H3T 1E2, Canada
| | - Michael Hier
- Department of Otolaryngology-Head and Neck Surgery, Lady Davis Institute for Medical Research and Segal Cancer Centre, Sir Mortimer B. Davis-Jewish General Hospital, McGill University, 3755 Côte Ste-Catherine Road, Montreal, QC, H3T 1E2, Canada
| | - Moulay A Alaoui-Jamali
- Segal Cancer Centre of the Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Mariana Maschietto
- Department of Structural and Functional Biology, Institute of Biology, Universidade Estadual de Campinas (UNICAMP) and Boldrini Children's Center, Campinas, Sao Paulo, Brazil
| | - Sabrina Daniela da Silva
- Department of Otolaryngology-Head and Neck Surgery, Lady Davis Institute for Medical Research and Segal Cancer Centre, Sir Mortimer B. Davis-Jewish General Hospital, McGill University, 3755 Côte Ste-Catherine Road, Montreal, QC, H3T 1E2, Canada. .,Segal Cancer Centre of the Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, McGill University, Montreal, QC, Canada.
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6
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Marthong L, Ghosh S, Palodhi A, Imran M, Shunyu NB, Maitra A, Ghosh S. Whole Genome DNA Methylation and Gene Expression Profiling of Oropharyngeal Cancer Patients in North-Eastern India: Identification of Epigenetically Altered Gene Expression Reveals Potential Biomarkers. Front Genet 2020; 11:986. [PMID: 33133131 PMCID: PMC7578381 DOI: 10.3389/fgene.2020.00986] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 08/05/2020] [Indexed: 12/31/2022] Open
Abstract
Oropharyngeal cancer is a subtype of head and neck squamous cell carcinoma that is associated with unique risk exposures like consumption of smokeless tobacco and areca nut and is highly prevalent in the northeastern region of India, especially Meghalaya. However, the underlying epigenetic and transcriptomic changes in this cancer type is yet to be delineated. We have undertaken a study on genome wide somatic alterations in the DNA methylation and transcriptome in oropharyngeal cancer patients from this region using genome wide techniques in paired tumors and adjacent normal tissues. By using integrative approaches, we have identified 194 epigenetically silenced and 241 epigenetically overexpressed genes in the tumor tissue of these patients. Pathways that are significantly enriched by these genes include the pathways of immune systems, such as the interleukin signaling pathways and Toll-like receptor signaling pathway. Also, osteoclast differentiation pathway was found to be epigenetically upregulated. The pathways enriched by the epigenetically downregulated genes were found to be predominantly those involved in xenobiotic metabolism and keratinization. Two major transcription factors - SPI1 and RUNX1 were identified as epigenetically dysregulated, which further modulates 129 downstream genes. Comparison of our observations with the head and neck cancer data from TCGA revealed distinct DNA methylation and gene expression landscapes which might be specific for oropharyngeal cancer. HPV DNA sequences were not detected in any of the tumor samples in RNA-Seq data. The results obtained in this study might provide improved understanding of the disease.
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Affiliation(s)
- Lastborn Marthong
- Department of Zoology, North Eastern Hill University (NEHU), Shillong, India
| | - Sahana Ghosh
- National Institute of Biomedical Genomics (NIBMG), Kalyani, India
| | - Arindam Palodhi
- National Institute of Biomedical Genomics (NIBMG), Kalyani, India
| | - Mohamed Imran
- National Institute of Biomedical Genomics (NIBMG), Kalyani, India
| | - Neizekhotuo Brian Shunyu
- Department of Otorhinolaryngology (ENT), North Eastern Indira Gandhi Regional Institute of Health and Medical Sciences (NEIGRIHMS), Shillong, India
| | - Arindam Maitra
- National Institute of Biomedical Genomics (NIBMG), Kalyani, India
| | - Srimoyee Ghosh
- Department of Zoology, North Eastern Hill University (NEHU), Shillong, India
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González-Pérez LV, Isaza-Guzmán DM, Arango-Pérez EA, Tobón-Arroyave SI. Analysis of salivary detection of P16INK4A and RASSF1A promoter gene methylation and its association with oral squamous cell carcinoma in a Colombian population. J Clin Exp Dent 2020; 12:e452-e460. [PMID: 32509227 PMCID: PMC7263777 DOI: 10.4317/jced.56647] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 02/24/2020] [Indexed: 01/19/2023] Open
Abstract
Background Epigenetic factors play a fundamental role in the etiopathogenesis of oral squamous cell carcinoma (OSCC). This study evaluated if salivary detection of P16INK4A/RASSF1A gene promoter methylation might be linked to the clinical/histological features of OSCC in a Colombian population.
Material and Methods Methylation-specific polymerase chain reaction (MSP-PCR) was used to detect the methylation frequency of P16INK4A/RASSF1A genes in DNA obtained from whole saliva collected of 40 healthy controls (HC) and 43 OSCC patients. Determination of the clinical performance of MSP-PCR assay was based on standard algorithms derived from two-way contingency table analysis. The association of methylation status of targeted genes with OSCC was analyzed in a multivariate binary logistic regression model.
Results There were significantly higher proportions of promoter methylation of these target genes in OSCC patients when compared with HC. The analysis of single methylated genes showed high specificity, good positive and negative predictive values, but was accompanied by a low sensitivity. OSCC cases with clinical stage III/IV, poorly differentiated, and severe cellular atypia showed a significantly greater proportion of methylated than that of unmethylated targeted genes in saliva samples. Logistic regression analysis indicated an independent association of P16INK4A and RASSF1A promoter methylation with OSCC diagnosis. A significant interaction effect between ageing and P16INK4A promoter methylation was also detected.
Conclusions Salivary detection of P16INK4A and RASSF1A promoter methylation appears to be independently associated with OSCC and may be linked to the tumor activity in the present population. Consequently, the targeting of these genes in saliva samples might constitute an important tool for diagnosis and prognosis purposes. Key words:Gene methylation, oral squamous cell carcinoma, P16INK4A, RASSF1A, saliva.
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Affiliation(s)
| | - Diana-María Isaza-Guzmán
- Titular Professor. Laboratory of Immunodetection and Bioanalysis, Faculty of Dentistry, University of Antioquia. Medellín, Colombia
| | - Eduin-Alonso Arango-Pérez
- Oral and Maxillofacial Surgeon Resident. Department of Oral and Maxillofacial Surgery, Faculty of Dentistry, University of Antioquia. Medellín, Colombia
| | - Sergio-Iván Tobón-Arroyave
- Titular Professor. Laboratory of Immunodetection and Bioanalysis, Faculty of Dentistry, University of Antioquia. Medellín, Colombia.,Stomatologist and Oral Surgeon. Stomatology and Maxillofacial Surgery Unit, San Vicente Foundation University Hospital, Medellín, Colombia
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Islam S, Uehara O, Matsuoka H, Kuramitsu Y, Adhikari BR, Hiraki D, Toraya S, Jayawardena A, Saito I, Muthumala M, Nagayasu H, Abiko Y, Chiba I. DNA hypermethylation of sirtuin 1 (SIRT1) caused by betel quid chewing-a possible predictive biomarker for malignant transformation. Clin Epigenetics 2020; 12:12. [PMID: 31931863 PMCID: PMC6958620 DOI: 10.1186/s13148-019-0806-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 12/30/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND DNA hypermethylation of tumor suppressor genes is observed in precancerous lesions and oral cancer of individuals with the habits of betel quid (BQ) chewing. SIRT1 has been identified as playing a role in the maintenance of epithelial integrity, and its alteration is often related to carcinogenesis. However, the methylation and transcription status of SIRT1 in patients with BQ chewing-related oral cancer has not been investigated. We examined the methylation status of SIRT1 in paraffin-embedded tissue samples of oral squamous cell carcinoma (OSCC) obtained from BQ chewing and non-chewing patients and in tissue samples from healthy control subjects. In addition, we examined whether the hypermethylation of SIRT1 followed by its transcriptional downregulation in the human gingival epithelial cells could be caused by arecoline, a major component of BQ. Furthermore, we investigated the methylation status of SIRT1 in smear samples of macroscopically healthy buccal mucosa from subjects with a habit of BQ chewing. RESULTS SIRT1 was significantly hypermethylated in tissue samples of OSCC from BQ chewers and non-chewers than in oral mucosa from healthy control subjects. Results also showed that the hypermethylation level of SIRT1 was significantly higher in OSCC of patients with BQ chewing habits than in those of non-chewing habits (p < 0.05). Our in vitro model showed that hypermethylation is followed by downregulation of the transcriptional level of SIRT1 (p < 0.05). The methylation levels of SIRT1 in the smear samples obtained from BQ chewing individuals were significantly higher than those in the samples obtained from individuals that did not chew BQ. The duration of BQ chewing habits was correlated positively to the frequency of SIRT1 hypermethylation (p < 0.05). CONCLUSIONS Our results suggest that DNA hypermethylation of SIRT1 is involved in the occurrence of oral cancer in BQ chewing patients and that hypermethylation in the oral mucosa of BQ chewers could be a predictive marker for the occurrence of malignant transformation. This is the first report that showed DNA hypermethylation in clinically healthy oral epithelium of BQ chewers. Our study shows evidence that DNA hypermethylation may be an early event of oral carcinogenesis prior to observable clinical changes.
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Affiliation(s)
- Shajedul Islam
- Division of Disease Control and Molecular Epidemiology, Department of Oral Growth and Development, School of Dentistry, Health Sciences University of Hokkaido, Hokkaido, 061-0293, Japan.,Division of Oral Medicine and Pathology, Department of Human Biology and Pathophysiology, School of Dentistry, Health Sciences University of Hokkaido, Hokkaido, 061-0293, Japan
| | - Osamu Uehara
- Division of Disease Control and Molecular Epidemiology, Department of Oral Growth and Development, School of Dentistry, Health Sciences University of Hokkaido, Hokkaido, 061-0293, Japan.,Research Institute of Cancer Prevention, Health Sciences University of Hokkaido, Hokkaido, 061-0293, Japan
| | - Hirofumi Matsuoka
- Division of Disease Control and Molecular Epidemiology, Department of Oral Growth and Development, School of Dentistry, Health Sciences University of Hokkaido, Hokkaido, 061-0293, Japan
| | - Yasuhiro Kuramitsu
- Research Institute of Cancer Prevention, Health Sciences University of Hokkaido, Hokkaido, 061-0293, Japan
| | - Bhoj Raj Adhikari
- Division of Oral Medicine and Pathology, Department of Human Biology and Pathophysiology, School of Dentistry, Health Sciences University of Hokkaido, Hokkaido, 061-0293, Japan
| | - Daichi Hiraki
- Division of Oral Medicine and Pathology, Department of Human Biology and Pathophysiology, School of Dentistry, Health Sciences University of Hokkaido, Hokkaido, 061-0293, Japan
| | - Seiko Toraya
- Division of Disease Control and Molecular Epidemiology, Department of Oral Growth and Development, School of Dentistry, Health Sciences University of Hokkaido, Hokkaido, 061-0293, Japan
| | - Asiri Jayawardena
- Department of General Education, School of Dental Medicine, Tsurumi University, Kanagawa, 230-8501, Japan
| | - Ichiro Saito
- Department of Pathology, School of Dental Medicine, Tsurumi University, Kanagawa, 230-8501, Japan
| | - Malsantha Muthumala
- Department of Oral and Maxillofacial Surgery, Army Hospital, Colombo, Sri Lanka
| | - Hiroki Nagayasu
- Division of Oral and Maxillofacial Surgery, Department of Human Biology and Pathophysiology, School of Dentistry, Health Sciences University of Hokkaido, Hokkaido, 061-0293, Japan
| | - Yoshihiro Abiko
- Division of Oral Medicine and Pathology, Department of Human Biology and Pathophysiology, School of Dentistry, Health Sciences University of Hokkaido, Hokkaido, 061-0293, Japan.
| | - Itsuo Chiba
- Division of Disease Control and Molecular Epidemiology, Department of Oral Growth and Development, School of Dentistry, Health Sciences University of Hokkaido, Hokkaido, 061-0293, Japan
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Liyanage C, Wathupola A, Muraleetharan S, Perera K, Punyadeera C, Udagama P. Promoter Hypermethylation of Tumor-Suppressor Genes p16INK4a, RASSF1A, TIMP3, and PCQAP/MED15 in Salivary DNA as a Quadruple Biomarker Panel for Early Detection of Oral and Oropharyngeal Cancers. Biomolecules 2019; 9:biom9040148. [PMID: 31013839 PMCID: PMC6523930 DOI: 10.3390/biom9040148] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 04/07/2019] [Accepted: 04/08/2019] [Indexed: 01/01/2023] Open
Abstract
Silencing of tumor-suppressor genes (TSGs) by DNA promoter hypermethylation is an early event in carcinogenesis; hence, TSGs may serve as early tumor biomarkers. We determined the promoter methylation levels of p16INK4a, RASSF1A, TIMP3, and PCQAP/MED15 TSGs in salivary DNA from oral cancer (OC) and oropharyngeal cancer (OPC) patients, using methylation-specific PCR coupled with densitometry analysis. We assessed the association between DNA methylation of individual TSGs with OC and OPC risk factors. The performance and the clinical validity of this quadruple-methylation marker panel were evaluated in discriminating OC and OPC patients from healthy controls using the CombiROC web tool. Our study reports that RASSF1A, TIMP3, and PCQAP/MED15 TSGs were significantly hypermethylated in OC and OPC cases compared to healthy controls. DNA methylation levels of TSGs were significantly augmented by smoking, alcohol use, and betel quid chewing, indicating the fact that frequent exposure to risk factors may drive oral and oropharyngeal carcinogenesis through TSG promoter hypermethylation. Also, this quadruple-methylation marker panel of p16INK4a, RASSF1A, TIMP3, and PCQAP/MED15 TSGs demonstrated excellent diagnostic accuracy in the early detection of OC at 91.7% sensitivity and 92.3% specificity and of OPC at 99.8% sensitivity and 92.1% specificity from healthy controls.
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Affiliation(s)
- Chamikara Liyanage
- Department of Zoology and Environment Sciences, University of Colombo, Colombo 03 00300, Sri Lanka.
| | - Asanga Wathupola
- Department of Zoology and Environment Sciences, University of Colombo, Colombo 03 00300, Sri Lanka.
| | - Sanjayan Muraleetharan
- Department of Zoology and Environment Sciences, University of Colombo, Colombo 03 00300, Sri Lanka.
| | - Kanthi Perera
- National Cancer Institute of Sri Lanka, Maharagama, 10280, Sri Lanka.
| | - Chamindie Punyadeera
- The School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD 4059, Australia.
- Translational Research Institute, 37 Kent Street, Woolloongabba, Brisbane, QLD 4102, Australia.
| | - Preethi Udagama
- Department of Zoology and Environment Sciences, University of Colombo, Colombo 03 00300, Sri Lanka.
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10
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Németh CG, Röcken C, Siebert R, Wiltfang J, Ammerpohl O, Gassling V. Recurrent chromosomal and epigenetic alterations in oral squamous cell carcinoma and its putative premalignant condition oral lichen planus. PLoS One 2019; 14:e0215055. [PMID: 30964915 PMCID: PMC6456184 DOI: 10.1371/journal.pone.0215055] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 03/26/2019] [Indexed: 12/31/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) affects about 700.000 individuals per year worldwide with oral squamous cell carcinoma (OSCC) as a major subcategory. Despite a comprehensive treatment concept including surgery, radiation, and chemotherapy the 5-year survival rate is still only about 50 percent. Chronic inflammation is one of the hallmarks of carcinogenesis. Until now, little is known about the premalignant status of oral lichen planus (OLP) and molecular alterations in OLP are still poorly characterized. Our study aims to delineate differential DNA methylation patterns in OLP, OSCC, and normal oral mucosa. By applying a bead chip approach, we identified altered chromosomal patterns characteristic for OSCC while finding no recurrent alterations in OLP. In contrast, we identified numerous alterations in the DNA methylation pattern in OLP, as compared to normal controls, that were also present in OSCC. Our data support the hypothesis that OLP is a precursor lesion of OSCC sharing multiple epigenetic alterations with OSCC.
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Affiliation(s)
- Christopher G Németh
- Department of Oral and Maxillofacial Surgery, University Hospital of Schleswig-Holstein, Kiel, Germany
| | - Christoph Röcken
- Department of Pathology, University Hospital of Schleswig-Holstein, Kiel, Germany
| | - Reiner Siebert
- Institute of Human Genetics, University Hospital of Schleswig-Holstein, Kiel, Germany.,Institute of Human Genetics, University Medical Centre, Ulm, Germany
| | - Jörg Wiltfang
- Department of Oral and Maxillofacial Surgery, University Hospital of Schleswig-Holstein, Kiel, Germany
| | - Ole Ammerpohl
- Institute of Human Genetics, University Hospital of Schleswig-Holstein, Kiel, Germany.,Institute of Human Genetics, University Medical Centre, Ulm, Germany
| | - Volker Gassling
- Department of Oral and Maxillofacial Surgery, University Hospital of Schleswig-Holstein, Kiel, Germany
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11
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Mohanta S, Sekhar Khora S, Suresh A. Cancer Stem Cell based molecular predictors of tumor recurrence in Oral squamous cell carcinoma. Arch Oral Biol 2019; 99:92-106. [PMID: 30641296 DOI: 10.1016/j.archoralbio.2019.01.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 01/02/2019] [Accepted: 01/04/2019] [Indexed: 02/01/2023]
Abstract
OBJECTIVE This study aimed to identify the cancer stem cell specific biomarkers that can be effective candidate prognosticators of oral squamous cell carcinoma. DESIGN Microarray-based meta-analysis derived transcriptional profile of head and neck cancers was compared with the Cancer Stem Cell database to arrive at a subset of markers. This subset was further co-related with clinico-pathological parameters, recurrence and survival of oral cancer patients (n = 313) in The Cancer Genome Atlas database and in oral cancer (n = 28) patients. RESULTS Meta-analysis in combination with database comparison identified a panel of 221 genes specific to head and neck cancers. Correlation of expression levels of these markers in the oral cancer cohort of The Cancer Genome Atlas (n = 313) with treatment outcome identified 54 genes (p < 0.05 or fold change >2) associated with disease recurrence, 8 genes (NQO1, UBE2C, EDNRB, FKBP4, STAT3, HOXA1, RIT1, AURKA) being significant with high fold change. Assessment of the efficacy of the subset (n = 54) as survival predictors identified an additional 4 genes (CDK1, GINS2, PHF5 A, ERBB2) that co-related with poor disease-free survival (p < 0.05). CDK1 showed a significant association with the clinical stage, margin status and with advanced pathological parameters. Initial patient validation indicated that CDK1 and NQO1 significantly co-related with the poor disease-free and overall survival (p < 0.05). CONCLUSION This panel of oral cancer specific, cancer stem cell associated markers identified in this study, a subset of which was validated, will be of clinical benefit subject to large scale validation studies.
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Affiliation(s)
- Simple Mohanta
- Integrated Head and Neck Oncology Program, Mazumdar Shaw Medical Foundation, Mazumdar Shaw Medical Center, Narayana Health City, Bommasandra Industrial Area, Anekal Taluk, Bangalore, 560099, Karnataka, India; Department of Head and Neck Oncology, Mazumdar Shaw Medical Center, Narayana Health City, Bommasandra Industrial Area, Anekal Taluk, Bangalore, 560099, Karnataka, India; School of Bio Sciences & Technology, VIT University, Vellore, 632014, Tamil Nadu, India
| | - Samanta Sekhar Khora
- School of Bio Sciences & Technology, VIT University, Vellore, 632014, Tamil Nadu, India
| | - Amritha Suresh
- Integrated Head and Neck Oncology Program, Mazumdar Shaw Medical Foundation, Mazumdar Shaw Medical Center, Narayana Health City, Bommasandra Industrial Area, Anekal Taluk, Bangalore, 560099, Karnataka, India; Department of Head and Neck Oncology, Mazumdar Shaw Medical Center, Narayana Health City, Bommasandra Industrial Area, Anekal Taluk, Bangalore, 560099, Karnataka, India; Mazumdar Shaw Medical Centre-Roswell Park Collaboration Program, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, 14263, New York, USA.
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12
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Strzelczyk JK, Krakowczyk Ł, Owczarek AJ. Aberrant DNA methylation of the p16, APC, MGMT, TIMP3 and CDH1 gene promoters in tumours and the surgical margins of patients with oral cavity cancer. J Cancer 2018; 9:1896-1904. [PMID: 29896273 PMCID: PMC5995944 DOI: 10.7150/jca.24477] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 03/10/2018] [Indexed: 12/15/2022] Open
Abstract
Oral cavity cancer is a type of head and neck squamous cell carcinoma (HNSCC) and contributes to significant morbidity and mortality each year. An epigenetic pathway of transcriptional inactivation for many genes has been described in various cancers, including HNSCC. For our study, we selected genes for which silencing caused by hypermethylation can promote cancer development. In 75 primary HNSCC tumours and paired surgical margins, we investigated the methylation status of the p16, APC, MGMT, TIMP3 and CDH1 gene promoters by methylation-specific PCR after bisulphite treatment. The promoter methylation rates of p16, APC, MGMT, TIMP3 and CDH1 in tumours were 58.67%, 49.33%, 58.67%, 50.67%, and 57.33% and 50.67%, 41.33%, 37.33%, 42.67%, and 25.33% in the surgical margin, respectively. Our observations confirm the presence of epigenetic changes not only in the cancer cells, but also in the surrounding mucosa and represent a basis for further analysis to unravel these complicated issues. Appropriate cancer risk assessment based on epigenetic alterations in surgical margins may influence a patient's diagnosis and cure.
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Affiliation(s)
- Joanna Katarzyna Strzelczyk
- Department of Medical and Molecular Biology, School of Medicine with the Division of Dentistry in Zabrze, Jordana 19 Str., 41-808 Zabrze, Medical University of Silesia in Katowice, Zabrze, Poland
| | - Łukasz Krakowczyk
- Clinic of Oncological and Reconstructive Surgery, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice Branch, Wybrzeże Armii Krajowej 15 Str., 44-101 Gliwice, Poland
| | - Aleksander Jerzy Owczarek
- Department of Statistics, Department of Instrumental Analysis, School of Pharmacy with the Division of Laboratory Medicine in Sosnowiec, Ostrogórska 30 Str., 41-200 Sosnowiec, Medical University of Silesia in Katowice, Sosnowiec, Poland
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13
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Ji X, Guan C, Jiang X, Li H. Diagnostic accuracy of DNA methylation for head and neck cancer varies by sample type and number of markers tested. Oncotarget 2018; 7:80019-80032. [PMID: 27683120 PMCID: PMC5346768 DOI: 10.18632/oncotarget.12219] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Accepted: 09/02/2016] [Indexed: 11/25/2022] Open
Abstract
Abnormal methylation of certain cancer related genes strongly predicts a diagnosis of head and neck cancer (HNC), while the predictive power of methylation of other DNA markers for HNC remains unclear. To systemically assess the diagnostic value of DNA methylation patterns for HNC and the effect of methylation platform techniques and sample types, we performed a PubMed search for studies of the correlation between DNA methylation and HNC completed before July 2016, and extracted the sensitivity and specificity for methylated biomarkers. Across these studies, DNA methylation showed high sensitivity for diagnosing HNC in solid tissue (0.57), and high specificity in saliva (0.89). Area under the curve (AUC) from summary receiver operating characteristic (SROC) curves revealed that DNA methylation had more diagnostic power in solid tissue (AUC = 0.82) than saliva (AUC = 0.80) or blood (AUC = 0.77). Combinations of multiple methylated genes were more sensitive diagnostic markers than single methylated genes. Our results suggest that the diagnostic accuracy of methylated biomarkers for HNC varied by sample type and were most accurate when results from multiple sample types were considered.
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Affiliation(s)
- Xu Ji
- Department of Otolaryngology, The First Affiliated Hospital of China Medical University, Shenyang, 110001, China
| | - Chao Guan
- Department of Otolaryngology, The First Affiliated Hospital of China Medical University, Shenyang, 110001, China
| | - Xuejun Jiang
- Department of Otolaryngology, The First Affiliated Hospital of China Medical University, Shenyang, 110001, China
| | - Hong Li
- Department of Otorhinolaryngology Head and Neck Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, 110032, China
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14
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Eljabo N, Nikolic N, Carkic J, Jelovac D, Lazarevic M, Tanic N, Milasin J. Genetic and epigenetic alterations in the tumour, tumour margins, and normal buccal mucosa of patients with oral cancer. Int J Oral Maxillofac Surg 2018; 47:976-982. [PMID: 29449053 DOI: 10.1016/j.ijom.2018.01.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 11/13/2017] [Accepted: 01/26/2018] [Indexed: 01/17/2023]
Abstract
Despite adequate surgical resection, oral squamous cell carcinoma (OSCC) shows a high rate of recurrence and metastasis, which could be explained by the presence of molecular alterations in seemingly normal tumour margins and the entire oral mucosa. The aims of this study were (1) to assess the presence of gene amplification (c-Myc and HER2) and promoter methylation (p14 and p16) in the tumours, tumour margins, and unaffected oral mucosa of 40 OSCC patients, and (2) to evaluate the possibility of using these alterations as prognostic markers. c-Myc and HER2 genes were quantified by means of real-time PCR (qPCR), and p14 and p16 methylation status was determined by methylation-specific PCR (MSP PCR). All tissues examined exhibited molecular alterations in various proportions. Tumour tissues, as expected, showed the highest prevalence of alterations, while oral mucosa showed the lowest. Multiple alterations (co-alterations) in tumours and tumour margins were significantly more frequent than in unaffected oral mucosa (P<0.001 and P=0.027, respectively). HER2 amplification in margin tissue (P<0.001) and swabs (P=0.013), as well as the existence of three co-alterations in margins (P=0.001) and macroscopically unaffected oral mucosa (P<0.001) were correlated with shorter disease-specific survival.
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Affiliation(s)
- N Eljabo
- Institute of Human Genetics, School of Dental Medicine, University of Belgrade, Belgrade, Serbia
| | - N Nikolic
- Institute of Human Genetics, School of Dental Medicine, University of Belgrade, Belgrade, Serbia
| | - J Carkic
- Institute of Human Genetics, School of Dental Medicine, University of Belgrade, Belgrade, Serbia
| | - D Jelovac
- Clinic for Maxillofacial Surgery, School of Dental Medicine, University of Belgrade, Belgrade, Serbia
| | - M Lazarevic
- Clinic for Maxillofacial Surgery, School of Dental Medicine, University of Belgrade, Belgrade, Serbia
| | - N Tanic
- Laboratory for Radiobiology and Molecular Genetics, Institute of Nuclear Sciences "Vinca", University of Belgrade, Belgrade, Serbia
| | - J Milasin
- Institute of Human Genetics, School of Dental Medicine, University of Belgrade, Belgrade, Serbia.
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15
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Association of Smoking, Alcohol Use, and Betel Quid Chewing with Epigenetic Aberrations in Cancers. Int J Mol Sci 2017; 18:ijms18061210. [PMID: 28587272 PMCID: PMC5486033 DOI: 10.3390/ijms18061210] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 05/26/2017] [Accepted: 06/02/2017] [Indexed: 12/16/2022] Open
Abstract
Numerous environmental factors such as diet, alcohol use, stress, and environmental chemicals are known to elicit epigenetic changes, leading to increased rates of cancers and other diseases. The incidence of head and neck cancer, one of the most common cancers in Taiwanese males, is increasing: oral cancer and nasopharyngeal carcinoma are ranked fourth and tenth respectively, among the top ten cancers in this group, and a major cause of cancer-related deaths in Taiwanese males. Previous studies have identified smoking, alcohol use, and betel quid chewing as the three major causes of head and neck cancers; these three social habits are commonly observed in Taiwanese males, resulting in an increasing morbidity rate of head and neck cancers in this population. In this literature review, we discuss the association between specific components of betel quid, alcohol, and tobacco, and the occurrence of head and neck cancers, lung cancer, gastrointestinal cancers, and urethral cancer. We focus on regulatory mechanisms at the epigenetic level and their oncogenic effects. The review further discusses the application of FDA-approved epigenetic drugs as therapeutic strategies against cancer.
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16
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Basu B, Chakraborty J, Chandra A, Katarkar A, Baldevbhai JRK, Dhar Chowdhury D, Ray JG, Chaudhuri K, Chatterjee R. Genome-wide DNA methylation profile identified a unique set of differentially methylated immune genes in oral squamous cell carcinoma patients in India. Clin Epigenetics 2017; 9:13. [PMID: 28174608 PMCID: PMC5292006 DOI: 10.1186/s13148-017-0314-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 01/19/2017] [Indexed: 01/06/2023] Open
Abstract
Background Oral squamous cell carcinoma (OSCC) is one of the common malignancies in Southeast Asia. Epigenetic changes, mainly the altered DNA methylation, have been implicated in many cancers. Considering the varied environmental and genotoxic exposures among the Indian population, we conducted a genome-wide DNA methylation study on paired tumor and adjacent normal tissues of ten well-differentiated OSCC patients and validated in an additional 53 well-differentiated OSCC and adjacent normal samples. Results Genome-wide DNA methylation analysis identified several novel differentially methylated regions associated with OSCC. Hypermethylation is primarily enriched in the CpG-rich regions, while hypomethylation is mainly in the open sea. Distinct epigenetic drifts for hypo- and hypermethylation across CpG islands suggested independent mechanisms of hypo- and hypermethylation in OSCC development. Aberrant DNA methylation in the promoter regions are concomitant with gene expression. Hypomethylation of immune genes reflect the lymphocyte infiltration into the tumor microenvironment. Comparison of methylome data with 312 TCGA HNSCC samples identified a unique set of hypomethylated promoters among the OSCC patients in India. Pathway analysis of unique hypomethylated promoters indicated that the OSCC patients in India induce an anti-tumor T cell response, with mobilization of T lymphocytes in the neoplastic environment. Survival analysis of these epigenetically regulated immune genes suggested their prominent role in OSCC progression. Conclusions Our study identified a unique set of hypomethylated regions, enriched in the promoters of immune response genes, and indicated the presence of a strong immune component in the tumor microenvironment. These methylation changes may serve as potential molecular markers to define risk and to monitor the prognosis of OSCC patients in India. Electronic supplementary material The online version of this article (doi:10.1186/s13148-017-0314-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Baidehi Basu
- Human Genetics Unit, Indian Statistical Institute, 203 B. T. Road, Kolkata, 700108 India
| | - Joyeeta Chakraborty
- Human Genetics Unit, Indian Statistical Institute, 203 B. T. Road, Kolkata, 700108 India
| | - Aditi Chandra
- Human Genetics Unit, Indian Statistical Institute, 203 B. T. Road, Kolkata, 700108 India
| | - Atul Katarkar
- Human Genetics Unit, Indian Statistical Institute, 203 B. T. Road, Kolkata, 700108 India.,Molecular Genetics Division, CSIR-Indian Institute of Chemical biology, 4 Raja S C Mullick Road, Kolkata, 700 032 India
| | | | | | - Jay Gopal Ray
- Dr. R Ahmed Dental College & Hospital, 114, A J C Bose Road, Kolkata, India
| | - Keya Chaudhuri
- Molecular Genetics Division, CSIR-Indian Institute of Chemical biology, 4 Raja S C Mullick Road, Kolkata, 700 032 India
| | - Raghunath Chatterjee
- Human Genetics Unit, Indian Statistical Institute, 203 B. T. Road, Kolkata, 700108 India
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17
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Lim Y, Sun CX, Tran P, Punyadeera C. Salivary epigenetic biomarkers in head and neck squamous cell carcinomas. Biomark Med 2016; 10:301-13. [DOI: 10.2217/bmm.16.2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The early detection of head and neck squamous cell carcinoma (HNSCC) continues to be a challenge to the clinician. Saliva as a diagnostic medium carries significant advantages including its close proximity to the region of interest, ease of collection and noninvasive nature. While the identification of biomarkers continues to carry significant diagnostic and prognostic utility in HNSCC, epigenetic alterations present a novel opportunity to serve this purpose. With the developments of novel and innovative technologies, epigenetic alterations are now emerging as attractive candidates in HNSCC. As such, this review will focus on two commonly aberrant epigenetic alterations: DNA methylation and microRNA expression in HNSCC and their potential clinical utility. Identification and validation of these salivary epigenetic biomarkers would not only enable early diagnosis but will also facilitate in the clinical management.
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Affiliation(s)
- Yenkai Lim
- The School of Biomedical Sciences, Institute of Health & Biomedical Innovations, Queensland University of Technology, 60 Musk Avenue, Kelvin Grove, Brisbane, QLD 4001, Australia
| | - Charles Xiaohang Sun
- The School of Biomedical Sciences, Institute of Health & Biomedical Innovations, Queensland University of Technology, 60 Musk Avenue, Kelvin Grove, Brisbane, QLD 4001, Australia
- School of Dentistry, The University of Queensland, 288 Herston Rd, Herston, Brisbane, QLD 4006, Australia
| | - Peter Tran
- The School of Biomedical Sciences, Institute of Health & Biomedical Innovations, Queensland University of Technology, 60 Musk Avenue, Kelvin Grove, Brisbane, QLD 4001, Australia
- School of Dentistry, The University of Queensland, 288 Herston Rd, Herston, Brisbane, QLD 4006, Australia
| | - Chamindie Punyadeera
- The School of Biomedical Sciences, Institute of Health & Biomedical Innovations, Queensland University of Technology, 60 Musk Avenue, Kelvin Grove, Brisbane, QLD 4001, Australia
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18
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D'Souza W, Saranath D. Clinical implications of epigenetic regulation in oral cancer. Oral Oncol 2015; 51:1061-8. [PMID: 26421863 DOI: 10.1016/j.oraloncology.2015.09.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 09/02/2015] [Accepted: 09/08/2015] [Indexed: 01/05/2023]
Abstract
Oral cancer is a high incidence cancer which is of major public health concern in India being the most common cancer in males and fifth most common cancer in females in India, contributing to 26% of the global oral cancer burden. The major risk factors of oral cancer are tobacco, alcohol and high risk Human Papilloma Virus type 16/18. However, only 3-12% of the high risk individuals with dysplasia develop oral cancer. Thus, individual genomic variants representing the genomic constitution and epigenetic alterations play a critical role in the development of oral cancer. Extensive epigenetic studies on the molecular lesions including oncogenes, tumor suppressor genes, genes associated with apoptosis, DNA damage repair have been reported. The current review highlights epigenetic regulation with a focus on molecular biomarkers and epidrug therapy in oral cancer. Epigenetic regulation by hypermethylation, histone modifications and specific microRNAs are often associated with early events and advanced stages in oral cancer, and thus indicate epidrug therapy for intervention. The presence of epigenetic marks in oral lesions, cancers and tumor associated mucosa emphasizes indications as biomarkers and epidrugs with therapeutic potential for better patient management.
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Affiliation(s)
- Wendy D'Souza
- Department of Biological Sciences, Sunandan Divatia School of Science, SVKM's NMIMS (Deemed-to-be) University, Mumbai 400056, India
| | - Dhananjaya Saranath
- Department of Biological Sciences, Sunandan Divatia School of Science, SVKM's NMIMS (Deemed-to-be) University, Mumbai 400056, India.
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19
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Tsaprouni LG, Yang TP, Bell J, Dick KJ, Kanoni S, Nisbet J, Viñuela A, Grundberg E, Nelson CP, Meduri E, Buil A, Cambien F, Hengstenberg C, Erdmann J, Schunkert H, Goodall AH, Ouwehand WH, Dermitzakis E, Spector TD, Samani NJ, Deloukas P. Cigarette smoking reduces DNA methylation levels at multiple genomic loci but the effect is partially reversible upon cessation. Epigenetics 2015; 9:1382-96. [PMID: 25424692 DOI: 10.4161/15592294.2014.969637] [Citation(s) in RCA: 243] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Smoking is a major risk factor in many diseases. Genome wide association studies have linked genes for nicotine dependence and smoking behavior to increased risk of cardiovascular, pulmonary, and malignant diseases. We conducted an epigenome wide association study in peripheral-blood DNA in 464 individuals (22 current smokers and 263 ex-smokers), using the Human Methylation 450 K array. Upon replication in an independent sample of 356 twins (41 current and 104 ex-smokers), we identified 30 probes in 15 distinct loci, all of which reached genome-wide significance in the combined analysis P < 5 × 10(-8). All but one probe (cg17024919) remained significant after adjusting for blood cell counts. We replicated all 9 known loci and found an independent signal at CPOX near GPR15. In addition, we found 6 new loci at PRSS23, AVPR1B, PSEN2, LINC00299, RPS6KA2, and KIAA0087. Most of the lead probes (13 out of 15) associated with cigarette smoking, overlapped regions of open chromatin (FAIRE and DNaseI hypersensitive sites) or/and H3K27Ac peaks (ENCODE data set), which mark regulatory elements. The effect of smoking on DNA methylation was partially reversible upon smoking cessation for longer than 3 months. We report the first statistically significant interaction between a SNP (rs2697768) and cigarette smoking on DNA methylation (cg03329539). We provide evidence that the metSNP for cg03329539 regulates expression of the CHRND gene located circa 95 Kb downstream of the methylation site. Our findings suggest the existence of dynamic, reversible site-specific methylation changes in response to cigarette smoking , which may contribute to the extended health risks associated with cigarette smoking.
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Key Words
- AHRR, aryl-hydrocarbon receptor repressor
- ALPP, alkaline phosphatase, placental
- AVPR1B, arginine vasopressin
- CHRND
- CHRND, cholinergic nicotinic receptor
- COPD, chronic obstructive pulmonary disease
- CPOX
- CPOX, coproporphyrinogen oxidase
- DNA methylation
- DNMT, DNA methyltransferase
- EWAS, epigenome wide association study
- FDR, false discovery rate
- GWAS, genome-wide association studies
- PRSS23, serine protease 23
- PSEN2, presenilin-2 gene
- RPS6KA2, ribosomal protein S6 kinase
- epigenome-wide screen
- gene network
- metQTL, methylation quantitative trait loci
- metQTLs
- rs2697768
- smoking
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20
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Association between P16INK4a promoter methylation and HNSCC: a meta-analysis of 21 published studies. PLoS One 2015; 10:e0122302. [PMID: 25835498 PMCID: PMC4383544 DOI: 10.1371/journal.pone.0122302] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 02/19/2015] [Indexed: 01/10/2023] Open
Abstract
Background The p16INK4a is an important tumor suppressor gene (TSG) and aberrant methylation of promoter is known to be a major inactivation mechanism of the tumor suppressor and tumor-related genes. Aberrant TSG methylation was considered an important epigenetic silencing mechanism in the progression of head and neck squamous cell carcinoma (HNSCC). However, some studies have reported differences in the methylation frequencies of P16INK4a promoter between cancer and the corresponding control group. Therefore, we conducted a meta-analysis to better identify the association. Methods PubMed, Ovid, ISI Web of Science, and EMBASE were searched to identify eligible studies to evaluate the association of p16INK4a promoter methylation and HNSCC. Odds ratio (ORs) and 95% confidence intervals (95%CI) were calculated to evaluate the strength of association between p16INK4a promoter methylation and HNSCC. Results A total of twenty-one studies with 1155 cases and 1017 controls were included in the meta-analysis. The frequencies of p16INK4a promoter methylation in the cancer group were significantly higher than those in the control group (cancer group: median: 46.67%, range = 7.84%-95.12%; control group: median: 18.37%, range = 0–83.33%; respectively). The pooled odds ratio was 3.37 (95%CI = 2.32–4.90) in the cancer group versus the corresponding control group under the random-effects model. Conclusion This meta-analysis of 21 published studies identified that aberrant methylation of p16INK4a promoter was found to be significantly associated with HNSCC.
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21
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Quantitative methodology is critical for assessing DNA methylation and impacts on correlation with patient outcome. Clin Epigenetics 2014; 6:22. [PMID: 25859283 PMCID: PMC4391486 DOI: 10.1186/1868-7083-6-22] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 10/17/2014] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND DNA hypermethylation is reported as a frequent event and prognostic marker in head and neck squamous cell carcinomas (HNSCC). Methylation has been commonly assessed with non-quantitative methodologies, such as methylation-specific PCR (MSP). We investigated previously reported hypermethylated genes with quantitative methodology in oral tongue squamous cell carcinomas (OTSCC). RESULTS The methylation status of 12 genes in 115 OTSCC samples was assessed by one or more of three quantitative analyses: methylation sensitive high resolution melting (MS-HRM), sensitive-melting analysis after real time-methylation specific PCR (SMART-MSP), and bisulfite pyrosequencing. In contrast to much of the literature, either no or infrequent locus-specific methylation was identified by MS-HRM for DAPK1, RASSF1A, MGMT, MLH1, APC, CDH1, CDH13, BRCA1, ERCC1, and ATM. The most frequently methylated loci were RUNX3 (18/108 methylated) and ABO (22/107 methylated). Interrogation of the Cancer Genome Atlas (TCGA) HNSCC cohort confirmed the frequency of significant methylation for the loci investigated. Heterogeneous methylation of RUNX3 (18/108) and ABO (22/107) detected by MS-HRM, conferred significantly worse survival (P = 0.01, and P = 0.03). However, following quantification of methylation levels using pyrosequencing, only four tumors had significant quantities (>15%) of RUNX3 methylation which correlated with a worse patient outcome (P <0.001), while the prognostic significance of ABO hypermethylation was lost. RUNX3 methylation was not prognostic for the TCGA cohort (P = 0.76). CONCLUSIONS We demonstrated the critical need for quantification of methylation levels and its impact on correlative analyses. In OTSCC, we found little evidence of significant or frequent hypermethylation of many loci reported to be commonly methylated. It is likely that previous reports have overestimated the frequency of significant methylation events as a consequence of the use of non-quantitative methodology.
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p16INK4A and p14ARF gene promoter hypermethylation as prognostic biomarker in oral and oropharyngeal squamous cell carcinoma: a review. DISEASE MARKERS 2014; 2014:260549. [PMID: 24803719 PMCID: PMC3997957 DOI: 10.1155/2014/260549] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 03/17/2014] [Indexed: 12/18/2022]
Abstract
Head and neck squamous cell carcinoma is a heterogeneous group of tumors with each subtype having a distinct histopathological and molecular profile. Most tumors share, to some extent, the same multistep carcinogenic pathways, which include a wide variety of genetic and epigenetic changes. Epigenetic alterations represent all changes in gene expression patterns that do not alter the actual DNA sequence. Recently, it has become clear that silencing of cancer related genes is not exclusively a result of genetic changes such as mutations or deletions, but it can also be regulated on epigenetic level, mostly by means of gene promoter hypermethylation. Results from recent studies have demonstrated that DNA methylation patterns contain tumor-type-specific signatures, which could serve as biomarkers for clinical outcome in the near future. The topic of this review discusses gene promoter hypermethylation in oral and oropharyngeal squamous cell carcinoma (OSCC). The main objective is to analyse the available data on gene promoter hypermethylation of the cell cycle regulatory proteins p16INK4A and p14ARF and to investigate their clinical significance as novel biomarkers in OSCC. Hypermethylation of both genes seems to possess predictive properties for several clinicopathological outcomes. We conclude that the methylation status of p16INK4A is definitely a promising candidate biomarker for predicting clinical outcome of OSCC, especially for recurrence-free survival.
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McKenzie GAG, Hinsley EE, Hunter K, Lambert DW. The endothelin axis in head and neck cancer: a promising therapeutic opportunity? J Oral Pathol Med 2013; 43:395-404. [DOI: 10.1111/jop.12108] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2013] [Indexed: 12/14/2022]
Affiliation(s)
- Gordon A. G. McKenzie
- College of Medical and Dental Sciences; University of Birmingham; Edgbaston UK
- Unit of Oral and Maxillofacial Pathology; School of Clinical Dentistry; University of Sheffield; Sheffield UK
| | - Emma E. Hinsley
- Unit of Oral and Maxillofacial Pathology; School of Clinical Dentistry; University of Sheffield; Sheffield UK
| | - Keith Hunter
- Unit of Oral and Maxillofacial Pathology; School of Clinical Dentistry; University of Sheffield; Sheffield UK
| | - Daniel W. Lambert
- Unit of Oral and Maxillofacial Pathology; School of Clinical Dentistry; University of Sheffield; Sheffield UK
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DNA methylation of PAX1 as a biomarker for oral squamous cell carcinoma. Clin Oral Investig 2013; 18:801-8. [PMID: 23907469 DOI: 10.1007/s00784-013-1048-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 07/03/2013] [Indexed: 12/25/2022]
Abstract
OBJECTIVES DNA methylation has been shown to be a promising cancer biomarker. The aim of this study was to evaluate DNA methylation of three transcription factors, sex-determining region Y-box 1 (SOX1), paired box gene 1 (PAX1), and zinc-finger 582 (ZNF582), in detecting oral squamous cell carcinoma (OSCC). MATERIALS AND METHODS A case-control study was conducted at Taipei Medical University Hospital in Taiwan with 31 cases of various oral cavity squamous cell carcinomas and 40 controls. Questionnaire data assessing environmental exposure, such as alcohol consumption, cigarette smoking, and betel nut chewing, were obtained from each participant. DNA from oral swabs were analyzed for methylation using quantitative methylation polymerase chain reaction with TaqMan probes. Methylation status was determined using a methylation index. RESULTS Methylation levels of SOX1, PAX1, and ZNF582 were significantly higher in cancer patients (p = 0.02, p = 0.02, and p = 0.03, respectively). Patients with highly methylated SOX1, PAX1, and ZNF582 had an increased cancer risk with odds ratios (ORs) of 16.50 (95 % CI = 2.85-96.65), 60.57 (95 % CI = 5.85-629.94), and 5.07 (95 % CI = 1.08-23.76), respectively. Area under the curve (AUC) values were 0.85, 0.78, and 0.78 for PAX1, SOX1, and ZNF582, respectively. When stratified based on environmental exposure, the AUC of PAX1 methylation (PAX1 (m) ) was 0.94 in environmental exposure-naïve subjects and 0.85 for SOX1 methylation in subjects who chewed betel nut. In general, the sensitivity and specificity of PAX1 (m) were 87 and 80 % for OSCC detection. The sensitivity of PAX1 (m) in subjects who chewed betel nut was 83 %, with a specificity of 75 %. CONCLUSIONS Testing PAX1 DNA methylation using oral swabs is a promising method for oral cancer detection. Combined assessments regarding betel nut consumption and DNA methylation can improve OSCC screening. CLINICAL RELEVANCE The double E (environmental and epigenetic) assessment is a potential strategy in OSCC screening.
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Abstract
PURPOSE OF REVIEW To evaluate recent developments in nutritional epigenomics and related challenges, opportunities, and implications for cancer control and prevention. RECENT FINDINGS Cancer is one of the leading causes of death worldwide, and understanding the factors that contribute to cancer development may facilitate the development of strategies for cancer prevention and control. Cancer development involves genetic and epigenetic alterations. Genetic marks are permanent, whereas epigenetic marks are dynamic, change with age, and are influenced by the external environment. Thus, epigenetics provides a link between the environment, diet, and cancer development. Proper food selection is imperative for better health and to avoid cancer and other diseases. Nutrients either contribute directly to cancer prevention or support the repair of genomic and epigenomic damage caused by exposure to cancer-causing agents such as toxins, free radicals, radiation, and infectious agents. Nutritional epigenomics provides an opportunity for cancer prevention because selected nutrients have the potential to reverse cancer-associated epigenetic marks in different tumor types. A number of natural foods and their bioactive components have been shown to have methylation-inhibitory and deacetylation-inhibitory properties. SUMMARY Natural foods and bioactive food components have characteristics and functions that are similar to epigenetic inhibitors and therefore have potential in cancer control and prevention.
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Affiliation(s)
- Mukesh Verma
- Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-7324, USA.
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Welch AK, Jacobs ME, Wingo CS, Cain BD. Early progress in epigenetic regulation of endothelin pathway genes. Br J Pharmacol 2013; 168:327-34. [PMID: 22220553 DOI: 10.1111/j.1476-5381.2012.01826.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Control of gene transcription is a major regulatory determinant for function of the endothelin pathway. Epigenetic mechanisms act on tissue-specific gene expression during development and in response to physiological stimuli. Most of the limited evidence available on epigenetic regulation of the endothelin pathway focuses on the EDN1 and EDNRB genes. Examination of whole genome databases suggests that both genes are influenced by histone modifications and DNA methylation. This interpretation is supported by studies directed at detecting epigenetic action on the two genes. The clearest illustration of epigenetic factors altering endothelin signalling is DNA methylation-associated EDNRB silencing during tumourigenesis. This review summarizes our current understanding of epigenetic regulation of the endothelin pathway genes. LINKED ARTICLES This article is part of a themed section on Endothelin. To view the other articles in this section visit http://dx.doi.org/10.1111/bph.2013.168.issue-1.
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Affiliation(s)
- A K Welch
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
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Abstract
Dysregulation of gene expression is a frequent occurrence in oral squamous cell carcinoma (OSCC). However, accumulating evidence suggests that in contrast to genetics, epigenetic modifications consisting of aberrant DNA methylation, histone modifications and altered expression of miRNAs induce OSCC tumorigenesis and perhaps play a more central role in the evolution and progression of this disease. The unifying theme among these three epigenetic mechanisms remains the same, which is aberrant regulation of gene expression. In this article, we provide a comprehensive review of the impact of epigenetics on oral tumorigenesis with a systematic report on aberrant DNA methylation, histone modifications and miRNA regulation in the pathogenesis of OSCC. We provide insights into recent studies on the prospect of biomarkers for early detection and indication of disease recurrence, and novel treatment modalities.
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Affiliation(s)
- Jacqueline A Gasche
- Division of Gastroenterology, Department of Internal Medicine, Charles A Sammons Cancer Center & Baylor Research Institute, Baylor University Medical Center, 3500 Gaston Avenue, Suite 250 Hoblitzelle, Dallas, TX 75246, USA
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Abstract
Oral Diseases (2012) Underlying molecular genetic mechanisms of diseases can be deciphered with unbiased strategies using recently developed technologies enabling genome-wide scale investigations. These technologies have been applied in scanning for genetic variations, gene expression profiles, and epigenetic changes for oral and craniofacial diseases. However, these approaches as applied to oral and craniofacial conditions are in the initial stages, and challenges remain to be overcome, including analysis of high throughput data and their interpretation. Here, we review methodology and studies using genome-wide approaches in oral and craniofacial diseases and suggest future directions.
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Affiliation(s)
- H Kim
- National Institute of Nursing Research, National Institutes of Health, Bethesda, MD School of Dentistry, University of Maryland, Baltimore, MD, USA
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Khojasteh A, Khodayari A, Rahimi F, Ghaderian MH, Jafarian M, Nayebi A, Akbarzadeh Najar R, Tabatabayipanah A, Jahangirnia A. Hypermethylation of p16 Tumor-Suppressor Gene in Ameloblastic Carcinoma, Ameloblastoma, and Dental Follicles. J Oral Maxillofac Surg 2013; 71:62-5. [DOI: 10.1016/j.joms.2012.04.033] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Revised: 04/20/2012] [Accepted: 04/20/2012] [Indexed: 02/02/2023]
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Correlation of epigenetic change and identification of risk factors for oral submucous fibrosis. Int J Biol Markers 2012; 27:e314-21. [PMID: 23250779 DOI: 10.5301/jbm.2012.9937] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/24/2012] [Indexed: 02/07/2023]
Abstract
BACKGROUND DNA methylation of certain genes is an epigenetic change that is essential for tumorigenesis. Oral submucous fibrosis (OSF) is a precancerous condition of oral mucosa with inflammation and progressive fibrosis of the lamina propria and deeper connective tissue. The hypermethylation of E-cadherin and cyclooxygenase 2 (COX-2) in chronic inflammation may demonstrate a mild lesion/mutation at epigenetic levels. This study compares the hypermethylation status of E-cadherin and COX-2 genes in patients with oral cancer and patients with OSF and also aims to identify risk factors for the development of OSF. METHODS DNA was extracted from blood samples of 50 healthy subjects, 50 patients with OSF and 60 patients with oral cancer. Methylation-specific polymerase chain reaction for E-cadherin and COX-2 was performed on these samples and the products were analyzed on 2% agarose gel. Surveys about oral health habits and clinical periodontal examinations in patients with OSF and healthy subjects were also conducted by well-trained dentists, and logistic regression was performed to identify risk factors for OSF. RESULTS Hypermethylation of E-cadherin and COX-2 was observed in 36% and 22% of oral cancer samples, respectively. In patients with OSF, the rates were 52% and 30%, and in healthy controls the rates were 4% and 6%. Hypermethylation was shown to be correlated between the 3 groups with statistical significance (p<0.01). Methylation of CpG islands in E-cadherin and COX-2 occurred more frequently in patients with OSF than in the control group, but less frequently than in patients with oral cancer. In the logistic regression analysis, smoking, brushing more than twice daily, periodontal probing depth and plaque index were identified as 4 major risk factors for OSF. CONCLUSIONS These data confirm that E-cadherin and COX-2 expressions are related to OSF. The epigenetic changes presented in patients with chronic inflammation might demonstrate an irreversible destruction in the tissues or organs similar to the effects of cancer. Chronic OSF was significantly associated with hypermethylation, a cancer risk factor.
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Expression of myelin and lymphocyte protein (MAL) in oral carcinogenesis. Med Mol Morphol 2012; 45:222-8. [DOI: 10.1007/s00795-011-0563-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Accepted: 09/12/2011] [Indexed: 11/26/2022]
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Rettori MM, de Carvalho AC, Bomfim Longo AL, de Oliveira CZ, Kowalski LP, Carvalho AL, Vettore AL. Prognostic significance of TIMP3 hypermethylation in post-treatment salivary rinse from head and neck squamous cell carcinoma patients. Carcinogenesis 2012; 34:20-7. [PMID: 23042095 DOI: 10.1093/carcin/bgs311] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Hypermethylation in the promoter regions of genes is associated with suppression of gene expression and has been considered a potential molecular marker for several tumor types, including head and neck squamous cell carcinomas (HNSCC). Moreover, hypermethylation can be detected in body fluids such as saliva and can be useful for the diagnosis and prognosis of patients suffering from cancer. To evaluate the hypermethylation profile as a tool for early detection of tumor recurrences, this study determines the methylation status of 24 genes in salivary rinses collected from HNSCC patients at diagnosis, just after the last curative treatment and in the patients' follow-up visit at 6 months after treatment. In the analysis of salivary rinse samples taken at diagnosis of HNSCC patients, five genes (CCNA1, DAPK, DCC, MGMT and TIMP3) showed high specificity and sensitivity. Hypermethylation in any of these five genes was correlated with the presence of tumors in the oral cavity. Patients with TIMP3 methylation in samples collected 6 months after the last curative treatment had lower local recurrence-free survival (P = 0.008). Multivariate analysis confirmed that this hypermethylation pattern remained as an independent prognostic factor for local recurrence (P = 0.025). This study presents, for the first time, the detection of TIMP3 promoter hypermethylation in post-treatment salivary rinse as an independent prognostic maker for local recurrence-free survival in patients with HNSCC, justifying the use of DNA hypermethylation detection in saliva as a tool for identifying and monitoring HNSCC patients' subgroups with high risk of developing local recurrence.
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de Freitas Cordeiro-Silva M, Stur E, Agostini LP, de Podestá JRV, de Oliveira JC, Soares MS, Mendonça EF, Gouvea SA, Von Zeidler SV, Louro ID. Promoter hypermethylation in primary squamous cell carcinoma of the oral cavity and oropharynx: a study of a Brazilian cohort. Mol Biol Rep 2012; 39:10111-9. [PMID: 22936053 DOI: 10.1007/s11033-012-1885-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 08/22/2012] [Indexed: 12/20/2022]
Abstract
Epigenetic silencing of cancer-related genes plays an important role in oral/oropharyngeal squamous cell carcinoma (OSCC). We evaluated promoter hypermethylation of 4 cancer-related genes in OSCCs of a Brazilian cohort and determined its relationship with exposure to alcohol, tobacco, HPV infection and clinicopathological parameters. CDKN2A (cyclin-dependent kinase inhibitor 2A or p16), SFN (stratifin or 14-3-3 σ), EDNRB (endothelin receptor B) and RUNX3 (runt-related transcript factor-3) had their methylation patterns evaluated by MSP analysis in OSCC tumors (n = 45). HPV detection was carried out by PCR/RFLP. Aberrant methylation was detected in 44/45 (97.8 %) OSCC; 24.4 % at CDKN2A, 77.8 % at EDNRB, 17.8 % at RUNX3 and 97.8 % at SFN gene. There was no significant association between methylation patterns and clinical parameters. HPV (subtype 16) was detected in 3 out of 45 patients (6 %). Our findings indicate that HPV infection is uncommon and methylation is frequent in Brazilian OSCCs, however, EDNRB and SFN gene methylation are not suitable OSCC biomarkers due to indistinct methylation in tumoral and normal samples. In contrast, CDKN2A and RUNX3 genes could be considered differentially methylated genes and potential tumor markers in OSCCs.
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Affiliation(s)
- Melissa de Freitas Cordeiro-Silva
- Núcleo de Genética Humana e Molecular Departamento de Ciências Biológicas, Centro de Ciências Humanas e Naturais Universidade Federal do Espírito Santo, Av. Marechal Campos, 1468. Maruípe, Vitoria, ES, CEP: 29040-090, Brazil
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Kusumoto T, Hamada T, Yamada N, Nagata S, Kanmura Y, Houjou I, Kamikawa Y, Yonezawa S, Sugihara K. Comprehensive Epigenetic Analysis Using Oral Rinse Samples: A Pilot Study. J Oral Maxillofac Surg 2012; 70:1486-94. [DOI: 10.1016/j.joms.2011.04.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Revised: 04/14/2011] [Accepted: 04/22/2011] [Indexed: 11/29/2022]
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Sun W, Zaboli D, Liu Y, Arnaoutakis D, Khan T, Wang H, Koch W, Khan Z, Califano JA. Comparison of promoter hypermethylation pattern in salivary rinses collected with and without an exfoliating brush from patients with HNSCC. PLoS One 2012; 7:e33642. [PMID: 22438973 PMCID: PMC3306276 DOI: 10.1371/journal.pone.0033642] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Accepted: 02/14/2012] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Salivary rinses have been recently proposed as a valuable resource for the development of epigenetic biomarkers for detection and monitoring of head and neck squamous cell carcinoma (HNSCC). Both salivary rinses collected with and without an exfoliating brush from patients with HNSCC are used in detection of promoter hypermethylation, yet their correlation of promoter hypermethylation has not been evaluated. This study was to evaluate the concordance of promoter hypermethylation between salivary rinses collected with and without an exfoliating brush from patients with HNSCC. METHODOLGY: 57 paired salivary rinses collected with or without an exfoliating brush from identical HNSCC patients were evaluated for promoter hypermethylation status using Quantitative Methylation-Specific PCR. Target tumor suppressor gene promoter regions were selected based on our previous studies describing a panel for HNSCC screening and surveillance, including P16, CCNA1, DCC, TIMP3, MGMT, DAPK and MINT31. PRINCIPAL FINDINGS In salivary rinses collected with and without brush, frequent methylation was detected in P16 (8.8% vs. 5.2%), CCNA1 (26.3% vs. 22.8%), DCC (33.3% vs. 29.8%), TIMP3 (31.6% vs. 36.8%), MGMT (29.8% vs. 38.6%), DAPK (14.0% vs. 19.2%), and MINT31 (10.5% vs. 8.8%). Spearman's rank correlation coefficient showed a positive correlation between salivary rinses collected with and without brush for P16 (ρ = 0.79), CCNA1 (ρ = 0.61), DCC (ρ = 0.58), TIMP3 (ρ = 0.10), MGMT (ρ = 0.70), DAPK (ρ = 0.51) and MINT31 (ρ = 0.72) (P<0.01). The percent agreement of promoter methylation between salivary rinses with brush and without brush were 96.5% for P16, 82.5% for CCNA1, 78.9% for DCC, 59.7% for TIMP3, 84.2% for MGMT, 84.2% for DAPK, and 94.7% for MINT31. CONCLUSIONS Our study demonstrated strong correlations of gene promoter hypermethylation between salivary rinses collected with and without an exfoliating brush. Salivary rinse collection without using an exfoliating brush may offer a cost effective, rapid, non-invasive, and reliable means for development of epigenetic salivary rinse biomarkers.
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Affiliation(s)
- Wenyue Sun
- Department of Otolaryngology-Head and Neck Surgery, Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - David Zaboli
- Department of Otolaryngology-Head and Neck Surgery, Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Yan Liu
- Department of Surgery, Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Demetri Arnaoutakis
- Department of Otolaryngology-Head and Neck Surgery, Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Tanbir Khan
- Department of Otolaryngology-Head and Neck Surgery, Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Hao Wang
- Division of Oncology Biostatistics, Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Wayne Koch
- Department of Otolaryngology-Head and Neck Surgery, Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Zubair Khan
- Department of Otolaryngology-Head and Neck Surgery, Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Joseph A. Califano
- Department of Otolaryngology-Head and Neck Surgery, Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
- Milton J. Dance Head and Neck Center, Greater Baltimore Medical Center, Baltimore, Maryland, United States of America
- * E-mail: .
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Mishra R. Biomarkers of oral premalignant epithelial lesions for clinical application. Oral Oncol 2012; 48:578-84. [PMID: 22342569 DOI: 10.1016/j.oraloncology.2012.01.017] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Revised: 01/17/2012] [Accepted: 01/26/2012] [Indexed: 12/15/2022]
Abstract
Oral cancer is the sixth most common form of cancer worldwide, and the majority of cases occur in India and Southeast Asia. Its major risk factors in the western world include smoking and drinking alcohol, whereas in Asia, it is primarily caused by tobacco/areca nut/betel leaf chewing and/or human papillomavirus (HPV) infections. Little is known about this type of cancer despite recent advances in cancer biology. The generally asymptomatic nature of the early oral lesions causes them to remain undetected in many cases. Thus, the disease progresses substantially before the patients seek treatment and is a major contributing factor to the severity of this disease. Therefore, there is a great need to create awareness for its prevention and early diagnosis. The application of advanced molecular biological and biochemical methodologies to elucidate its biomarkers may aid in early detection; however, much more work must be done for this information to be effectively applied in the clinical setting. This review focuses on the need for systematic diagnoses in the early detection of oral cancer using molecular and biochemical approaches, thereby reducing the number of advanced cases in the chewing tobacco-dominated oral cancer population.
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Affiliation(s)
- Rajakishore Mishra
- Centre for Life Sciences, School of Natural Sciences, Central University of Jharkhand, Ratu-Lohardaga Road, Brambe, Jharkhand, India.
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Demokan S, Chuang A, Suoğlu Y, Ulusan M, Yalnız Z, Califano JA, Dalay N. Promoter methylation and loss of p16(INK4a) gene expression in head and neck cancer. Head Neck 2011; 34:1470-5. [PMID: 22106032 DOI: 10.1002/hed.21949] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Revised: 07/25/2011] [Accepted: 09/05/2011] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Silencing of tumor suppressor genes plays a vital role in head and neck carcinogenesis. In this study we aimed to evaluate aberrant p16(INK4a) gene promoter methylation in patients with head and neck cancer. METHODS Methylation of the gene was investigated by bisulfite modification/methylation-specific polymerase chain reaction and gene expression levels were analyzed by quantitative reverse transcription-polymerase chain reaction in tumors and matched normal tissue samples from Turkish patients with head and neck cancer. RESULTS The promoter region of the p16(INK4a) gene was methylated in 67.5% and 28.6% of the primary tumors and the corresponding normal tissue, respectively. This difference was highly significant. In concordance, p16(INK4a) gene expression was downregulated in 67.5% of the tumor samples. Methylation and the absence of expression in the tumors were observed in 48% of the patients. CONCLUSIONS Our data indicate that methylation of the p16(INK4a) gene is a frequent event in primary head and neck cancer and that it plays a major role in the silencing of p16(INK4a) gene expression during tumor development.
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Affiliation(s)
- Semra Demokan
- Department of Basic Oncology, Oncology Institute, Istanbul University, Istanbul, Turkey
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Role of DNA methylation in head and neck cancer. Clin Epigenetics 2011; 2:123-50. [PMID: 22704334 PMCID: PMC3365391 DOI: 10.1007/s13148-011-0045-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Accepted: 06/14/2011] [Indexed: 02/07/2023] Open
Abstract
Head and neck cancer (HNC) is a heterogenous and complex entity including diverse anatomical sites and a variety of tumor types displaying unique characteristics and different etilogies. Both environmental and genetic factors play a role in the development of the disease, but the underlying mechanism is still far from clear. Previous studies suggest that alterations in the genes acting in cellular signal pathways may contribute to head and neck carcinogenesis. In cancer, DNA methylation patterns display specific aberrations even in the early and precancerous stages and may confer susceptibility to further genetic or epigenetic changes. Silencing of the genes by hypermethylation or induction of oncogenes by promoter hypomethylation are frequent mechanisms in different types of cancer and achieve increasing diagnostic and therapeutic importance since the changes are reversible. Therefore, methylation analysis may provide promising clinical applications, including the development of new biomarkers and prediction of the therapeutic response or prognosis. In this review, we aimed to analyze the available information indicating a role for the epigenetic changes in HNC.
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Sun WZ, Han GX. Detection of the promoter methylation status of the EDNRB gene in human gastric cancer cell line KATO III. Shijie Huaren Xiaohua Zazhi 2010; 18:3448-3451. [DOI: 10.11569/wcjd.v18.i32.3448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To detect the promoter methylation status and mRNA expression of the endothelin receptor type B (EDNRB) gene in human gastric cancer cell line KATO III and to analyze their clinical significance.
METHODS: Genomic DNA and total RNA were extracted from healthy adult peripheral blood samples and KATO III cells. Bisulfite sequencing PCR and reverse transcription-PCR were performed to analyze the promoter methylation status and mRNA expression of the EDNRB gene, respectively.
RESULTS: In KATO III cells, some CG loci (≤20%) were not or lowly methylated, while some others (≥50%) were hypermethylated. In healthy adult peripheral blood samples, only one CG locus (10%) was methylated, while the others were not methylated. The promoter methylation extent of the EDNRB gene in KATO III cells was higher than that in healthy adult peripheral blood samples. The mRNA expression was inhibited significantly in KATO III cells compared with healthy adult peripheral blood samples.
CONCLUSION: EDNRB gene promoter is hypermethylated in KATO III cells. The promoter methylation of the EDNRB gene may play an important role in the pathogenesis of gastric cancer.
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Abstract
As part of the PLoS Epigenetics Collection, Caroline Relton and George Davey Smith discuss the potential of epigenetics for the treatment and prevention of common complex diseases, including cancer.
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Affiliation(s)
- Caroline L Relton
- Human Nutrition Research Centre, Institute of Human Genetics, Newcastle University, Newcastle upon Tyne, United Kingdom.
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