1
|
Lao TD, Le TAH. Hypermethylation of genes on chromosome 3p as a biomarker for nasopharyngeal carcinoma diagnosis: A Vietnamese case-control study. Int J Biol Markers 2024:3936155241268431. [PMID: 39149888 DOI: 10.1177/03936155241268431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
BACKGROUND The crucial event driving nasopharyngeal tumorigenesis is the hypermethylation of chromosome 3p-located tumor suppressor genes. This case-control study aims to investigate the methylation characteristics of RASSF1A, Blu, ADAMTS9, and DLEC1 to potentially develop effective diagnostic biomarkers for nasopharyngeal carcinoma, either individually or in combination. METHODS The methylation of RASSF1A, Blu, ADAMTS9, and DLEC1 in the collection of 93 biopsy samples and 100 healthy swab specimens were evaluated by Nested methylation-specific polymerase chain reaction. The strength of the correlation between candidate genes and nasopharyngeal carcinoma was estimated by the evaluation of odds ratios (ORs). RESULTS Promoter hypermethylation of RASSF1A, Blu, ADAMTS9, and DLEC1 were found in 60.22%, 80.65%, 62.37%, and 74.19%, respectively, in nasopharyngeal carcinoma tumors. A significant association between the methylation status of candidate genes with nasopharyngeal carcinoma was reported. The methylation of candidate genes significantly increased the risk of nasopharyngeal carcinoma in cancerous samples compared with control samples (OR > 1). Based on the value of the methylation index, methylation of at least one gene was found in 95.70% of nasopharyngeal tumors. Additionally, the methylation index among 93 tumors significantly correlated with advanced stage nasopharyngeal tumors. CONCLUSION The study explored a higher frequency of hypermethylation at least one candidate gene. Methylation of a panel of potential genes can be utilized to discriminate between nasopharyngeal carcinoma and non-cancer cells, particularly in the advanced stages of nasopharyngeal carcinoma. Thus, it could serve as a valuable marker for the diagnosis and monitoring of nasopharyngeal carcinoma.
Collapse
Affiliation(s)
- Thuan Duc Lao
- Faculty of Biotechnology, Ho Chi Minh City Open University, Ho Chi Minh City, Viet Nam
| | - Thuy Ai Huyen Le
- Faculty of Biotechnology, Ho Chi Minh City Open University, Ho Chi Minh City, Viet Nam
| |
Collapse
|
2
|
Lao TD, Truong PK, Le TAH. Diagnostic Value of DAPK Methylation for Nasopharyngeal Carcinoma: Meta-Analysis. Diagnostics (Basel) 2023; 13:2926. [PMID: 37761293 PMCID: PMC10529083 DOI: 10.3390/diagnostics13182926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/01/2023] [Accepted: 08/01/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND Methylation of DAPK has been reported to play a key role in the initiation and progression of nasopharyngeal cancer. However, there are differences between the studies on it. This meta-analysis was performed to evaluate the diagnostic value of DAPK promoter methylation for NPC. METHOD The study method involves the systematic research of eligible studies based on criteria. The frequency, odds ratios (OR), sensitivity as well as specificity with the corresponding 95% confidence intervals (CIs) were used to assess the effect sizes. RESULTS A total of 13 studies, including 1048 NPC samples and 446 non-cancerous samples, were used for the meta-analysis. The overall frequencies of DAPK methylation were 56.94% and 9.28% in NPC samples and non-cancerous samples, respectively. The association between DAPK methylation and risk of NPC was also confirmed by calculating the OR value which was 13.13 (95%CI = 54.24-40.72) based on a random-effect model (Q = 64.74; p < 0.0001; I2 = 81.47% with 95%CI for I2 = 69.39-88.78). Additionally, the study results suggest that testing for DAPK methylation in tissue samples or brushing may provide a promising method for diagnosing NPC. CONCLUSION This is the first meta-analysis that provided scientific evidence that methylation of the DAPK gene could serve as a potential biomarker for diagnosis, prognosis, and early screening of NPC patients.
Collapse
Affiliation(s)
- Thuan Duc Lao
- Department of Pharmaceutical and Medical Biotechnology, Faculty of Biotechnology, Ho Chi Minh City Open University, Ho Chi Minh City 700000, Vietnam; (P.K.T.); (T.A.H.L.)
| | | | | |
Collapse
|
3
|
Lao TD, Thieu HH, Nguyen DH, Le TAH. Hypermethylation of the RASSF1A gene promoter as the tumor DNA marker for nasopharyngeal carcinoma. Int J Biol Markers 2021; 37:31-39. [PMID: 34935528 DOI: 10.1177/17246008211065472] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND RASSF1A is a tumor suppressor gene. The methylation of RASSF1A has been reported to be associated with nasopharyngeal tumorigenesis. However, the heterogeneity was high among different studies. A meta-analysis was performed to evaluate the value of RASSF1A methylation for the diagnosis and early screening of nasopharyngeal carcinoma. METHODS Relevant articles were identified by searching the MEDLINE database. Frequency and odds ratio (OR) were applied to estimate the effect of CDH-1 methylation based on random-/fixed-effect models. The meta-analysis was performed by using MedCalc® software. Subgroup analyses were performed by test method, ethnicity, and source of nasopharyngeal carcinoma samples to determine likely sources of heterogeneity. RESULTS A total of 17 studies, including 1688 samples (1165 nasopharyngeal carcinoma samples, and 523 from non-cancerous samples) were used for the meta-analysis. The overall frequencies of RASSF1A methylation were 59.68% and 2.65% in case-group and control-group, respectively. By removing the poor relative studies, the heterogeneity was not observed among the studies included. The association between RASSF1A gene methylation and the risk of nasopharyngeal carcinoma was also confirmed by calculating the OR value of 30.32 (95%CI = 18.22-50.47) in the fixed-effect model (Q = 16.41, p = 0.36,I2 = 8.62, 95% CI = 0.00-45.27). Additionally, the significant association was also found between the methylation of the RASSF1A gene and the subgroups. CONCLUSIONS This is the first meta-analysis that has provided scientific evidence that the methylation of RASSF1A is the potential diagnosis, prognosis, and early screening biomarker for nasopharyngeal carcinoma.
Collapse
Affiliation(s)
- Thuan Duc Lao
- Faculty of Biotechnology, 486019Ho Chi Minh City Open University, HCMC, Vietnam
| | - Hue Hong Thieu
- Faculty of Biotechnology, 486019Ho Chi Minh City Open University, HCMC, Vietnam
| | - Dung Huu Nguyen
- University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Thuy Ai Huyen Le
- Faculty of Biotechnology, 486019Ho Chi Minh City Open University, HCMC, Vietnam
| |
Collapse
|
4
|
Promoter Hypermethylation of Tumor Suppressor Genes Located on Short Arm of the Chromosome 3 as Potential Biomarker for the Diagnosis of Nasopharyngeal Carcinoma. Diagnostics (Basel) 2021; 11:diagnostics11081404. [PMID: 34441339 PMCID: PMC8391633 DOI: 10.3390/diagnostics11081404] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/30/2021] [Accepted: 08/02/2021] [Indexed: 11/16/2022] Open
Abstract
DNA methylation, the most common epigenetic alteration, has been proven to play important roles in nasopharyngeal carcinoma (NPC). Numerous tumor suppressor genes located on the chromosome 3p, particularly in the region of 3p21, are frequently methylated in NPC, thus suggesting great potential for diagnosis of NPC. In this review, we summarize recent findings of tumor suppressor genes on chromosome 3 that likely drive nasopharyngeal tumor development and progression, based on previous studies related to the hypermethylation of these target genes. Better understanding will allow us to design further experiments to establish a potential test for diagnosis of NPC, as well as bring about methylated therapies to improve the treatment of NPC.
Collapse
|
5
|
Shi QP, Wang X, Liu ZX, Zhang JJ, Wang ZY. Autoantibody Signatures as a Biomarker Panel for the Detection of Nasopharyngeal Carcinoma. Arch Med Res 2021; 52:620-626. [PMID: 33653596 DOI: 10.1016/j.arcmed.2021.02.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 02/01/2021] [Accepted: 02/11/2021] [Indexed: 02/05/2023]
Abstract
OBJECTIVE The early symptoms of nasopharyngeal carcinoma (NPC) are not obvious, and it is difficult to make early diagnosis. A case-control study was conducted to identify potential biomarkers and established a diagnosis model for nasopharyngeal carcinoma. METHODS Plasma samples of 131 cases of NPC and 132 cases of healthy individuals were incubated with the Ray Biotech Human Lung Cancer IgG Autoantibody Detection Array G1, and signal values were used to develop a risk prediction model for NPC diagnosis. RESULTS Of the 30 autoantibodies, high expression of MAGE-A4, NY-ESO-1, HuD, Survivin, IMDH2, Ubiquilin-1, IMP1, PGP9.5, IMP3, C-Myc and low expression of Cyclin B1 were potential biomarkers for NPC diagnosis (p <0.05), among which Survivin, MAGE-A4 and IMP3 shows higher AUC of 0.674, 0.652 and 0.650 respectively, the specificity of them was 89.39% (95% CI: 82.85-94.08%), 90.15% (95% CI: 83.75-94.65%) and 88.64% (81.95-93.50%).The risk probability analysis for NPC diagnosis based on the panel of Cyclin B1, NY-ESO-1, Survivin, and IMP3 displayed the best diagnosis performance with an AUC of 0.779, p (Yi = 1) = 1/(1+EXP[8.316+1.672*CyclinB1-1.152*NY-ESO-1-2.052*Survivin-0.950*IMP3]), the specificity of that was 86.36% (95% CI: 79.31-91.71%). CONCLUSIONS Our findings demonstrated that the panel of Cyclin B1, NY-ESO-1, Survivin, and IMP3 has a good performance in the detection of NPC, and all 11 autoantibodies may also have a certain significance for the prognosis of NPC.
Collapse
Affiliation(s)
- Qian-Ping Shi
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, Guangdong, China; Department of Preventive Medicine, Shantou University Medical College, Shantou, Guangdong, China; Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong, China
| | - Xuan Wang
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, Guangdong, China; Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong, China
| | - Zhi-Xi Liu
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, Guangdong, China; Department of Preventive Medicine, Shantou University Medical College, Shantou, Guangdong, China; Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong, China
| | - Jian-Jun Zhang
- Department of Preventive Medicine, Shantou University Medical College, Shantou, Guangdong, China.
| | - Zhao-Yang Wang
- Department of Radiation Oncology, Shenzhen People's Hospital, Second Clinical Medicine College of Jinan University, Shenzhen, Guangdong, China.
| |
Collapse
|
6
|
Bryzgunova OE, Konoshenko MY, Laktionov PP. Concentration of cell-free DNA in different tumor types. Expert Rev Mol Diagn 2020; 21:63-75. [PMID: 33270495 DOI: 10.1080/14737159.2020.1860021] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Introduction: Cell-free DNA (cfDNA) circulates in the blood for a long time. The levels of cfDNA in the blood are assayed in cancer diagnostics because they are closely related to the tumor burden of patients.Areas covered: cfDNA escapes the action of DNA-hydrolyzing enzymes, being a part of supramolecular complexes or interacting with the plasma membrane of blood cells. cfDNA has heterogeneous size and composition, which impose various restrictions on both isolation methods and subsequent analysis. cfDNA concentration and structural changes with the development of diseases highlight the high potential of cfDNA as a diagnostic and prognostic marker. The concentration of cfDNA released in the blood by tumor cells determines the specificity of such diagnostics and the required blood volume. The present review aimed to synthesize the available data on cfDNA concentration in the cancer patient's blood as well as pre-analytical, analytical, and biological factors, which interfere with cfDNA concentration.Expert opinion: The concentration of cfDNA and tumor cell DNA (ctDNA), and the over-presentation of DNA loci in cfDNA must be considered when looking for tumor markers. Some inconsistent data on cfDNA concentrations (like those obtained by different methods) suggest that the study of cfDNA should be continued.
Collapse
Affiliation(s)
- O E Bryzgunova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia.,Meshalkin Siberian Federal Biomedical Research Center, Ministry of Public Health of the Russian Federation, Novosibirsk, Russia
| | - M Yu Konoshenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia.,Meshalkin Siberian Federal Biomedical Research Center, Ministry of Public Health of the Russian Federation, Novosibirsk, Russia
| | - P P Laktionov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia.,Meshalkin Siberian Federal Biomedical Research Center, Ministry of Public Health of the Russian Federation, Novosibirsk, Russia
| |
Collapse
|
7
|
Tan R, Phua SKA, Soong YL, Oon LLE, Chan KS, Lucky SS, Mong J, Tan MH, Lim CM. Clinical utility of Epstein-Barr virus DNA and other liquid biopsy markers in nasopharyngeal carcinoma. Cancer Commun (Lond) 2020; 40:564-585. [PMID: 32989921 PMCID: PMC7668470 DOI: 10.1002/cac2.12100] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/14/2020] [Indexed: 12/22/2022] Open
Abstract
Nasopharyngeal carcinoma (NPC) is a malignant epithelial tumor ubiquitously associated with the Epstein-Barr virus (EBV), which is highly prevalent in South China, Southeast Asia, and North Africa. Despite being a highly radio-sensitive and treatable cancer, a majority of NPC patients are diagnosed in their advanced stage, and locoregional and distant relapses following definitive treatment contribute largely to cancer-specific mortality among these patients. Given that EBV-driven NPC is the predominant variant seen in endemic regions, various EBV detection methods have been developed and are utilized in screening, prognostication, and post-treatment surveillance of NPC patients. While the Immunoglobulin A (IgA) serology assay is the most extensively studied EBV detection method, the detection of plasma EBV DNA released during replication or cellular apoptosis has shown superior outcomes in endemic population screening, prognostication, and detection of distant relapse. Furthermore, there is emerging evidence on the use of circulating tumor cells, microRNAs, DNA hypermethylation, and combination assays in various clinical scenarios. Herein, this paper provides a comprehensive overview of the relevant studies using various EBV detection techniques in the management of NPC. Specifically, the recent advances, clinical evidence, and challenges associated with the clinical application of EBV liquid biopsies in population screening, prognostication, and surveillance of NPC are presented.
Collapse
Affiliation(s)
- Rong Tan
- Yong Loo Lin School of MedicineNational University of SingaporeSingapore117599Singapore
| | - Sean Kean Ann Phua
- Yong Loo Lin School of MedicineNational University of SingaporeSingapore117599Singapore
| | - Yoke Lim Soong
- Department of Radiation OncologyNational Cancer CenterSingapore169608Singapore
| | - Lynette Lin Ean Oon
- Department of Molecular PathologySingapore General HospitalSingapore169608Singapore
| | - Kian Sing Chan
- Department of Molecular PathologySingapore General HospitalSingapore169608Singapore
| | | | - Jamie Mong
- Institute of Bioengineering and NanotechnologySingapore138669Singapore
| | - Min Han Tan
- Institute of Bioengineering and NanotechnologySingapore138669Singapore
- Lucence DiagnosticsSingapore159552Singapore
| | - Chwee Ming Lim
- Institute of Bioengineering and NanotechnologySingapore138669Singapore
- Department of Otorhinolaryngology‐Head and Neck SurgerySingapore General HospitalSingapore169608Singapore
- Surgery Academic Clinical ProgrammeDuke‐NUS Graduate Medical SchoolSingapore169857Singapore
| |
Collapse
|
8
|
E. A. R. ENS, Irekeola AA, Yean Yean C. Diagnostic and Prognostic Indications of Nasopharyngeal Carcinoma. Diagnostics (Basel) 2020; 10:E611. [PMID: 32825179 PMCID: PMC7554987 DOI: 10.3390/diagnostics10090611] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 08/11/2020] [Accepted: 08/18/2020] [Indexed: 02/06/2023] Open
Abstract
Nasopharyngeal carcinoma (NPC) is a disease that is highly associated with the latent infection of Epstein-Barr virus. The absence of obvious clinical signs at the early stage of the disease has made early diagnosis practically impossible, thereby promoting the establishment and progression of the disease. To enhance the stride for a reliable and less invasive tool for the diagnosis and prognosis of NPC, we synopsize biomarkers belonging to the two most implicated biological domains (oncogenes and tumor suppressors) in NPC disease. Since no single biomarker is sufficient for diagnosis and prognosis, coupled with the fact that the known established methods such as methylation-specific polymerase chain reaction (PCR), multiplex methylation-specific PCR, microarray assays, etc., can only accommodate a few biomarkers, we propose a 10-biomarker panel (KIT, LMP1, PIKC3A, miR-141, and miR-18a/b (oncogenic) and p16, RASSF1A, DAP-kinase, miR-9, and miR-26a (tumor suppressors)) based on their diagnostic and prognostic values. This marker set could be explored in a multilevel or single unified assay for the diagnosis and prognosis of NPC. If carefully harnessed and standardized, it is hoped that the proposed marker set would help transform the diagnostic and prognostic realm of NPC, and ultimately, help prevent the life-threatening late-stage NPC disease.
Collapse
Affiliation(s)
- Engku Nur Syafirah E. A. R.
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia; (E.N.S.E.A.R.); (A.A.I.)
| | - Ahmad Adebayo Irekeola
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia; (E.N.S.E.A.R.); (A.A.I.)
- Department of Biological Sciences, Microbiology Unit, College of Natural and Applied Sciences, Summit University Offa, Offa PMB 4412, Kwara State, Nigeria
| | - Chan Yean Yean
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia; (E.N.S.E.A.R.); (A.A.I.)
- Hospital Universiti Sains Malaysia, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia
| |
Collapse
|
9
|
Pall AH, Jakobsen KK, Grønhøj C, von Buchwald C. Circulating tumour DNA alterations as biomarkers for head and neck cancer: a systematic review. Acta Oncol 2020; 59:845-850. [PMID: 32223478 DOI: 10.1080/0284186x.2020.1742930] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Background: Head and neck squamous cell carcinoma (HNSCC) is a significant global burden. The development of a diagnostic or recurrence monitoring test could evolve from the exploitation of molecular markers such as tumour-specific DNA alterations in plasma. The aim of this study was to report specific genetic alterations of DNA in plasma from HNSCC patients, report the diagnostic accuracy, and discuss potentials for a diagnostic or recurrence monitoring test based on circulating tumour DNA (ctDNA).Methods: A systematic search was performed in PubMed, Embase, and Cochrane Library for articles published in English between 1 January 1980 and 24 October 2018. The search terms used were related to ctDNA methylations and mutations in HNSCC patients.Results: We identified 16 studies from four countries (p = 1156 patients, c = 601 controls) examining ctDNA alterations of HNSCC patients. CtDNA methylations were significantly increased in HNSCC patients compared to controls. Five studies investigated ctDNA mutations in HNSCC. The most frequent examined gene mutation was TP53. Eleven studies investigated ctDNA methylations in HNSCC. Nine studies calculated the diagnostic accuracy of ctDNA methylations in HNSCC compared to controls. The most frequent examined gene methylations were CDKN2A, DAPK1, RASSF1, and P15.Conclusion: We found that increasing the number of ctDNA genetic methylations resulted in an increase in diagnostic sensitivity accuracy. No studies investigating ctDNA mutations included a control group. A combination of multiple human ctDNA gene alterations with viral ctDNA are promising tools for developing a ctDNA biomarker for HNSCC.
Collapse
Affiliation(s)
- Amalie Hartvig Pall
- Department of Otorhinolaryngology, Head and Neck Surgery and Audiology, University Hospital Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Kathrine Kronberg Jakobsen
- Department of Otorhinolaryngology, Head and Neck Surgery and Audiology, University Hospital Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Christian Grønhøj
- Department of Otorhinolaryngology, Head and Neck Surgery and Audiology, University Hospital Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Christian von Buchwald
- Department of Otorhinolaryngology, Head and Neck Surgery and Audiology, University Hospital Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
10
|
Zhao S, Zhang Y, Liang X, Li M, Peng F, Chen Z, Chen Y. Detection and Analysis of RNAs Expression Profile for Methylated Candidate Tumor Suppressor Genes in Nasopharyngeal Carcinoma. Anticancer Agents Med Chem 2019; 19:772-782. [PMID: 30714531 DOI: 10.2174/1871520619666190204094815] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 01/21/2019] [Accepted: 01/24/2019] [Indexed: 12/25/2022]
Abstract
BACKGROUND DNA methylation, which acts as an expression regulator for multiple Tumor Suppressor Genes (TSGs), is believed to play an important role in Nasopharyngeal Carcinoma (NPC) development. METHODS We compared the effects of 5-aza-2-deoxycytidine (decitabine, DAC) on gene expression using RNA sequencing in NPC cells. RESULTS We analyzed Differentially Expressed Genes (DEGs) in NPC cells using DAC demethylation treatment and found that 2182 genes were significantly upregulated (≥ 2-fold change), suggesting that they may play a key role in cell growth, proliferation, development, and death. For data analysis, we used the Gene Ontology database and pathway enrichment analysis of the DEGs to discover differential patterns of DNA methylation associated with changes in gene expression. Furthermore, we evaluated 74 methylated candidate TSGs from the DEGs in NPC cells and summarized these genes in several important signaling pathways frequently disrupted by promoter methylation in NPC tumorigenesis. CONCLUSION Our study analyzes the DEGs and identifies a set of genes whose promoter methylation in NPC cells is reversed by DAC. These genes are potential substrates of DNMT inhibitors and may serve as tumor suppressors in NPC cells.
Collapse
Affiliation(s)
- Shuang Zhao
- Key Laboratory of Cancer Proteomics of National Health Commission, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Ye Zhang
- Key Laboratory of Cancer Proteomics of National Health Commission, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Xujun Liang
- Key Laboratory of Cancer Proteomics of National Health Commission, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Maoyu Li
- Key Laboratory of Cancer Proteomics of National Health Commission, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Fang Peng
- Key Laboratory of Cancer Proteomics of National Health Commission, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Zhuchu Chen
- Key Laboratory of Cancer Proteomics of National Health Commission, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Yongheng Chen
- Key Laboratory of Cancer Proteomics of National Health Commission, Xiangya Hospital, Central South University, Changsha 410008, China
| |
Collapse
|
11
|
Zhang J, Shen Z, Liu H, Liu S, Shu W. Diagnostic potential of methylated DAPK in brushing samples of nasopharyngeal carcinoma. Cancer Manag Res 2018; 10:2953-2964. [PMID: 30214290 PMCID: PMC6118259 DOI: 10.2147/cmar.s171796] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Background The death-associated protein kinase (DAPK) gene is an important member of the apoptotic pathway and is inactivated by abnormal methylation in numerous cancers, including nasopharyngeal carcinoma (NPC). However, the diagnostic value of DAPK methylation in brushing samples and tissue samples of NPC remains unclear. Methods We conducted a systematic meta-analysis based on 17 studies (including 386 tissue cases, 233 brushing cases, and 296 blood cases). Results Our results revealed an association between methylated DAPK and increased risk of NPC in blood, brushing, and tissue samples. In addition, the comparison of the pooled sensitivity, specificity, and area under the curve of methylated DAPK in brushing and tissue samples demonstrated the non-inferior effectiveness of methylated DAPK in brushing samples to monitor the development of NPC.
Collapse
Affiliation(s)
- Jian Zhang
- Department of Otorhinolaryngology Head and Neck Surgery, Ningbo Medical Center Lihuili Hospital, Ningbo, People's Republic of China
| | - Zhisen Shen
- Department of Otorhinolaryngology Head and Neck Surgery, Ningbo Medical Center Lihuili Hospital, Ningbo, People's Republic of China
| | - Huigao Liu
- Department of Otorhinolaryngology Head and Neck Surgery, Ningbo Zhenhai Longsai Hospital, Ningbo, People's Republic of China
| | - Shuai Liu
- Department of Radiology, Ningbo Medical Center Lihuili Eastern Hospital, Ningbo, People's Republic of China
| | - Wenxiu Shu
- Department of Oncology and Hematology, Ningbo Medical Center Lihuili Eastern Hospital, Ningbo, People's Republic of China,
| |
Collapse
|
12
|
Li L, Ma BBY, Chan ATC, Chan FKL, Murray P, Tao Q. Epstein-Barr Virus-Induced Epigenetic Pathogenesis of Viral-Associated Lymphoepithelioma-Like Carcinomas and Natural Killer/T-Cell Lymphomas. Pathogens 2018; 7:pathogens7030063. [PMID: 30022006 PMCID: PMC6161003 DOI: 10.3390/pathogens7030063] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 07/13/2018] [Accepted: 07/17/2018] [Indexed: 12/13/2022] Open
Abstract
Cancer genome studies of Epstein-Barr virus (EBV)-associated tumors, including lymphoepithelioma-like carcinomas (LELC) of nasopharyngeal (NPC), gastric (EBVaGC) and lung tissues, and natural killer (NK)/T-cell lymphoma (NKTCL), reveal a unique feature of genomic alterations with fewer gene mutations detected than other common cancers. It is known now that epigenetic alterations play a critical role in the pathogenesis of EBV-associated tumors. As an oncogenic virus, EBV establishes its latent and lytic infections in B-lymphoid and epithelial cells, utilizing hijacked cellular epigenetic machinery. EBV-encoded oncoproteins modulate cellular epigenetic machinery to reprogram viral and host epigenomes, especially in the early stage of infection, using host epigenetic regulators. The genome-wide epigenetic alterations further inactivate a series of tumor suppressor genes (TSG) and disrupt key cellular signaling pathways, contributing to EBV-associated cancer initiation and progression. Profiling of genome-wide CpG methylation changes (CpG methylome) have revealed a unique epigenotype of global high-grade methylation of TSGs in EBV-associated tumors. Here, we have summarized recent advances of epigenetic alterations in EBV-associated tumors (LELCs and NKTCL), highlighting the importance of epigenetic etiology in EBV-associated tumorigenesis. Epigenetic study of these EBV-associated tumors will discover valuable biomarkers for their early detection and prognosis prediction, and also develop effective epigenetic therapeutics for these cancers.
Collapse
Affiliation(s)
- Lili Li
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, State Key Laboratory of Oncology in South China, Sir YK Pao Center for Cancer and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.
| | - Brigette B Y Ma
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, State Key Laboratory of Oncology in South China, Sir YK Pao Center for Cancer and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.
| | - Anthony T C Chan
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, State Key Laboratory of Oncology in South China, Sir YK Pao Center for Cancer and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.
| | - Francis K L Chan
- Institute of Digestive Disease and State Key Laboratory of Digestive Diseases, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China.
| | - Paul Murray
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, UK.
| | - Qian Tao
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, State Key Laboratory of Oncology in South China, Sir YK Pao Center for Cancer and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.
| |
Collapse
|
13
|
Wu C, Peng S, Sun W, Luo M, Su B, Liu D, Hu G. Association of E-cadherin methylation with risk of nasopharyngeal cancer: A meta-analysis. Head Neck 2018; 40:2538-2545. [PMID: 29947108 DOI: 10.1002/hed.25319] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 03/13/2018] [Accepted: 04/03/2018] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Various studies have assessed the association between E-cadherin methylation and risk of nasopharyngeal cancer (NPC) but the conclusion remains unclear. This meta-analysis was conducted to evaluate the effects of E-cadherin methylation on the incidence and clinicopathological characteristics of NPC. METHODS Ten studies published up to June 30, 2016, were collected. Odds ratios (ORs) with corresponding confidence intervals (CIs) were calculated and summarized, respectively. RESULTS The E-cadherin methylation in NPC was significantly higher than those in normal groups (OR 16.23; 95% CI 8.34-31.60; P < .001). Ethnicity-stratified analysis indicated that E-cadherin methylation was strongly correlated with NPC among both Asians (OR 16.98; 95% CI 8.45-34.14; P < .001) and North Africans (OR 10.67; 95% CI 1.21-93.72; P = .033). However, further analysis showed that E-cadherin methylation was not strongly associated with clinicopathological feathers in patients with NPC. CONCLUSION The E-cadherin methylation is strongly associated with the incidence of NPC, which can serve as an effective biomarker for early detection of NPC.
Collapse
Affiliation(s)
- Cheng Wu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| | - Shan Peng
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| | - Wei Sun
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| | - Min Luo
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| | - Beibei Su
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| | - Dongbo Liu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| | - Guoqing Hu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| |
Collapse
|
14
|
Zanetti-Dällenbach RA, Schmid S, Wight E, Holzgreve W, Ladewing A, Hahn S, Zhong XY. Levels of Circulating Cell-Free Serum DNA in Benign and Malignant Breast Lesions. Int J Biol Markers 2018; 22:95-9. [PMID: 17549664 DOI: 10.1177/172460080702200202] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Purposes of the study: We analyzed circulating cell-free DNA in the serum of patients with benign and malignant breast disease and in healthy individuals to determine its diagnostic value. Basic procedures: Serum samples were obtained from 50 healthy individuals, 33 patients with malignant breast disease and 32 patients with benign breast disease. Circulatory DNA was extracted from serum samples. Cell-free DNA was quantified by real-time quantitative PCR for the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene. Tissue samples from patients with malignant and benign breast lesions were histopathologically examined. Main findings: The mean levels of circulating cell-free DNA in serum samples were 41,149 genome equivalents (GE)/mL in patients with malignant disease, 30,826 GE/mL in patients with benign disease, and 13,267 GE/mL in healthy individuals. Healthy individuals had significantly lower levels of cell-free DNA than patients with malignant or benign breast disease (p=0.001, p=0.031). No significant difference was observed between malignant and benign disease. There was a correlation between cell-free DNA levels and tumor size but not with other tumor characteristics. Principal conclusion: Our results suggest that levels of circulating cell-free DNA in serum could have diagnostic value to discriminate between healthy individuals and patients with breast lesions but not between patients with malignant and benign breast lesions.
Collapse
|
15
|
Arantes LMRB, De Carvalho AC, Melendez ME, Lopes Carvalho A. Serum, plasma and saliva biomarkers for head and neck cancer. Expert Rev Mol Diagn 2017; 18:85-112. [PMID: 29134827 DOI: 10.1080/14737159.2017.1404906] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
INTRODUCTION Head and neck squamous cell carcinoma (HNSCC) encompasses tumors arising from several locations (oral and nasal cavities, paranasal sinuses, salivary glands, pharynx, and larynx) and currently stands as the sixth most common cancer worldwide. The most important risk factors identified so far are tobacco and alcohol consumption, and, for a subgroup of HNSCCs, infection with high-risk types of human papillomavirus (HPV). Despite several improvements in the treatment of these tumors in the last decades, overall survival rates have only improved marginally, mainly due to the advanced clinical stage at diagnosis and the high rates of treatment failure associated with this late diagnosis. Areas covered: This review will focus on the feasibility of evaluating molecular-based biomarkers (mRNA, microRNA, lncRNA, DNA methylation and protein expression) in body fluids (serum, plasma, and saliva) as markers for diagnosis, prognosis, and surveillance. Expert commentary: The potential use of those markers in the clinical setting would allow for early diagnosis, prediction of treatment response, improvement in treatment selection and provide disease monitoring for early detection of tumor recurrence. It can ultimately be translated into better survival rates and improved quality of life for HNSCC patients.
Collapse
Affiliation(s)
| | | | - Matias Eliseo Melendez
- a Molecular Oncology Research Center , Barretos Cancer Hospital , Barretos - SP , Brazil
| | - André Lopes Carvalho
- a Molecular Oncology Research Center , Barretos Cancer Hospital , Barretos - SP , Brazil
| |
Collapse
|
16
|
Diagnostic Capacity of RASSF1A Promoter Methylation as a Biomarker in Tissue, Brushing, and Blood Samples of Nasopharyngeal Carcinoma. EBioMedicine 2017; 18:32-40. [PMID: 28396012 PMCID: PMC5405182 DOI: 10.1016/j.ebiom.2017.03.038] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Revised: 03/17/2017] [Accepted: 03/27/2017] [Indexed: 12/12/2022] Open
Abstract
Methylation of the RAS association domain family protein 1A (RASSF1A) promoter has been observed in nasopharyngeal carcinoma (NPC). This study investigated the correlation of RASSF1A promoter methylation with clinicopathological features and its utility as a diagnostic biomarker in NPC. A total of 926 patients with NPC and 495 non-tumor controls were analyzed in this study. RASSF1A promoter methylation was notably higher in NPC compared with non-tumor tissue, brushing and blood samples. RASSF1A promoter methylation was associated with clinical stage, lymph node status, distant metastasis, and T classification of patients with NPC, although it was not linked to age and sex. The pooled sensitivity, specificity, and AUC (area under the curve) of RASSF1A promoter methylation were determined in NPC samples vs. non-tumor samples (tissue: sensitivity=0.72, specificity=0.99, AUC=0.98; brushing: sensitivity=0.56, specificity=1.00, AUC=0.94; blood: sensitivity=0.11, specificity=0.98, AUC=0.97). Our findings show that RASSF1A promoter methylation may be correlated with the development, progression and metastasis of NPC. RASSF1A promoter methylation is a promising noninvasive biomarker for the diagnosis of NPC from tissue and brushing samples.
Collapse
|
17
|
Fathi A, Amani F, Davoodi M, Bahadoram S, Bahadoram M. A Rare Presentation of Primary Nasopharyngeal Carcinoma (NPC) in Mediastinum. IRANIAN JOURNAL OF CANCER PREVENTION 2016; 9:e4277. [PMID: 27761207 PMCID: PMC5055759 DOI: 10.17795/ijcp-4277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 02/22/2016] [Accepted: 05/30/2016] [Indexed: 12/05/2022]
Abstract
Introduction Nasopharyngeal carcinoma among the children has been rare accounting for only 1% of all pediatric malignancies. Both genetic and environmental factors have contributed to the development of nasopharyngeal carcinoma. Among the children there was a higher rate of undifferentiated histology. The mean age of nasopharyngeal carcinoma diagnosis has been 11 years old age; and the most common site was nasopharynx. Palpable lymphadenopathy, dysphasia and neural defect were common associated signs. Case Presentation A 15-year-old boy has presented with a mass that located near by the heart in the left side of mediastinum with invasion to anterior mediastinum from two years ago. In biopsy, nasopharyngeal carcinoma, non-keratinizing type, has diagnosed while there was no involvement of nasopharyngeal region. Patient has treated by 70 Gy (2.0 Gy/fraction) radiotherapy plus concomitant chemotherapy with base of docetaxel. But the mass had no regression. Then, the patient has treated with Cisplatin 100 mg/m2 IV on days 1, 22, and 43 with radiation, then cisplatin 80 mg/m2 IV on day 1 plus fluorouracil (5-FU) 1000 mg/m2/day by continuous IV infusion on days 1 - 4 every 4wk for 3 cycles and after remission interferon beta has added to treatment for 6 months duration as a maintenance therapy. After 1 year follow up; the patient was in complete remission. In the course of therapy, only hypothyroidism has occurred. Conclusions Nasopharyngeal carcinoma in childhood, without nasopharyngeal involvement, initially could be detected in other sites such as pericardium. Also good results could be respected by cisplatin and 5-fluorouracil based neoadjuvant chemotherapy before radiotherapy plus interferon beta as a maintenance therapy in childhood aggressive nasopharyngeal carcinoma.
Collapse
Affiliation(s)
- Afshin Fathi
- Associate Professor of Pediatric Haematology Oncology, Faculty of Medicine, Ardabil University of Medical Sciences, Ardabil, IR Iran
| | - Firuz Amani
- Associate Professor of Biostatistics and Epidemiology, Ardabil University of Medical Sciences, Ardabil, IR Iran
| | - Mohammad Davoodi
- Department of Radiology, Golestan Hospital, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, IR Iran
| | - Sara Bahadoram
- Department of Pediatrics, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, IR Iran
| | - Mohammad Bahadoram
- Medical Student Research Committee & Social Determinant of Health Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, IR Iran
| |
Collapse
|
18
|
Warton K, Mahon KL, Samimi G. Methylated circulating tumor DNA in blood: power in cancer prognosis and response. Endocr Relat Cancer 2016; 23:R157-71. [PMID: 26764421 PMCID: PMC4737995 DOI: 10.1530/erc-15-0369] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/13/2016] [Indexed: 12/12/2022]
Abstract
Circulating tumor DNA (ctDNA) in the plasma or serum of cancer patients provides an opportunity for non-invasive sampling of tumor DNA. This 'liquid biopsy' allows for interrogations of DNA such as quantity, chromosomal alterations, sequence mutations and epigenetic changes, and can be used to guide and improve treatment throughout the course of the disease. This tremendous potential for real-time 'tracking' in a cancer patient has led to substantial research efforts in the ctDNA field. ctDNA can be distinguished from non-tumor DNA by the presence of tumor-specific mutations and copy number variations, and also by aberrant DNA methylation, with both DNA sequence and methylation changes corresponding to those found in the tumor. Aberrant methylation of specific promoter regions can be a very consistent feature of cancer, in contrast to mutations, which typically occur at a wide range of sites. This consistency makes ctDNA methylation amenable to the design of widely applicable clinical assays. In this review, we examine ctDNA methylation in the context of monitoring disease status, treatment response and determining the prognosis of cancer patients.
Collapse
Affiliation(s)
- Kristina Warton
- Garvan Institute of Medical ResearchThe Kinghorn Cancer Centre and St Vincent's Clinical School, 370 Victoria Street, Darlinghurst, Sydeny, New South Wales, AustraliaChris O'Brien LifehouseCamperdown, New South Wales, Australia
| | - Kate L Mahon
- Garvan Institute of Medical ResearchThe Kinghorn Cancer Centre and St Vincent's Clinical School, 370 Victoria Street, Darlinghurst, Sydeny, New South Wales, AustraliaChris O'Brien LifehouseCamperdown, New South Wales, Australia Garvan Institute of Medical ResearchThe Kinghorn Cancer Centre and St Vincent's Clinical School, 370 Victoria Street, Darlinghurst, Sydeny, New South Wales, AustraliaChris O'Brien LifehouseCamperdown, New South Wales, Australia
| | - Goli Samimi
- Garvan Institute of Medical ResearchThe Kinghorn Cancer Centre and St Vincent's Clinical School, 370 Victoria Street, Darlinghurst, Sydeny, New South Wales, AustraliaChris O'Brien LifehouseCamperdown, New South Wales, Australia
| |
Collapse
|
19
|
Abstract
Viral and bacterial infections are involved in the development of human cancers, such as liver, nasopharyngeal, cervical, head and neck, and gastric cancers. Aberrant DNA methylation is frequently present in these cancers, and some of the aberrantly methylated genes are causally involved in cancer development and progression. Notably, aberrant DNA methylation can be present even in non-cancerous or precancerous tissues, and its levels correlate with the risk of cancer development, producing a so-called 'epigenetic field for cancerization'. Mechanistically, most viral or bacterial infections induce DNA methylation indirectly via chronic inflammation, but recent studies have indicated that some viruses have direct effects on the epigenetic machinery of host cells. From a translational viewpoint, a recent multicenter prospective cohort study demonstrated that assessment of the extent of alterations in DNA methylation in non-cancerous tissues can be used to predict cancer risk. Furthermore, suppression of aberrant DNA methylation was shown to be a useful strategy for cancer prevention in an animal model. Here, we review the involvement of aberrant DNA methylation in various types of infection-associated cancers, along with individual induction mechanisms, and we discuss the application of these findings for cancer prevention, diagnosis, and therapy.
Collapse
Affiliation(s)
- Naoko Hattori
- Division of Epigenomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Toshikazu Ushijima
- Division of Epigenomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
| |
Collapse
|
20
|
Jiang W, Cai R, Chen QQ. DNA Methylation Biomarkers for Nasopharyngeal Carcinoma: Diagnostic and Prognostic Tools. Asian Pac J Cancer Prev 2016; 16:8059-65. [DOI: 10.7314/apjcp.2015.16.18.8059] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
21
|
Salvianti F, Orlando C, Massi D, De Giorgi V, Grazzini M, Pazzagli M, Pinzani P. Tumor-Related Methylated Cell-Free DNA and Circulating Tumor Cells in Melanoma. Front Mol Biosci 2016; 2:76. [PMID: 26779490 PMCID: PMC4705904 DOI: 10.3389/fmolb.2015.00076] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 12/14/2015] [Indexed: 12/18/2022] Open
Abstract
Solid tumor release into the circulation cell-free DNA (cfDNA) and circulating tumor cells (CTCs) which represent promising biomarkers for cancer diagnosis. Circulating tumor DNA may be studied in plasma from cancer patients by detecting tumor specific alterations, such as genetic or epigenetic modifications. Ras association domain family 1 isoform A (RASSF1A) is a tumor suppressor gene silenced by promoter hypermethylation in a variety of human cancers including melanoma. The aim of the present study was to assess the diagnostic performance of a tumor-related methylated cfDNA marker in melanoma patients and to compare this parameter with the presence of CTCs. RASSF1A promoter methylation was quantified in cfDNA by qPCR in a consecutive series of 84 melanoma patients and 68 healthy controls. In a subset of 68 cases, the presence of CTCs was assessed by a filtration method (Isolation by Size of Epithelial Tumor Cells, ISET) as well as by an indirect method based on the detection of tyrosinase mRNA by RT-qPCR. The distribution of RASSF1A methylated cfDNA was investigated in cases and controls and the predictive capability of this parameter was assessed by means of the area under the ROC curve (AUC). The percentage of cases with methylated RASSF1A promoter in cfDNA was significantly higher in each class of melanoma patients (in situ, invasive and metastatic) than in healthy subjects (Pearson chi-squared test, p < 0.001). The concentration of RASSF1A methylated cfDNA in the subjects with a detectable quantity of methylated alleles was significantly higher in melanoma patients than in controls. The biomarker showed a good predictive capability (in terms of AUC) in discriminating between melanoma patients and healthy controls. This epigenetic marker associated to cfDNA did not show a significant correlation with the presence of CTCs, but, when the two parameters are jointly considered, we obtain a higher sensitivity of the detection of positive cases in invasive and metastatic melanomas. Our data suggest that cell-free tumor DNA and CTCs represent two complementary aspects of the liquid biopsy which may improve the diagnosis and the clinical management of melanoma patients.
Collapse
Affiliation(s)
- Francesca Salvianti
- Department of Clinical, Experimental and Biomedical Sciences, University of Florence Florence, Italy
| | - Claudio Orlando
- Department of Clinical, Experimental and Biomedical Sciences, University of Florence Florence, Italy
| | - Daniela Massi
- Division of Pathology, Department of Surgery and Translational Medicine, University of Florence Florence, Italy
| | - Vincenzo De Giorgi
- Division of Dermatology, Department of Surgery and Traslational Medicine, University of Florence Florence, Italy
| | - Marta Grazzini
- Division of Dermatology, Department of Surgery and Traslational Medicine, University of Florence Florence, Italy
| | - Mario Pazzagli
- Department of Clinical, Experimental and Biomedical Sciences, University of Florence Florence, Italy
| | - Pamela Pinzani
- Department of Clinical, Experimental and Biomedical Sciences, University of Florence Florence, Italy
| |
Collapse
|
22
|
Pei N, Wan R, Chen X, Li A, Zhang Y, Li J, Du H, Chen B, Wei W, Qi Y, Zhang Y, Katovich MJ, Sumners C, Zheng H, Li H. Angiotensin-(1-7) Decreases Cell Growth and Angiogenesis of Human Nasopharyngeal Carcinoma Xenografts. Mol Cancer Ther 2015; 15:37-47. [PMID: 26671566 DOI: 10.1158/1535-7163.mct-14-0981] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 10/27/2015] [Indexed: 11/16/2022]
Abstract
Angiotensin-(1-7) [Ang-(1-7)] is an endogenous, heptapeptide hormone acting through the Mas receptor (MasR), with antiproliferative and antiangiogenic properties. Recent studies have shown that Ang-(1-7) has an antiproliferative action on lung adenocarcinoma cells and prostate cancer cells. In this study, we report that MasR levels were significantly upregulated in nasopharyngeal carcinoma (NPC) specimens and NPC cell lines. Viral vector-mediated expression of Ang-(1-7) dramatically suppressed NPC cell proliferation and migration in vitro. These effects were completely blocked by the specific Ang-(1-7) receptor antagonist A-779, suggesting that they are mediated by the Ang-(1-7) receptor Mas. In this study, Ang-(1-7) not only caused a significant reduction in the growth of human nasopharyngeal xenografts, but also markedly decreased vessel density, suggesting that the heptapeptide inhibits angiogenesis to reduce tumor size. Mechanistic investigations revealed that Ang-(1-7) inhibited the expression of the proangiogenic factors VEGF and PlGF. Taken together, the data suggest that upregulation of MasR could be used as a diagnostic marker of NPC and Ang-(1-7) may be a novel therapeutic agent for nasopharyngeal cancer therapy because it exerts significant antiangiogenic activity.
Collapse
Affiliation(s)
- Nana Pei
- School of Biotechnology, Southern Medical University, Guangzhou, Guangdong, China. Department of Clinical Pathology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, China
| | - Renqiang Wan
- Department of Otolaryngology-Head and Neck Surgery, Guangdong NO.2 Provincial People's Hospital, Guangzhou, Guangdong, China
| | - Xinglu Chen
- School of Biotechnology, Southern Medical University, Guangzhou, Guangdong, China
| | - Andrew Li
- Department of Biomedical Engineering, The Johns University School of Medicine, Baltimore, Maryland
| | - Yanling Zhang
- School of Biotechnology, Southern Medical University, Guangzhou, Guangdong, China
| | - Jinlong Li
- School of Biotechnology, Southern Medical University, Guangzhou, Guangdong, China
| | - Hongyan Du
- School of Biotechnology, Southern Medical University, Guangzhou, Guangdong, China
| | - Baihong Chen
- School of Biotechnology, Southern Medical University, Guangzhou, Guangdong, China
| | - Wenjin Wei
- Beijing Minhai Biotechnology Co. Ltd., Beijing, China
| | - Yanfei Qi
- Department of Physiology and Functional Genomics, University of Florida, Gainesville, Florida
| | - Yi Zhang
- Department of Pharmacology, University of Florida, Gainesville, Florida
| | - Michael J Katovich
- Department of Pharmacodynamics, University of Florida, Gainesville, Florida
| | - Colin Sumners
- Department of Physiology and Functional Genomics, University of Florida, Gainesville, Florida
| | - Haifa Zheng
- Beijing Minhai Biotechnology Co. Ltd., Beijing, China.
| | - Hongwei Li
- School of Biotechnology, Southern Medical University, Guangzhou, Guangdong, China.
| |
Collapse
|
23
|
Bruce JP, Yip K, Bratman SV, Ito E, Liu FF. Nasopharyngeal Cancer: Molecular Landscape. J Clin Oncol 2015; 33:3346-55. [DOI: 10.1200/jco.2015.60.7846] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Nasopharyngeal carcinoma (NPC) is a unique epithelial malignancy arising from the superior aspect of the pharyngeal mucosal space, associated with latent Epstein-Barr virus infection in most cases. The capacity to characterize cancer genomes in unprecedented detail is now providing insights into the genesis and molecular underpinnings of this disease. Herein, we provide an overview of the molecular aberrations that likely drive nasopharyngeal tumor development and progression. The contributions of major Epstein-Barr virus–encoded factors, including proteins, small RNAs, and microRNAs, along with their interactions with pathways regulating cell proliferation and survival are highlighted. We review recent analyses that clearly define the role of genetic and epigenetic variations affecting the human genome in NPC. These findings point to the impact of DNA methylation and histone modifications on gene expression programs that promote this malignancy. The molecular interactions that allow NPC cells to evade immune recognition and elimination, which is crucial for the survival of cells expressing potentially immunogenic viral proteins, are also described. Finally, the potential utility of detecting host and viral factors for the diagnosis and prognosis of NPC is discussed. Altogether, the studies summarized herein have greatly expanded our knowledge of the molecular biology of NPC, yet much remains to be uncovered. Emerging techniques for using and analyzing well-annotated biospecimens from patients with NPC will ultimately lead to a greater level of understanding, and enable improvements in precision therapies and clinical outcomes.
Collapse
Affiliation(s)
- Jeff P. Bruce
- Jeff P. Bruce, Kenneth Yip, Scott V. Bratman, Emma Ito, and Fei-Fei Liu, University Health Network; and Scott V. Bratman, Emma Ito, and Fei-Fei Liu, University of Toronto, Toronto, Ontario, Canada
| | - Kenneth Yip
- Jeff P. Bruce, Kenneth Yip, Scott V. Bratman, Emma Ito, and Fei-Fei Liu, University Health Network; and Scott V. Bratman, Emma Ito, and Fei-Fei Liu, University of Toronto, Toronto, Ontario, Canada
| | - Scott V. Bratman
- Jeff P. Bruce, Kenneth Yip, Scott V. Bratman, Emma Ito, and Fei-Fei Liu, University Health Network; and Scott V. Bratman, Emma Ito, and Fei-Fei Liu, University of Toronto, Toronto, Ontario, Canada
| | - Emma Ito
- Jeff P. Bruce, Kenneth Yip, Scott V. Bratman, Emma Ito, and Fei-Fei Liu, University Health Network; and Scott V. Bratman, Emma Ito, and Fei-Fei Liu, University of Toronto, Toronto, Ontario, Canada
| | - Fei-Fei Liu
- Jeff P. Bruce, Kenneth Yip, Scott V. Bratman, Emma Ito, and Fei-Fei Liu, University Health Network; and Scott V. Bratman, Emma Ito, and Fei-Fei Liu, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
24
|
Jiang W, Liu N, Chen XZ, Sun Y, Li B, Ren XY, Qin WF, Jiang N, Xu YF, Li YQ, Ren J, Cho WCS, Yun JP, Zeng J, Liu LZ, Li L, Guo Y, Mai HQ, Zeng MS, Kang TB, Jia WH, Shao JY, Ma J. Genome-Wide Identification of a Methylation Gene Panel as a Prognostic Biomarker in Nasopharyngeal Carcinoma. Mol Cancer Ther 2015; 14:2864-73. [PMID: 26443805 DOI: 10.1158/1535-7163.mct-15-0260] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 08/21/2015] [Indexed: 11/16/2022]
Abstract
DNA methylation, the best known epigenetic marker, can be used as a prognostic biomarker in many cancers. We examined DNA methylation status and survival in nasopharyngeal carcinoma (NPC) patients. Aberrant DNA-methylated genes in 24 NPC tissues and 24 noncancer nasopharyngitis biopsy tissues (NCNBT) were identified using Illumina 450K BeadChip. Correlations between DNA methylation and clinical outcomes were evaluated using bisulfite pyrosequencing in 454 NPC patients. Genome-wide methylation analysis demonstrated that NPC tissues had distinct DNA methylation patterns compared with NCNBT. Among all significant CpG sites, 2,173 CpG sites with β change ≥ 0.2 (1,880 hypermethylated, 293 hypomethylated) were identified (P < 0.05). A methylation gene panel comprising six hypermethylated genes was constructed with the average Z-score method. Patients in the training cohort with high methylation had poorer disease-free survival [DFS, HR, 2.26; 95% confidence interval (CI), 1.28-4.01; P, 0.005] and overall survival (OS, HR, 2.47; 95% CI, 1.30-4.71; P, 0.006) than those with low methylation. There were similar results in the validation (DFS, HR, 2.07; 95% CI, 1.17-3.67; P, 0.013; OS, HR, 1.83; 95% CI, 1.01-3.31; P, 0.046) and independent cohorts (DFS, HR, 1.94; 95% CI, 1.08-3.47; P, 0.026; OS, HR, 2.09; 95% CI, 1.10-3.98; P, 0.022). Analysis indicated that the methylation gene panel was an independent prognostic factor. Furthermore, patients with low methylation had a favorable response to concurrent chemotherapy with an improved DFS (P = 0.045) and OS (P = 0.031), whereas patients with high methylation did not benefit from concurrent chemotherapy. The six-hypermethylated gene panel was associated with poor survival in patients with NPC, demonstrating its potential usefulness as a prognostic biomarker to clinicians in NPC management.
Collapse
Affiliation(s)
- Wei Jiang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, People's Republic of China
| | - Na Liu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, People's Republic of China
| | - Xiao-Zhong Chen
- Department of Radiation Oncology, Zhejiang Cancer Hospital, Hangzhou, People's Republic of China
| | - Ying Sun
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, People's Republic of China
| | - Bin Li
- Department of Radiation Oncology, Zhejiang Cancer Hospital, Hangzhou, People's Republic of China
| | - Xian-Yue Ren
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, People's Republic of China
| | - Wei-Feng Qin
- Department of Radiation Oncology, Zhejiang Cancer Hospital, Hangzhou, People's Republic of China
| | - Ning Jiang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, People's Republic of China
| | - Ya-Fei Xu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, People's Republic of China
| | - Ying-Qin Li
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, People's Republic of China
| | - Jian Ren
- School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - William C S Cho
- Department of Radiation Oncology, Queen Elizabeth Hospital, Hong Kong, People's Republic of China
| | - Jing-Ping Yun
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, People's Republic of China
| | - Jing Zeng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, People's Republic of China
| | - Li-Zhi Liu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, People's Republic of China
| | - Li Li
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, People's Republic of China
| | - Ying Guo
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, People's Republic of China
| | - Hai-Qiang Mai
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, People's Republic of China
| | - Mu-Sheng Zeng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, People's Republic of China
| | - Tie-Bang Kang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, People's Republic of China
| | - Wei-Hua Jia
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, People's Republic of China
| | - Jian-Yong Shao
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, People's Republic of China
| | - Jun Ma
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, People's Republic of China.
| |
Collapse
|
25
|
Wu K, Xu XN, Chen Y, Pu XL, Wang BY, Tang XD. RASSF1A Gene Methylation is Associated with Nasopharyngeal Carcinoma Risk in Chinese. Asian Pac J Cancer Prev 2015; 16:2283-7. [DOI: 10.7314/apjcp.2015.16.6.2283] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
26
|
Koffler J, Sharma S, Hess J. Predictive value of epigenetic alterations in head and neck squamous cell carcinoma. Mol Cell Oncol 2014; 1:e954827. [PMID: 27308324 PMCID: PMC4905189 DOI: 10.1080/23723548.2014.954827] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 07/14/2014] [Accepted: 07/17/2014] [Indexed: 12/31/2022]
Abstract
Head and neck cancer collectively describes malignant tumors originating from the mucosal surface of the upper aerodigestive tract. These tumors pose a great threat to public health because of their high incidence and mortality. Traditional risk factors are tobacco and alcohol abuse. More recently, infection by high-risk types of human papilloma virus (HPV) has been identified as an additional risk factor, especially for oropharyngeal squamous cell carcinoma (OPSCC). Moreover, HPV-positive OPSCC is considered a distinct tumor entity with an improved clinical outcome compared to HPV-negative OPSCC. Epigenetic alterations act as key events in the pathogenesis of cancer and are of special interest for basic and translational oncology because of their reversible nature. This review provides a comprehensive summary of alterations of the epigenome in head and neck squamous cell carcinoma (HNSCC) with a focus on the methylome (hypomethylation and hypermethylation) and its predictive value in the evaluation of pathologic states and clinical outcome, or monitoring response rates to certain therapies.
Collapse
Affiliation(s)
- Jennifer Koffler
- Section Experimental and Translational Head and Neck Oncology; Department of Otolaryngology; Head and Neck Surgery; University Hospital Heidelberg ; Heidelberg, Germany
| | - Sarika Sharma
- Section Experimental and Translational Head and Neck Oncology; Department of Otolaryngology; Head and Neck Surgery; University Hospital Heidelberg ; Heidelberg, Germany
| | - Jochen Hess
- Section Experimental and Translational Head and Neck Oncology; Department of Otolaryngology; Head and Neck Surgery; University Hospital Heidelberg; Heidelberg, Germany; Research Group Molecular Mechanisms of Head and Neck Tumors; German Cancer Research Center (DKFZ); Heidelberg, Germany
| |
Collapse
|
27
|
Yang X, Dai W, Kwong DLW, Szeto CYY, Wong EHW, Ng WT, Lee AWM, Ngan RKC, Yau CC, Tung SY, Lung ML. Epigenetic markers for noninvasive early detection of nasopharyngeal carcinoma by methylation-sensitive high resolution melting. Int J Cancer 2014; 136:E127-35. [PMID: 25196065 DOI: 10.1002/ijc.29192] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 08/16/2014] [Accepted: 08/25/2014] [Indexed: 12/22/2022]
Abstract
Nasopharyngeal carcinoma (NPC) is a human malignancy that is closely associated with Epstein-Barr Virus (EBV). Early diagnosis of NPC will greatly improve the overall survival. However, current EBV DNA marker detection still lacks the predictive value to perform well in high-risk populations for early detection of NPC. Since aberrant promoter hypermethylation of tumor suppressor genes (TSGs) is widely considered to be an important epigenetic change in early carcinogenesis, this study identified a panel of methylation markers for early detection of NPC and also assessed the clinical usefulness of these markers with noninvasive plasma specimens instead of biopsies. MS-HRM assays were carried out to assess the methylation status of a selected panel of four TSGs (RASSF1A, WIF1, DAPK1 and RARβ2) in biopsies, NP brushings and cell-free plasma from NPC patients. High-risk and cancer-free groups were used as controls. DNA methylation panel showed higher sensitivity and specificity than EBV DNA marker in cell-free plasma from NPC patients at early Stages (I and II) and in addition to the EBV DNA marker, MS-HRM test for plasma and NP brushing DNA methylation significantly increased the detection rate at all NPC stages as well as local recurrence, using this selected four-gene panel (p<0.05). MS-HRM assay on a selected gene panel has great potential to become a noninvasive and complementary test for NPC early and recurrent detection in combination with the EBV DNA test to increase the sensitivity for NPC detection at an early stage.
Collapse
Affiliation(s)
- Xuesong Yang
- Department of Clinical Oncology and Center for Cancer Research, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Shao Y, Jiang H, Wu X, Luo Y, Tang W. p16 promoter hypermethylation is associated with increased risk of nasopharyngeal carcinoma. Mol Clin Oncol 2014; 2:1121-1124. [PMID: 25279209 DOI: 10.3892/mco.2014.396] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 07/22/2014] [Indexed: 01/31/2023] Open
Abstract
The present study aimed to investigate the effects of p16 hypermethylation on the risk of nasopharyngeal carcinoma (NPC) quantitatively, through a meta-analysis of available case-control studies including malignant and normal NPC tissue samples. Crude odds ratios (ORs) with 95% confidence intervals (CIs) were extracted and pooled to assess the strength of the association between p16 hypermethylation and NPC risk. A total of 9 studies, including 406 NPC and 376 control cases, were identified for meta-analysis. Statistically significant ORs of p16 hypermethylation were obtained from the NPC and control groups (OR=19.53; 95% CI: 9.54-39.97; P=0.685). The meta-analysis indicated that p16 hypermethylation significantly increases NPC risk.
Collapse
Affiliation(s)
- Yang Shao
- Laboratory of Molecular Genetics of Aging and Tumor, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, P.R. China
| | - Hongguo Jiang
- Laboratory of Molecular Genetics of Aging and Tumor, Faculty of Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, P.R. China
| | - Xiaoming Wu
- Laboratory of Molecular Genetics of Aging and Tumor, Faculty of Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, P.R. China
| | - Ying Luo
- Laboratory of Molecular Genetics of Aging and Tumor, Faculty of Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, P.R. China
| | - Wenru Tang
- Laboratory of Molecular Genetics of Aging and Tumor, Faculty of Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, P.R. China
| |
Collapse
|
29
|
Abstract
DNA methylation is a significant regulator of gene expression, and its role in carcinogenesis recently has been a subject of remarkable interest. The aim of this review is to analyze the mechanism and cell regulatory effects of both hypo- and hyper-DNA methylation on cancer. In this review, we report new developments and their implications regarding the effects of DNA methylation on cancer development. Indeed, alteration of the pattern of DNA methylation has been a constant finding in cancer cells of the same type and differences in the pattern of DNA methylation not only occur in a variety of tumor types, but also in developmental processes Furthermore, the pattern of histone modification appears to be a predicator of the risk of recurrence of human cancers. It is well known that hypermethylation represses transcription of the promoter sections of tumor-suppressor genes leading to gene silencing. However, hypomethylation also has been identified as a cause of oncogenesis. Furthermore, experiments concerning the mechanism of methylation and its control have led to the discovery of many regulatory enzymes and proteins. This review reports on methods developed for the detection of 5-hydroxymethylcytosine methylation at the 5-methylcytosine of protein domains in the CpG context compared to non-methylated DNA, histone modification, and microRNA change.
Collapse
|
30
|
Arantes LMRB, de Carvalho AC, Melendez ME, Carvalho AL, Goloni-Bertollo EM. Methylation as a biomarker for head and neck cancer. Oral Oncol 2014; 50:587-92. [PMID: 24656975 DOI: 10.1016/j.oraloncology.2014.02.015] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 02/13/2014] [Accepted: 02/20/2014] [Indexed: 02/08/2023]
Abstract
Head and neck cancer is a collective term that describes malignant tumors of the oral cavity, pharynx, and larynx characterized by high incidence and mortality rates. Although most HNSCC originate from the mucosal surface of the upper aerodigestive tract, where they can be easily detected during a routine clinical examination. Often the definitive diagnosis is delayed because of the difficulty in differentiating from other similar lesions. Activation of proto-oncogenes and inactivation of tumor suppressor genes are the major molecular alterations involved in carcinogenesis. In addition, epigenetic changes can alter the expression of critical genes important in the development of a variety of cancers. The detection of aberrant gene promoter methylation as a tool for the detection of tumors or its use as prognostic marker have been described for many different cancers including HNSCC. The search for biomarkers has as its main aim the evaluation and measurement of the status of normal and pathological biological processes as well as pharmacological responses to certain treatments. The tracking of these biomarkers is an important part for the identification of individuals in the early stages of head and neck cancer for its diagnostic and prognostic relevance reflecting in high survival rates, better quality of life and less cost to the healthcare system. Therefore, assuming that cancer results from genetic and epigenetic changes, analyzes based on gene methylation profile in combination with the pathological diagnosis would be useful in predicting the behavior of these head and neck tumors.
Collapse
Affiliation(s)
- L M R B Arantes
- Department of Molecular Biology, São José do Rio Preto Medical School (FAMERP), São José do Rio Preto - SP, Brazil; Center for Research in Molecular Oncology, Barretos Cancer Hospital - Pio XII, Barretos - SP, Brazil
| | - A C de Carvalho
- Center for Research in Molecular Oncology, Barretos Cancer Hospital - Pio XII, Barretos - SP, Brazil
| | - M E Melendez
- Center for Research in Molecular Oncology, Barretos Cancer Hospital - Pio XII, Barretos - SP, Brazil
| | - A L Carvalho
- Center for Research in Molecular Oncology, Barretos Cancer Hospital - Pio XII, Barretos - SP, Brazil
| | - E M Goloni-Bertollo
- Department of Molecular Biology, São José do Rio Preto Medical School (FAMERP), São José do Rio Preto - SP, Brazil.
| |
Collapse
|
31
|
Xiao L, Xiao T, Wang ZM, Cho WCS, Xiao ZQ. Biomarker discovery of nasopharyngeal carcinoma by proteomics. Expert Rev Proteomics 2014; 11:215-25. [PMID: 24611579 DOI: 10.1586/14789450.2014.897613] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Nasopharyngeal carcinoma (NPC) is one of the most common malignant tumors in southern China and southern Asia, and poses one of the most serious public health problems in these areas. Early diagnosis, predicting metastasis, recurrence, prognosis and therapeutic response of NPC remain a challenge. Discovery of diagnostic and predictive biomarkers is an ideal way to achieve these objectives. Proteomics has great potential in identifying cancer biomarkers. Comparative proteomics has identified a large number of potential biomarkers associated with NPC, although the clinical performance of such biomarkers needs to be further validated. In this article, we review the latest discovery and progress of biomarkers for early diagnosis, predicting metastasis, recurrence, prognosis and therapeutic response of NPC, inform the readers of the current status of proteomics-based NPC biomarker findings and suggest avenues for future work.
Collapse
Affiliation(s)
- Liang Xiao
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | | | | | | | | |
Collapse
|
32
|
The plasma DNA concentration as a potential breast cancer screening marker. Indian J Clin Biochem 2013; 30:55-8. [PMID: 25646041 DOI: 10.1007/s12291-013-0407-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 11/11/2013] [Indexed: 12/27/2022]
Abstract
Increased levels of plasma DNA have frequently been noticed in the blood plasma of cancer patients. The possibility of using plasma DNA level as the indicator of tumor stage in breast cancer was investigated in plasma samples obtained from 100 breast cancer patients and 100 healthy women who were included as controls. Circulatory plasma free DNA was extracted from plasma samples and quantified by fluorometer. The median concentration of plasma DNA in the plasma samples from breast cancer patients classified by TNM staging system as stage I, II, III, IV and breast surgical patients were 0.5, 235, 422, 1,280 and 0.5 ng/ml, respectively. The level of plasma DNA in the stage II- IV group was significantly higher than those in the surgical group with breast cancer and control group (P value < 0.001). The plasma DNA concentration in stage II, III and IV of breast cancer were higher when compared with healthy group. These tumor size, TNM stage and metastasis were significantly correlated with plasma DNA. The cut point of 120 ng/ml was early screening and treatment follow up breast cancer.
Collapse
|
33
|
Yang Q, Gao J, Xu L, Zeng Z, Sung JJY, Yu J. Promoter hypermethylation of BCL6B gene is a potential plasma DNA biomarker for gastric cancer. Biomarkers 2013; 18:721-5. [PMID: 24191714 DOI: 10.3109/1354750x.2013.853839] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We previously showed that BCL6B acts as a tumor suppressor in gastric cancer and up to 66% gastric cancer patients have promoter hypermethylation in tumor tissues. We aimed to evaluate the feasibility of detecting BCL6B methylation in plasma DNA as a potential biomarker for gastric cancer. Hypermethylation of the CpG islands in BCL6B promoter was detected in 42.5% (17/40) plasma DNA samples from gastric cancer patients, while no methylation was found in the plasma DNA of healthy controls (p < 0.001). BCL6B methylation may serve as a novel potential non-invasive plasma biomarker for the detection of gastric cancer.
Collapse
Affiliation(s)
- Qingfan Yang
- Institute of Digestive Disease and Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin , NT , Hong Kong
| | | | | | | | | | | |
Collapse
|
34
|
Tian F, Yip SP, Kwong DLW, Lin Z, Yang Z, Wu VWC. Promoter hypermethylation of tumor suppressor genes in serum as potential biomarker for the diagnosis of nasopharyngeal carcinoma. Cancer Epidemiol 2013; 37:708-13. [PMID: 23790641 DOI: 10.1016/j.canep.2013.05.012] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 05/28/2013] [Accepted: 05/31/2013] [Indexed: 11/26/2022]
Abstract
PURPOSE Promoter hypermethylation of tumor suppressor genes may serve as a promising biomarker for the diagnosis of cancer. Cell-free circulating DNA (cf-DNA) shares hypermethylation status with primary tumors. This study investigated promoter hypermethylation of five tumor suppressor genes as markers in the detection of nasopharyngeal carcinoma (NPC) in serum samples. METHODS cf-DNA was extracted from serum collected from 40 NPC patients and 41 age- and sex-matched healthy subjects. The promoter hypermethylation status of the five genes (RASSF1, CDKN2A, DLEC1, DAPK1 and UCHL1) was assessed by methylation-specific PCR after sodium bisulfite conversion. Differences in the methylation status of these five genes between NPC patients and healthy subjects were compared. RESULTS The concentration of cf-DNA in the serum of NPC patients was significantly higher than that in normal controls. The five tumor suppressor genes - RASSF1, CDKN2A, DLEC1, DAPK1 and UCHL1 - were found to be methylated in 17.5%, 22.5%, 25.0%, 51.4% and 64.9% of patients, respectively. The combination of four-gene marker - CDKN2A, DLEC1, DAPK1 and UCHL1 - had the highest sensitivity and specificity in predicting NPC. CONCLUSION Screening DNA hypermethylation of tumor suppressor genes in serum was a promising approach for the diagnosis of NPC.
Collapse
Affiliation(s)
- Fangyun Tian
- Department of Health Technology and Informatics, Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong.
| | | | | | | | | | | |
Collapse
|
35
|
Shu XS, Li L, Ji M, Cheng Y, Ying J, Fan Y, Zhong L, Liu X, Tsao SW, Chan ATC, Tao Q. FEZF2, a novel 3p14 tumor suppressor gene, represses oncogene EZH2 and MDM2 expression and is frequently methylated in nasopharyngeal carcinoma. Carcinogenesis 2013; 34:1984-93. [PMID: 23677067 DOI: 10.1093/carcin/bgt165] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Nasopharyngeal carcinoma (NPC) is an Epstein-Barr virus-associated tumor prevalent in southern China and southeast Asia, with the 3p14-p12 locus reported as a critical tumor suppressor gene (TSG) region during its pathogenesis. We identified a novel 3p14.2 TSG, FEZF2 (FEZ family zinc finger 2), for NPC. FEZF2 is readily expressed in normal tissues including upper respiratory epithelium, testis, brain and ovary tissues, as well as in immortalized nasopharyngeal epithelial cell line NP69, but it is completely silenced in NPC cell lines due to CpG methylation of its promoter, although no homozygous deletion of FEZF2 was detected. 5-Aza-2'-deoxycytidine treatment restored FEZF2 expression in NPC cell lines along with its promoter demethylation. FEZF2 was frequently downregulated in NPC tumors, with promoter methylation detected in 75.5% of tumors, but only in 7.1% of normal nasopharyngeal tissues. Restored FEZF2 expression suppressed NPC cell clonogenicity through inducing G2/M cell cycle arrest and apoptosis and also inhibited NPC cell migration and stemness. FEZF2 acted as a histone deacetylase-associated repressor downregulating multiple oncogenes including EZH2 and MDM2, through direct binding to their promoters. Concomitantly, overexpression of EZH2 was frequently detected in NPC tumors. Thus, we have identified FEZF2 as a novel 3p14.2 TSG frequently inactivated by promoter methylation in NPC, which functions as a repressor downregulating multiple oncogene expression.
Collapse
Affiliation(s)
- Xing-Sheng Shu
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, State Key Laboratory of Oncology in South China, Sir YK Pao Center for Cancer and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong and CUHK Shenzhen Research Institute, Shatin, Hong Kong
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
36
|
La Rosa S, Furlan D, Franzi F, Battaglia P, Frattini M, Zanellato E, Marando A, Sahnane N, Turri-Zanoni M, Castelnuovo P, Capella C. Mixed exocrine-neuroendocrine carcinoma of the nasal cavity: clinico-pathologic and molecular study of a case and review of the literature. Head Neck Pathol 2013; 7:76-84. [PMID: 22740238 PMCID: PMC3597157 DOI: 10.1007/s12105-012-0379-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Accepted: 06/12/2012] [Indexed: 01/05/2023]
Abstract
Sinonasal intestinal-type adenocarcinomas (ITACs) are rare neoplasms histologically resembling intestinal adenocarcinomas. Although a neuroendocrine differentiation in ITACs has been described, true mixed exocrine-neuroendocrine carcinomas, neoplasms in which each component represents at least 30 % of the lesion, are extremely rare and their molecular alterations are largely unknown. We describe herein the clinico-pathologic features, the methylation profile, chromosomal gains and losses, and mutation analysis of KRAS, BRAF and p53 in a nasal mixed exocrine-neuroendocrine carcinoma resected in a 79-year-old man. The tumor was composed of an ITAC and a poorly differentiated neuroendocrine carcinoma. Both exocrine and neuroendocrine components were CK8, CK20, CDX2 and p53 positive, and CK7 and TTF1 negative. The neuroendocrine component also showed immunoreactivity for chromogranin A, synaptophysin, serotonin and glicentin. Gains and losses were found at following chromosome regions: 17p13 (TP53), 14q24 (MLH3), 19q13 (KLK3), 5q21 (APC), 7q21 (CDK6), 9q34 (DAPK1), 12p13 (TNFRSF 1A, CDKN1B), 13q12 (BRCA2), 17p13.3 (HIC1), 18q21 (BCL2), and 22q12 (TIMP3). Aberrant methylation was detected only in the neuroendocrine component and involved APC and DAPK1 genes. No mutation of KRAS (exons 2-4), BRAF (exon 15), and p53 (exons 4-10) was found in both components. The results suggest a monoclonal origin of the tumor from a pluripotent cell undergoing a biphenotypic differentiation and that the neuroendocrine differentiation may be from an exocrine to an endocrine pathway. We have also reviewed the literature on sinonasal mixed exocrine-neuroendocrine carcinomas to give to the reader a comprehensive overview of these very rare tumor types.
Collapse
Affiliation(s)
- Stefano La Rosa
- Department of Pathology, Ospedale di Circolo, viale Borri 57, 21100 Varese, Italy.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Bukurova YA, Krasnov GS, Nikitina IG, Karpov VL, Lisitsyn NA, Beresten SF. Methods of searching for markers for serological serum diagnosis of tumors. Mol Biol 2013. [DOI: 10.1134/s0026893313010032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
38
|
Biological Tools for NPC Population Screening and Disease Monitoring. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013. [DOI: 10.1007/978-1-4614-5947-7_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
39
|
Li L, Choi JY, Lee KM, Sung H, Park SK, Oze I, Pan KF, You WC, Chen YX, Fang JY, Matsuo K, Kim WH, Yuasa Y, Kang D. DNA methylation in peripheral blood: a potential biomarker for cancer molecular epidemiology. J Epidemiol 2012; 22:384-94. [PMID: 22863985 PMCID: PMC3798632 DOI: 10.2188/jea.je20120003] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Aberrant DNA methylation is associated with cancer development and progression. There are several types of specimens from which DNA methylation pattern can be measured and evaluated as an indicator of disease status (from normal biological process to pathologic condition) and even of pharmacologic response to therapy. Blood-based specimens such as cell-free circulating nucleic acid and DNA extracted from leukocytes in peripheral blood may be a potential source of noninvasive cancer biomarkers. In this article, we describe the characteristics of blood-based DNA methylation from different biological sources, detection methods, and the factors affecting DNA methylation. We provide a comprehensive literature review of blood-based DNA methylation as a cancer biomarker and focus on the study of DNA methylation using peripheral blood leukocytes. Although DNA methylation patterns measured in peripheral blood have great potential to be useful and informative biomarkers of cancer risk and prognosis, large systematic and unbiased prospective studies that consider biological plausibility and data analysis issues will be needed in order to develop a clinically feasible blood-based assay.
Collapse
Affiliation(s)
- Lian Li
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Benesova L, Belsanova B, Suchanek S, Kopeckova M, Minarikova P, Lipska L, Levy M, Visokai V, Zavoral M, Minarik M. Mutation-based detection and monitoring of cell-free tumor DNA in peripheral blood of cancer patients. Anal Biochem 2012; 433:227-34. [PMID: 22750103 DOI: 10.1016/j.ab.2012.06.018] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Revised: 06/15/2012] [Accepted: 06/20/2012] [Indexed: 12/18/2022]
Abstract
Prognosis of solid cancers is generally more favorable if the disease is treated early and efficiently. A key to long cancer survival is in radical surgical therapy directed at the primary tumor followed by early detection of possible progression, with swift application of subsequent therapeutic intervention reducing the risk of disease generalization. The conventional follow-up care is based on regular observation of tumor markers in combination with computed tomography/endoscopic ultrasound/magnetic resonance/positron emission tomography imaging to monitor potential tumor progression. A recent development in methodologies allowing screening for a presence of cell-free DNA (cfDNA) brings a new viable tool in early detection and management of major cancers. It is believed that cfDNA is released from tumors primarily due to necrotization, whereas the origin of nontumorous cfDNA is mostly apoptotic. The process of cfDNA detection starts with proper collection and treatment of blood and isolation and storage of blood plasma. The next important steps include cfDNA extraction from plasma and its detection and/or quantification. To distinguish tumor cfDNA from nontumorous cfDNA, specific somatic DNA mutations, previously localized in the primary tumor tissue, are identified in the extracted cfDNA. Apart from conventional mutation detection approaches, several dedicated techniques have been presented to detect low levels of cfDNA in an excess of nontumorous (nonmutated) DNA, including real-time polymerase chain reaction (PCR), "BEAMing" (beads, emulsion, amplification, and magnetics), and denaturing capillary electrophoresis. Techniques to facilitate the mutant detection, such as mutant-enriched PCR and COLD-PCR (coamplification at lower denaturation temperature PCR), are also applicable. Finally, a number of newly developed miniaturized approaches, such as single-molecule sequencing, are promising for the future.
Collapse
Affiliation(s)
- L Benesova
- Laboratory of Molecular Genetics and Oncology, Genomac Research Institute, 155 41 Prague, Czech Republic
| | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Egger G, Wielscher M, Pulverer W, Kriegner A, Weinhäusel A. DNA methylation testing and marker validation using PCR: diagnostic applications. Expert Rev Mol Diagn 2012; 12:75-92. [PMID: 22133121 DOI: 10.1586/erm.11.90] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
DNA methylation provides a fundamental epigenetic mechanism to establish and promote cell-specific gene-expression patterns, which are inherited by subsequent cell generations. Thus, the epigenome determines the differentiation into a cell lineage but can also program cells to become abnormal or malignant. In humans, different germline and somatic diseases have been linked to faulty DNA methylation. In this article, we will discuss the available PCR-based technologies to assess differences in DNA methylation levels mainly affecting 5-methylcytosine in the CpG dinucleotide context in hereditary syndromal and somatic pathological conditions. We will discuss some of the current diagnostic applications and provide an outlook on how DNA methylation-based biomarkers might provide novel tools for diagnosis, prognosis or patient stratification for diseases such as cancer.
Collapse
Affiliation(s)
- Gerda Egger
- Clinical Institute of Pathology, Medical University of Vienna, Austria
| | | | | | | | | |
Collapse
|
42
|
Gourzones C, Barjon C, Busson P. Host-tumor interactions in nasopharyngeal carcinomas. Semin Cancer Biol 2012; 22:127-36. [PMID: 22249142 DOI: 10.1016/j.semcancer.2012.01.002] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Revised: 12/29/2011] [Accepted: 01/03/2012] [Indexed: 12/13/2022]
Abstract
Like other human solid tumors, nasopharyngeal carcinoma (NPC) is a tissue and a systemic disease as much as a cell disease. Tumor cell population in NPC is highly heterogeneous. Heavy infiltration by non-malignant leucocytes results at least in part from the production of abundant inflammatory cytokines by the malignant epithelial cells. There is indirect evidence that interactions between stromal and malignant cells contribute to tumor development. Peripheral blood samples collected from NPC patients contain multiple products derived from the tumor, including cytokines, non-cytokine tumor proteins, tumor exosomes and viral nucleic acids. These products represent a potential source of biomarkers for assessment of tumor aggressiveness, indirect exploration of cellular interactions and monitoring of tumor response to therapeutic agents. Most NPC patients are immunocompetent with evidence of active humoral and cellular immune responses against EBV-antigens at the systemic level. Tumor development is facilitated by local immunosuppressive factors which are not fully understood. Local accumulation of regulatory T-cells is probably one important factor. At least two NPC tumor products are suspected to contribute to their expansion, the cytokine CCL20 and the tumor exosomes carrying galectin 9. In the future, new therapeutic modalities will probably aim at breaking immune tolerance or at blocking cellular interactions critical for tumor growth.
Collapse
Affiliation(s)
- Claire Gourzones
- Université Paris-Sud-11, CNRS-UMR 8126 and Institut de cancérologie Gustave Roussy, 39 rue Camille Desmoulins, F-94805 Villejuif, France
| | | | | |
Collapse
|
43
|
Hutajulu SH, Indrasari SR, Indrawati LPL, Harijadi A, Duin S, Haryana SM, Steenbergen RDM, Greijer AE, Middeldorp JM. Epigenetic markers for early detection of nasopharyngeal carcinoma in a high risk population. Mol Cancer 2011; 10:48. [PMID: 21535891 PMCID: PMC3114786 DOI: 10.1186/1476-4598-10-48] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Accepted: 05/02/2011] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Undifferentiated nasopharyngeal carcinoma (NPC) is strongly related to Epstein-Barr virus (EBV) infection, allowing aberrant antibodies against EBV and viral DNA load as screening tools in high risk populations. Methylation analysis in the promoter of tumor suppressor genes (TSGs) may serve as a complementary marker for identifying early cases. This study determined methylation status of multiple TSGs and evaluated whether it may improve early detection. METHODS Nasopharyngeal brushings were taken from 53 NPC patients, 22 high risk subjects and 25 healthy EBV carriers. Corresponding NPC paraffin tissue was included. DNA was bisulfite-modified preceding analysis by methylation-specific PCR (MSP). Ten TSGs were studied. RESULTS NPC paraffin and brushing DNA revealed an 81.8% concordance so that MSP analysis was done using either one of both specimens. NPC samples showed methylation for individual TSGs (DAPK1 79.2%, CDH13 77.4%, DLC1 76.9%, RASSF1A 75.5%, CADM1 69.8%, p16 66.0%, WIF1 61.2%, CHFR 58.5%, RIZ1 56.6% and RASSF2A 29.2%). High risk individuals, having elevated EBV IgA and viral load, showed high frequency of methylation of CDH13, DAPK1, DLC1 and CADM1, but low frequency of methylation of p16 and WIF1 and undetectable methylation of RASSF1A, CHFR, RIZ1 and RASSF2A. Healthy subjects showed similar patterns as high risk individuals. A combination of RASSF1A and p16 gave good discrimination between NPC and non-NPC, but best results were combined analysis of five methylation markers (RASSF1A, p16, WIF1, CHFR and RIZ1) with detection rate of 98%. CONCLUSION Multiple marker MSP is proposed as a complementary test for NPC risk assessment in combination with EBV-based markers.
Collapse
Affiliation(s)
- Susanna H Hutajulu
- Faculty of Medicine/Dr Sardjito Hospital, Universitas Gadjah Mada,Yogyakarta, Indonesia
| | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Yi L, Li D, Li X, Deng J, Liao Y, Liang Y, Chen Z, Xiao Z. Serum Metabolic Fingerprinting to Detect Human Nasopharyngeal Carcinoma Based on Gas Chromatography-Mass Spectrometry and Partial Least Squares-Linear Discriminant Analysis. ANAL LETT 2011. [DOI: 10.1080/00032719.2010.512685] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
45
|
Li LL, Shu XS, Wang ZH, Cao Y, Tao Q. Epigenetic disruption of cell signaling in nasopharyngeal carcinoma. CHINESE JOURNAL OF CANCER 2011; 30:231-9. [PMID: 21439244 PMCID: PMC4013349 DOI: 10.5732/cjc.011.10080] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Revised: 03/09/2011] [Accepted: 03/09/2011] [Indexed: 12/18/2022]
Abstract
Nasopharyngeal carcinoma (NPC) is a malignancy with remarkable ethnic and geographic distribution in southern China and Southeast Asia. Alternative to genetic changes, aberrant epigenetic events disrupt multiple genes involved in cell signaling pathways through DNA methylation of promoter CpG islands and/or histone modifications. These epigenetic alterations grant cell growth advantage and contribute to the initiation and progression of NPC. In this review, we summarize the epigenetic deregulation of cell signaling in NPC tumorigenesis and highlight the importance of identifying epigenetic cell signaling regulators in NPC research. Developing pharmacologic strategies to reverse the epigenetic-silencing of cell signaling regulators might thus be useful to NPC prevention and therapy.
Collapse
Affiliation(s)
- Li-Li Li
- Shenzhen Key Laboratory of Cancer Nanotechnology, Institute of Biomedical and Health Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences-CUHK, Shenzhen, Guangdong 518055, P. R. China;
- Cancer Epigenetics Laboratory, Sir YK Pao Center for Cancer, Department of Clinical Oncology, The Chinese University of Hong Kong, Hong Kong and CUHK Shenzhen Research Institute, Shenzhen, Guangdong 518057, P. R. China;
- Cancer Research Institute, Xiangya School of Medicine, Central South University, Changsha, Hunan 410078, P. R. China.
| | - Xing-Sheng Shu
- Cancer Epigenetics Laboratory, Sir YK Pao Center for Cancer, Department of Clinical Oncology, The Chinese University of Hong Kong, Hong Kong and CUHK Shenzhen Research Institute, Shenzhen, Guangdong 518057, P. R. China;
| | - Zhao-Hui Wang
- Shenzhen Key Laboratory of Cancer Nanotechnology, Institute of Biomedical and Health Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences-CUHK, Shenzhen, Guangdong 518055, P. R. China;
- Cancer Epigenetics Laboratory, Sir YK Pao Center for Cancer, Department of Clinical Oncology, The Chinese University of Hong Kong, Hong Kong and CUHK Shenzhen Research Institute, Shenzhen, Guangdong 518057, P. R. China;
| | - Ya Cao
- Cancer Research Institute, Xiangya School of Medicine, Central South University, Changsha, Hunan 410078, P. R. China.
| | - Qian Tao
- Shenzhen Key Laboratory of Cancer Nanotechnology, Institute of Biomedical and Health Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences-CUHK, Shenzhen, Guangdong 518055, P. R. China;
- Cancer Epigenetics Laboratory, Sir YK Pao Center for Cancer, Department of Clinical Oncology, The Chinese University of Hong Kong, Hong Kong and CUHK Shenzhen Research Institute, Shenzhen, Guangdong 518057, P. R. China;
| |
Collapse
|
46
|
Loyo M, Brait M, Kim MS, Ostrow KL, Jie CC, Chuang AY, Califano JA, Liégeois NJ, Begum S, Westra WH, Hoque MO, Tao Q, Sidransky D. A survey of methylated candidate tumor suppressor genes in nasopharyngeal carcinoma. Int J Cancer 2011; 128:1393-403. [PMID: 20473931 DOI: 10.1002/ijc.25443] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Nasopharyngeal carcinoma (NPC) is a rare malignancy with unique genetic, viral and environmental characteristic that distinguishes it from other head and neck carcinomas. The clinical management of NPC remains challenging largely due to the lack of early detection strategies for this tumor. In our study, we have sought to identify novel genes involved in the pathogenesis of NPC that might provide insight into this tumor's biology and could potentially be used as biomarkers. To identify these genes, we studied the epigenetics of NPC by characterizing a panel of methylation markers. Eighteen genes were evaluated by quantitative methylation-specific polymerase chain reaction (PCR) in cell lines as well as in tissue samples including 50 NPC tumors and 28 benign nasopharyngeal biopsies. Significance was evaluated using Fisher's exact test and quantitative values were optimized using cut off values derived from receiver-operator characteristic curves. The methylation status of AIM1, APC, CALCA, deleted in colorectal carcinomas (DCC), DLEC, deleted in liver cancer 1 (DLC1), estrogen receptor alpha (ESR), FHIT, KIF1A and PGP9.5 was significantly associated with NPC compared to controls. The sensitivity of the individual genes ranged from 26 to 66% and the specificity was above 92% for all genes except FHIT. The combination of PGP9.5, KIF1A and DLEC had a sensitivity of 84% and a specificity of 92%. Ectopic expression of DCC and DLC1 lead to decrease in colony formation and invasion properties. Our results indicate that methylation of novel biomarkers in NPC could be used to enhance early detection approaches. Additionally, our functional studies reveal previously unknown tumor suppressor roles in NPC.
Collapse
Affiliation(s)
- Myriam Loyo
- Department of Otolaryngology-Head and Neck Surgery, Greater Baltimore Medical Center, Baltimore, MD 21231, USA
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Radpour R, Barekati Z, Kohler C, Lv Q, Bürki N, Diesch C, Bitzer J, Zheng H, Schmid S, Zhong XY. Hypermethylation of tumor suppressor genes involved in critical regulatory pathways for developing a blood-based test in breast cancer. PLoS One 2011; 6:e16080. [PMID: 21283676 PMCID: PMC3025923 DOI: 10.1371/journal.pone.0016080] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2010] [Accepted: 12/06/2010] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Aberrant DNA methylation patterns might be used as a biomarker for diagnosis and management of cancer patients. METHODS AND FINDINGS To achieve a gene panel for developing a breast cancer blood-based test we quantitatively assessed the DNA methylation proportion of 248 CpG sites per sample (total of 31,248 sites in all analyzed samples) on 10 candidate genes (APC, BIN1, BMP6, BRCA1, CST6, ESR-b, GSTP1, P16, P21 and TIMP3). The number of 126 samples consisting of two different cohorts was used (first cohort: plasma samples from breast cancer patients and normal controls; second cohort: triple matched samples including cancerous tissue, matched normal tissue and serum samples). In the first cohort, circulating cell free methylated DNA of the 8 tumor suppressor genes (TSGs) was significantly higher in patients with breast cancer compared to normal controls (P<0.01). In the second cohort containing triple matched samples, seven genes showed concordant hypermethylated profile in tumor tissue and serum samples compared to normal tissue (P<0.05). Using eight genes as a panel to develop a blood-based test for breast cancer, a sensitivity and specificity of more than 90% could be achieved in distinguishing between tumor and normal samples. CONCLUSIONS Our study suggests that the selected TSG panel combined with the high-throughput technology might be a useful tool to develop epigenetic based predictive and prognostic biomarker for breast cancer relying on pathologic methylation changes in tumor tissue, as well as in circulation.
Collapse
Affiliation(s)
- Ramin Radpour
- Laboratory for Gynecological Oncology, Department of Biomedicine, Women's Hospital, University of Basel, Basel, Switzerland
| | - Zeinab Barekati
- Laboratory for Gynecological Oncology, Department of Biomedicine, Women's Hospital, University of Basel, Basel, Switzerland
| | - Corina Kohler
- Laboratory for Gynecological Oncology, Department of Biomedicine, Women's Hospital, University of Basel, Basel, Switzerland
| | - Qing Lv
- Department of Breast Surgery, West China Hospital, West China School of Medicine, Sichuan University, Chengdu, China
| | - Nicole Bürki
- Department of Obstetrics and Gynecology, Kantonsspital, Liestal, Switzerland
| | - Claude Diesch
- Department of Obstetrics and Gynecology, Kantonsspital, Liestal, Switzerland
| | - Johannes Bitzer
- Department of Obstetrics and Gynecology, Women's Hospital, University of Basel, Basel, Switzerland
| | - Hong Zheng
- Laboratory of Molecular Diagnosis of Cancer, Department of Oncology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China School of Medicine, Sichuan University, Chengdu, China
| | - Seraina Schmid
- Department of Obstetrics and Gynecology, Women's Hospital, University of Basel, Basel, Switzerland
- * E-mail: (XYZ); (SS)
| | - Xiao Yan Zhong
- Laboratory for Gynecological Oncology, Department of Biomedicine, Women's Hospital, University of Basel, Basel, Switzerland
- * E-mail: (XYZ); (SS)
| |
Collapse
|
48
|
Tamkovich SN, Vlassov VV, Laktionov PP. Circulating DNA in the blood and its application in medical diagnosis. Mol Biol 2011. [DOI: 10.1134/s0026893308010020] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
49
|
Selection of reliable reference genes for gene expression study in nasopharyngeal carcinoma. Acta Pharmacol Sin 2010; 31:1487-94. [PMID: 21052085 DOI: 10.1038/aps.2010.115] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
AIM To construct a system for selecting reference genes (RGs) and to select the most optimal RGs for gene expression studies in nasopharyngeal carcinoma (NPC). METHODS The total RNAs from 20 NPC samples were each labeled with Cy5-dUTP. To create a common control, the total RNA from 15 nasopharyngeal phlogistic (NP) tissues was mixed and labeled via reverse transcription with Cy3-dUTP. cDNA microarrays containing 14 112 genes were then performed. A mathematical approach was constructed to screen stably expressed genes from the microarray data. Using this method, three genes (YARS, EIF3S7, and PFDN1) were selected as candidate RGs. Furthermore, 7 commonly used RGs (HPRT1, GAPDH, TBP, ACTB, B2M, G6PDH, and HBB) were selected as additional potential RGs. Real-time PCR was used to detect these 10 candidate genes' expression levels and the geNorm program was used to find the optimal RGs for NPC studies. RESULTS On the basis of the 10 candidate genes' expression stability level, geNorm analysis identified the optimal single RG (YARS or HPRT1) and the most suitable set of RGs (HPRT1, YARS, and EIF3S7) for NPC gene expression studies. In addition, this analysis determined that B2M, G6PDH, and HBB were not appropriate for use as RGs. Interestingly, ACTB was the least stable RG in our study, even though previous studies had indicated that it was one of the most stable RGs. Three novel candidate genes (YARS, EIF3S7, and PFDN1), which were selected from microarray data, were all identified as suitable RGs for NPC research. A RG-selecting system was then constructed, which combines microarray data analysis, a literature screen, real-time PCR, and bioinformatic analysis. CONCLUSION We construct a RG-selecting system that helps find the optimal RGs. This process, applied to NPC research, determined the single RG (YARS or HPRT1) and the set of RGs (HPRT1, YARS, and EIF3S7) that are the most suitable internal controls.
Collapse
|
50
|
Jung K, Fleischhacker M, Rabien A. Cell-free DNA in the blood as a solid tumor biomarker--a critical appraisal of the literature. Clin Chim Acta 2010; 411:1611-24. [PMID: 20688053 DOI: 10.1016/j.cca.2010.07.032] [Citation(s) in RCA: 242] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Revised: 07/24/2010] [Accepted: 07/25/2010] [Indexed: 12/21/2022]
Abstract
Circulating cell-free DNA (cfDNA) has been suggested as a cancer biomarker. Several studies assessed the usefulness of quantitative and qualitative tumor-specific alterations of cfDNA, such as DNA strand integrity, frequency of mutations, abnormalities of microsatellites, and methylation of genes, as diagnostic, prognostic, and monitoring markers in cancer patients. Most of the papers that could be evaluated in this review resulted in a positive conclusion. However, methodical diversity without the traceability of data and differently designed and often underpowered studies resulted in divergent results between studies. In addition, the limited diagnostic sensitivity and specificity of cfDNA alterations temper the effusive hope of novel tumor markers, raising similar issues as those for other tumor markers. To validate the actual clinical validity of various cfDNA alterations as potential cancer biomarkers in practice for individual tumor types, the main problems of the observed uncertainties must be considered in future studies. These include methodical harmonization concerning sample collection, processing, and analysis with the traceability of measurement results as well as the realization of well-designed prospective studies based on power analysis and sample size calculations.
Collapse
Affiliation(s)
- Klaus Jung
- Department of Urology, Research Division, University Hospital Charité, Schumannstr. 20/21, 10117 Berlin, Germany.
| | | | | |
Collapse
|