1
|
Jeddi F, Faghfuri E, Mehranfar S, Soozangar N. The common bisulfite-conversion-based techniques to analyze DNA methylation in human cancers. Cancer Cell Int 2024; 24:240. [PMID: 38982390 PMCID: PMC11234524 DOI: 10.1186/s12935-024-03405-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 06/11/2024] [Indexed: 07/11/2024] Open
Abstract
DNA methylation is an important molecular modification that plays a key role in the expression of cancer genes. Evaluation of epigenetic changes, hypomethylation and hypermethylation, in specific genes are applied for cancer diagnosis. Numerous studies have concentrated on describing DNA methylation patterns as biomarkers for cancer diagnosis monitoring and predicting response to cancer therapy. Various techniques for detecting DNA methylation status in cancers are based on sodium bisulfite treatment. According to the application of these methods in research and clinical studies, they have a number of advantages and disadvantages. The current review highlights sodium bisulfite treatment-based techniques, as well as, the advantages, drawbacks, and applications of these methods in the evaluation of human cancers.
Collapse
Affiliation(s)
- Farhad Jeddi
- Zoonoses Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
- Department of Genetics and Pathology, School of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Elnaz Faghfuri
- Digestive Diseases Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Sahar Mehranfar
- Department of Genetics and Immunology, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Narges Soozangar
- Zoonoses Research Center, Ardabil University of Medical Sciences, Ardabil, Iran.
- Digestive Diseases Research Center, Ardabil University of Medical Sciences, Ardabil, Iran.
| |
Collapse
|
2
|
Yadav S, Meena S, Kalwan G, Jain PK. DNA methylation: an emerging paradigm of gene regulation under drought stress in plants. Mol Biol Rep 2024; 51:311. [PMID: 38372841 DOI: 10.1007/s11033-024-09243-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 01/11/2024] [Indexed: 02/20/2024]
Abstract
Drought is an enormous threat to global crop production. In order to ensure food security for the burgeoning population, we must develop drought tolerant crop varieties. This necessitates the identification of drought-responsive genes and understanding the mechanisms involved in their regulation. DNA methylation is a widely studied mechanism of epigenetic regulation of gene expression, which is known to play vital role in conferring tolerance to various biotic and abiotic stress factors. The recent advances in next-generation sequencing (NGS) technologies, has allowed unprecedented access to genome-wide methylation marks, with single base resolution. The most important roles of DNA methylation have been studied in terms of gene body methylation (gbM), which is associated with regulation of both transcript abundance and its stability. The availability of mutants for the various genes encoding enzymes involved in methylation of DNA has allowed ascertainment of the biological significance of methylation. Even though a vast number of reports have emerged in the recent past, where both genome-wide methylation landscape and locus specific changes in DNA methylation have been studied, a conclusive picture with regards to the biological role of DNA methylation is still lacking. Compounding this, is the lack of sufficient evidence supporting the heritability of these epigenetic changes. Amongst the various epigenetic variations, the DNA methylation changes are observed to be the most stable. This review describes the drought-induced changes in DNA methylation identified across different plant species. We also briefly describe the stress memory contributed by these changes. The identification of heritable, drought-induced methylation marks would broaden the scope of crop improvement in the future.
Collapse
Affiliation(s)
- Sheel Yadav
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
- PG School, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - Shashi Meena
- PG School, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Gopal Kalwan
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
- PG School, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - P K Jain
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India.
| |
Collapse
|
3
|
Yokoyama S, Matsuo K, Tanimoto A. Methylation-Specific Electrophoresis. Methods Mol Biol 2024; 2763:259-268. [PMID: 38347417 DOI: 10.1007/978-1-0716-3670-1_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
Methylation of CpG sites in the promoter region of genomic DNA is an important epigenetic modification that plays a critical role in gene regulation, particularly in gene silencing. Epigenetic abnormalities, along with genetic alterations, are implicated in carcinogenesis and cancer progression. Numerous studies have investigated the role of epigenetics in cancer using various tools to assess DNA methylation. However, conventional analysis methods for DNA methylation require a large amount of DNA but lack higher sensitivity, making them unsuitable for analysis of samples with high heterogeneity, such as tumor tissues. In this study, we introduce a novel electrophoresis method named "methylation-specific electrophoresis (MSE)," which utilizes a denaturing gradient acrylamide gel. We demonstrate the applicability of the MSE method for DNA methylation analysis of the mucin gene as an example.
Collapse
Affiliation(s)
- Seiya Yokoyama
- Department of Pathology, Kagoshima University Graduate school of Medical and Dental Sciences, Kagoshima, Japan.
| | - Kei Matsuo
- Department of Pathology, Kagoshima University Graduate school of Medical and Dental Sciences, Kagoshima, Japan
| | - Akihide Tanimoto
- Department of Pathology, Kagoshima University Graduate school of Medical and Dental Sciences, Kagoshima, Japan
| |
Collapse
|
4
|
Current Advances in DNA Methylation Analysis Methods. BIOMED RESEARCH INTERNATIONAL 2021; 2021:8827516. [PMID: 33824878 PMCID: PMC8007345 DOI: 10.1155/2021/8827516] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 02/04/2021] [Accepted: 03/01/2021] [Indexed: 12/18/2022]
Abstract
DNA methylation is one of the epigenetic changes, which plays a major role in regulating gene expression and, thus, many biological processes and diseases. There are several methods for determining the methylation of DNA samples. However, selecting the most appropriate method for answering biological questions appears to be a challenging task. The primary methods in DNA methylation focused on identifying the state of methylation of the examined genes and determining the total amount of 5-methyl cytosine. The study of DNA methylation at a large scale of genomic levels became possible following the use of microarray hybridization technology. The new generation of sequencing platforms now allows the preparation of genomic maps of DNA methylation at the single-open level. This review includes the majority of methods available to date, introducing the most widely used methods, the bisulfite treatment, biological identification, and chemical cutting along with their advantages and disadvantages. The techniques are then scrutinized according to their robustness, high throughput capabilities, and cost.
Collapse
|
5
|
Yokoyama S, Hamada T, Higashi M, Matsuo K, Maemura K, Kurahara H, Horinouchi M, Hiraki T, Sugimoto T, Akahane T, Yonezawa S, Kornmann M, Batra SK, Hollingsworth MA, Tanimoto A. Predicted Prognosis of Patients with Pancreatic Cancer by Machine Learning. Clin Cancer Res 2020; 26:2411-2421. [PMID: 31992588 DOI: 10.1158/1078-0432.ccr-19-1247] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 08/20/2019] [Accepted: 01/23/2020] [Indexed: 12/30/2022]
Abstract
PURPOSE Pancreatic cancer remains a disease of high mortality despite advanced diagnostic techniques. Mucins (MUC) play crucial roles in carcinogenesis and tumor invasion in pancreatic cancers. MUC1 and MUC4 expression are related to the aggressive behavior of human neoplasms and a poor patient outcome. In contrast, MUC2 is a tumor suppressor, and we have previously reported that MUC2 is a favorable prognostic factor in pancreatic neoplasia. This study investigates whether the methylation status of three mucin genes from postoperative tissue specimens from patients with pancreatic neoplasms could serve as a predictive biomarker for outcome after surgery. EXPERIMENTAL DESIGN We evaluated the methylation status of MUC1, MUC2, and MUC4 promoter regions in pancreatic tissue samples from 191 patients with various pancreatic lesions using methylation-specific electrophoresis. Then, integrating these results and clinicopathologic features, we used support vector machine-, neural network-, and multinomial-based methods to develop a prognostic classifier. RESULTS Significant differences were identified between the positive- and negative-prediction classifiers of patients in 5-year overall survival (OS) in the cross-validation test. Multivariate analysis revealed that these prognostic classifiers were independent prognostic factors analyzed by not only neoplastic tissues but also nonneoplastic tissues. These classifiers had higher predictive accuracy for OS than tumor size, lymph node metastasis, distant metastasis, and age and can complement the prognostic value of the TNM staging system. CONCLUSIONS Analysis of epigenetic changes in mucin genes may be of diagnostic utility and one of the prognostic predictors for patients with pancreatic ductal adenocarcinoma.
Collapse
Affiliation(s)
- Seiya Yokoyama
- Department of Pathology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Taiji Hamada
- Department of Pathology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Michiyo Higashi
- Department of Pathology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan.
| | - Kei Matsuo
- Department of Pathology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Kosei Maemura
- Center for the Research of Advanced Diagnosis and Therapy of Cancer, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan.,Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima, Japan
| | - Hiroshi Kurahara
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima, Japan
| | - Michiko Horinouchi
- Department of Pathology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Tsubasa Hiraki
- Department of Pathology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Tomoyuki Sugimoto
- Graduate School of Science and Engineering (Science), Kagoshima University, Kagoshima, Japan
| | - Toshiaki Akahane
- Department of Pathology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Suguru Yonezawa
- Department of Pathology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Marko Kornmann
- Department of General and Visceral Surgery, University of Ulm, Ulm, Germany
| | - Surinder K Batra
- Department of Biochemistry and Molecular Biology, Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska
| | - Michael A Hollingsworth
- Fred and Pamela Buffet Cancer Center, Eppley Institute for Research in Cancer, University of Nebraska Medical Center, Omaha, Nebraska
| | - Akihide Tanimoto
- Department of Pathology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| |
Collapse
|
6
|
Fujita K, Hashimoto M. Separation-free single-base extension assay with fluorescence resonance energy transfer for rapid and convenient determination of DNA methylation status at specific cytosine and guanine dinucleotide sites. Electrophoresis 2018; 40:281-288. [PMID: 30280389 DOI: 10.1002/elps.201800144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 09/15/2018] [Accepted: 09/29/2018] [Indexed: 11/08/2022]
Abstract
A separation-free single-base extension (SBE) assay utilizing fluorescence resonance energy transfer (FRET) was developed for rapid and convenient interrogation of DNA methylation status at specific cytosine and guanine dinucleotide sites. In this assay, the SBE was performed in a tube using an allele-specific oligonucleotide primer (i.e., extension primer) labeled with Cy3 as a FRET donor fluorophore at the 5'-end, a nucleotide terminator (dideoxynucleotide triphosphate) labeled with Cy5 as a FRET acceptor, a PCR amplicon derived from bisulfite-converted genomic DNA, and a DNA polymerase. A single base-extended primer (i.e., SBE product) that was 5'-Cy3- and 3'-Cy5-tagged was formed by incorporation of the Cy5-labeled terminator into the 3'-end of the extension primer, but only if the terminator added was complementary to the target nucleotide. The resulting SBE product brought the Cy3 donor and the Cy5 acceptor into close proximity. Illumination of the Cy3 donor resulted in successful FRET and excitation of the Cy5 acceptor, generating fluorescence emission from the acceptor. The capacity of the developed assay to discriminate as low as 10% methylation from a mixture of methylated and unmethylated DNA was demonstrated at multiple cytosine and guanine dinucleotide sites.
Collapse
Affiliation(s)
- Keisuke Fujita
- Department of Chemical Engineering and Materials Science, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto, Japan
| | - Masahiko Hashimoto
- Department of Chemical Engineering and Materials Science, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto, Japan
| |
Collapse
|
7
|
Huang Y, Wei L, Sun AM, Li B, Sun CJ, Liang WB, Liu QY, Yu XQ, He JY, Qin Y. Application of multiplex methylated-specific PCR with capillary electrophoresis to explore prognostic value of TSGs hypermethylation for hepatocellular carcinoma. J Clin Lab Anal 2018. [PMID: 29516551 DOI: 10.1002/jcla.22430] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is a malignant tumor that severely threatens human health. To date, early detection for HCC patients is particularly significant due to their poor survival rates even after liver resection. METHODS Therefore, an efficient and sensitive detection method for monitoring liver cancer, multiplex methylation-specific PCR (MSP) coupled with capillary electrophoresis, is developed. RESULTS Simulations demonstrated that the methylation status of RASSF1A, p16, SFRP1, and ELF could be detected even when DNA equaled or exceeded 12.5 ng simultaneously. Also, its accuracy for methylation detection outweighed polyacrylamide gel electrophoresis (87.5%) and agarose electrophoresis (84.3%), reaching 92.1%. Subsequently, we implemented multiplex MSP with capillary electrophoresis to investigate methylation status of the four tumor suppressor genes in tissue specimens and explore the prognostic value for HCC patients. As the data suggested, multivariate cox regression analysis revealed that the recurrence-free survival of 46 patients was greatly associated with portal vein tumor thrombus (PVTT) and p16 methylation and receiver operating characteristic (ROC) curves demonstrated that the predictive range of portal vein tumor thrombus (PVTT) combined with p16 hypermethylation was more sensitive than that of either PVTT or p16 hypermethylation alone with regard to disease recurrence in patients with HCC, which could be testified as a valuable biomarker in Clinical application. CONCLUSION Multiplex MSP coupled with capillary electrophoresis has an excellent prospect of clinical application for monitoring early liver cancer and screening valuable biomarkers for prognosis of HCC patients.
Collapse
Affiliation(s)
- Yuan Huang
- Department of Biochemistry and Molecular Biology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Ling Wei
- Department of Biochemistry and Molecular Biology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Ai-Min Sun
- Analytical & testing center, Sichuan University, Chengdu, China
| | - Bo Li
- Division of Liver Transplantation, Department of Liver Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Cheng-Jun Sun
- West China School of Public Health, Sichuan University, Chengdu, China
| | - Wei-Bo Liang
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, China
| | - Qiu-Ying Liu
- Department of Biochemistry and Molecular Biology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Xiao-Qin Yu
- Department of Biochemistry and Molecular Biology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Jing-Yang He
- Department of Biochemistry and Molecular Biology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Yang Qin
- Department of Biochemistry and Molecular Biology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China.,Sichuan University, "985 project -Science and technology innovation platform for novel drug development", Chengdu, China
| |
Collapse
|
8
|
Yokoyama S, Higashi M, Kitamoto S, Oeldorf M, Knippschild U, Kornmann M, Maemura K, Kurahara H, Wiest E, Hamada T, Kitazono I, Goto Y, Tasaki T, Hiraki T, Hatanaka K, Mataki Y, Taguchi H, Hashimoto S, Batra SK, Tanimoto A, Yonezawa S, Hollingsworth MA. Aberrant methylation of MUC1 and MUC4 promoters are potential prognostic biomarkers for pancreatic ductal adenocarcinomas. Oncotarget 2018; 7:42553-42565. [PMID: 27283771 PMCID: PMC5173155 DOI: 10.18632/oncotarget.9924] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 05/01/2016] [Indexed: 01/14/2023] Open
Abstract
Pancreatic cancer is still a disease of high mortality despite availability of diagnostic techniques. Mucins (MUC) play crucial roles in carcinogenesis and tumor invasion in pancreatic neoplasms. MUC1 and MUC4 are high molecular weight transmembrane mucins. These are overexpressed in many carcinomas, and high expression of these molecules is a risk factor associated with poor prognosis. We evaluated the methylation status of MUC1 and MUC4 promoter regions in pancreatic tissue samples from 169 patients with various pancreatic lesions by the methylation specific electrophoresis (MSE) method. These results were compared with expression of MUC1 and MUC4, several DNA methylation/demethylation factors (e.g. ten-eleven translocation or TET, and activation-induced cytidine deaminase or AID) and CAIX (carbonic anhydrase IX, as a hypoxia biomarker). These results were also analyzed with clinicopathological features including time of overall survival of PDAC patients. We show that the DNA methylation status of the promoters of MUC1 and MUC4 in pancreatic tissue correlates with the expression of MUC1 and MUC4 mRNA. In addition, the expression of several DNA methylation/demethylation factors show a significant correlation with MUC1 and MUC4 methylation status. Furthermore, CAIX expression significantly correlates with the expression of MUC1 and MUC4. Interestingly, our results indicate that low methylation of MUC1 and/or MUC4 promoters correlates with decreased overall survival. This is the first report to show a relationship between MUC1 and/or MUC4 methylation status and prognosis. Analysis of epigenetic changes in mucin genes may be of diagnostic utility and one of the prognostic predictors for patients with PDAC.
Collapse
Affiliation(s)
- Seiya Yokoyama
- Department of Pathology, Research Field in Medicine and Health Sciences, Medical and Dental Sciences Area, Research and Education Assembly, Kagoshima University, Kagoshima, Japan.,Center for the Research of Advanced Diagnosis and Therapy of Cancer, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan.,Eppley Institute for Research in Cancer, Fred and Pamela Buffet Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Michiyo Higashi
- Department of Pathology, Research Field in Medicine and Health Sciences, Medical and Dental Sciences Area, Research and Education Assembly, Kagoshima University, Kagoshima, Japan.,Center for the Research of Advanced Diagnosis and Therapy of Cancer, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Sho Kitamoto
- Department of Pathology, Research Field in Medicine and Health Sciences, Medical and Dental Sciences Area, Research and Education Assembly, Kagoshima University, Kagoshima, Japan
| | - Monika Oeldorf
- Department of General and Visceral Surgery, University of Ulm, Ulm, Germany
| | - Uwe Knippschild
- Department of General and Visceral Surgery, University of Ulm, Ulm, Germany
| | - Marko Kornmann
- Department of General and Visceral Surgery, University of Ulm, Ulm, Germany
| | - Kosei Maemura
- Center for the Research of Advanced Diagnosis and Therapy of Cancer, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan.,Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima, Japan
| | - Hiroshi Kurahara
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima, Japan
| | - Edwin Wiest
- Eppley Institute for Research in Cancer, Fred and Pamela Buffet Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Tomofumi Hamada
- Department of Oral Surgery, Kagoshima University Medical and Dental Hospital, Kagoshima, Japan
| | - Ikumi Kitazono
- Department of Pathology, Research Field in Medicine and Health Sciences, Medical and Dental Sciences Area, Research and Education Assembly, Kagoshima University, Kagoshima, Japan
| | - Yuko Goto
- Department of Pathology, Research Field in Medicine and Health Sciences, Medical and Dental Sciences Area, Research and Education Assembly, Kagoshima University, Kagoshima, Japan
| | - Takashi Tasaki
- Department of Pathology, Research Field in Medicine and Health Sciences, Medical and Dental Sciences Area, Research and Education Assembly, Kagoshima University, Kagoshima, Japan
| | - Tsubasa Hiraki
- Department of Pathology, Research Field in Medicine and Health Sciences, Medical and Dental Sciences Area, Research and Education Assembly, Kagoshima University, Kagoshima, Japan
| | - Kazuhito Hatanaka
- Department of Pathology, Research Field in Medicine and Health Sciences, Medical and Dental Sciences Area, Research and Education Assembly, Kagoshima University, Kagoshima, Japan
| | - Yuko Mataki
- Department of Pathology, Research Field in Medicine and Health Sciences, Medical and Dental Sciences Area, Research and Education Assembly, Kagoshima University, Kagoshima, Japan
| | - Hiroki Taguchi
- Department of Digestive and Life-Style Related Diseases, Human and Environmental Sciences, Health Research, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Shinichi Hashimoto
- Department of Digestive and Life-Style Related Diseases, Human and Environmental Sciences, Health Research, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Surinder K Batra
- Department of Biochemistry and Molecular Biology, Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
| | - Akihide Tanimoto
- Department of Pathology, Research Field in Medicine and Health Sciences, Medical and Dental Sciences Area, Research and Education Assembly, Kagoshima University, Kagoshima, Japan
| | - Suguru Yonezawa
- Department of Pathology, Research Field in Medicine and Health Sciences, Medical and Dental Sciences Area, Research and Education Assembly, Kagoshima University, Kagoshima, Japan
| | - Michael A Hollingsworth
- Eppley Institute for Research in Cancer, Fred and Pamela Buffet Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| |
Collapse
|
9
|
Yokoyama S, Higashi M, Tsutsumida H, Wakimoto J, Hamada T, Wiest E, Matsuo K, Kitazono I, Goto Y, Guo X, Hamada T, Yamada S, Hiraki T, Yonezawa S, Batra SK, Hollingsworth MA, Tanimoto A. TET1-mediated DNA hypomethylation regulates the expression of MUC4 in lung cancer. Genes Cancer 2017; 8:517-527. [PMID: 28680536 PMCID: PMC5489649 DOI: 10.18632/genesandcancer.139] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Lung cancer remains a disease of high mortality, despite advanced diagnostic techniques. Mucins (MUC) play crucial roles in carcinogenesis and tumor invasion in lung neoplasms. Our immunohistochemistry (IHC) studies have shown that high MUC4 expression correlates with a poor outcome. We have also shown that the expression of several mucin genes in cancer cell lines is regulated by DNA methylation. We evaluated the expression level of MUC4, mRNA and several DNA hypomethylation factors in lung tissue samples from 33 patients with various lung lesions. The results indicated that the DNA methylation status of MUC4 matched the expression level of mRNA. In addition, the TET1 (Ten-Eleven Translocation) mRNA showed a significant correlation with the status of DNA methylation of MUC4. Furthermore, the treatment of a lung cancer cell line with TET1 siRNA caused a reduction in MUC4 mRNA expression. Thus, we suggest that TET1 mediated DNA hypomethylation plays a key role in the expression of MUC4. This is the first report that TET1 mediated DNA hypomethylation regulates the expression of MUC4 in lung cancer. The analysis of these epigenetic changes may be useful for diagnosing carcinogenic risk.
Collapse
Affiliation(s)
- Seiya Yokoyama
- Department of Pathology, Research Field in Medicine and Health Sciences, Medical and Dental Sciences Area, Research and Education Assembly, Kagoshima University, Sakuragoaka, Japan.,Center for the Research of Advanced Diagnosis and Therapy of Cancer, Graduate School of Medical and Dental Sciences, Kagoshima University, Japan.,Eppley Institute for Research in Cancer, Fred and Pamela Buffet Cancer Center, University of Nebraska Medical Center, NE, USA
| | - Michiyo Higashi
- Department of Pathology, Research Field in Medicine and Health Sciences, Medical and Dental Sciences Area, Research and Education Assembly, Kagoshima University, Sakuragoaka, Japan.,Center for the Research of Advanced Diagnosis and Therapy of Cancer, Graduate School of Medical and Dental Sciences, Kagoshima University, Japan
| | - Hideaki Tsutsumida
- Department of Pathology, Research Field in Medicine and Health Sciences, Medical and Dental Sciences Area, Research and Education Assembly, Kagoshima University, Sakuragoaka, Japan
| | - Jouji Wakimoto
- Department of Respiratory Medicine, Minami-kyushu National Hospital, Aira, Japan
| | - Tomofumi Hamada
- Department of Oral Surgery, Kagoshima University Medical and Dental Hospital, Sakuragoaka, Japan
| | - Edwin Wiest
- Eppley Institute for Research in Cancer, Fred and Pamela Buffet Cancer Center, University of Nebraska Medical Center, NE, USA
| | - Kei Matsuo
- Department of Pathology, Research Field in Medicine and Health Sciences, Medical and Dental Sciences Area, Research and Education Assembly, Kagoshima University, Sakuragoaka, Japan
| | - Ikumi Kitazono
- Department of Pathology, Research Field in Medicine and Health Sciences, Medical and Dental Sciences Area, Research and Education Assembly, Kagoshima University, Sakuragoaka, Japan
| | - Yuko Goto
- Department of Pathology, Research Field in Medicine and Health Sciences, Medical and Dental Sciences Area, Research and Education Assembly, Kagoshima University, Sakuragoaka, Japan
| | - Xin Guo
- Department of Pathology, Research Field in Medicine and Health Sciences, Medical and Dental Sciences Area, Research and Education Assembly, Kagoshima University, Sakuragoaka, Japan
| | - Taiji Hamada
- Department of Pathology, Research Field in Medicine and Health Sciences, Medical and Dental Sciences Area, Research and Education Assembly, Kagoshima University, Sakuragoaka, Japan
| | - Sohsuke Yamada
- Department of Pathology, Research Field in Medicine and Health Sciences, Medical and Dental Sciences Area, Research and Education Assembly, Kagoshima University, Sakuragoaka, Japan
| | - Tsubasa Hiraki
- Department of Pathology, Research Field in Medicine and Health Sciences, Medical and Dental Sciences Area, Research and Education Assembly, Kagoshima University, Sakuragoaka, Japan
| | - Suguru Yonezawa
- Department of Pathology, Research Field in Medicine and Health Sciences, Medical and Dental Sciences Area, Research and Education Assembly, Kagoshima University, Sakuragoaka, Japan
| | - Surinder K Batra
- Department of Biochemistry and Molecular Biology, Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, NE, USA
| | - Michael A Hollingsworth
- Eppley Institute for Research in Cancer, Fred and Pamela Buffet Cancer Center, University of Nebraska Medical Center, NE, USA
| | - Akihide Tanimoto
- Department of Pathology, Research Field in Medicine and Health Sciences, Medical and Dental Sciences Area, Research and Education Assembly, Kagoshima University, Sakuragoaka, Japan
| |
Collapse
|
10
|
Daneshpour M, moradi LS, Izadi P, Omidfar K. Femtomolar level detection of RASSF1A tumor suppressor gene methylation by electrochemical nano-genosensor based on Fe 3 O 4 /TMC/Au nanocomposite and PT-modified electrode. Biosens Bioelectron 2016; 77:1095-103. [DOI: 10.1016/j.bios.2015.11.007] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 10/20/2015] [Accepted: 11/02/2015] [Indexed: 10/22/2022]
|
11
|
Kurdyukov S, Bullock M. DNA Methylation Analysis: Choosing the Right Method. BIOLOGY 2016; 5:biology5010003. [PMID: 26751487 PMCID: PMC4810160 DOI: 10.3390/biology5010003] [Citation(s) in RCA: 343] [Impact Index Per Article: 42.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 12/16/2015] [Accepted: 12/22/2015] [Indexed: 01/10/2023]
Abstract
In the burgeoning field of epigenetics, there are several methods available to determine the methylation status of DNA samples. However, choosing the method that is best suited to answering a particular biological question still proves to be a difficult task. This review aims to provide biologists, particularly those new to the field of epigenetics, with a simple algorithm to help guide them in the selection of the most appropriate assay to meet their research needs. First of all, we have separated all methods into two categories: those that are used for: (1) the discovery of unknown epigenetic changes; and (2) the assessment of DNA methylation within particular regulatory regions/genes of interest. The techniques are then scrutinized and ranked according to their robustness, high throughput capabilities and cost. This review includes the majority of methods available to date, but with a particular focus on commercially available kits or other simple and straightforward solutions that have proven to be useful.
Collapse
Affiliation(s)
- Sergey Kurdyukov
- Genomics Core facility, Kolling Institute of Medical Research, University of Sydney, Sydney 2065, Australia.
| | - Martyn Bullock
- Cancer Genetics Laboratory, Kolling Institute of Medical Research, University of Sydney, Sydney 2065, Australia.
| |
Collapse
|
12
|
Yokoyama S, Kitamoto S, Higashi M, Goto Y, Hara T, Ikebe D, Yamaguchi T, Arisaka Y, Niihara T, Nishimata H, Tanaka S, Takaori K, Batra SK, Yonezawa S. Diagnosis of pancreatic neoplasms using a novel method of DNA methylation analysis of mucin expression in pancreatic juice. PLoS One 2014; 9:e93760. [PMID: 24714692 PMCID: PMC3979708 DOI: 10.1371/journal.pone.0093760] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 03/06/2014] [Indexed: 12/19/2022] Open
Abstract
Mucins (MUC) play crucial roles in carcinogenesis and tumor invasion in pancreatic ductal adenocarcinoma (PDAC) and intraductal papillary mucinous neoplasms (IPMNs). Our immunohistochemistry (IHC) studies have shown a consensus position on mucin expression profiles in pancreatic neoplasms as follows: MUC1-positive but MUC2-negative expression in PDACs; MUC1-negative but MUC2-positive expression in intestinal-type IPMNs (dangerous type); MUC1-negative and MUC2-negative expression in gastric-type IPMNs (safe type); High MUC4 expression in PDAC patients with a poor outcome; and MUC4-positive expression in intestinal-type IPMNs. We also showed that three mucin genes (MUC1, MUC2 and MUC4) expression in cancer cell line was regulated by DNA methylation. We have developed a novel 'methylation-specific electrophoresis (MSE)' method to analyze the DNA methylation status of mucin genes by high sensitivity and resolution. By using the MSE method, we evaluated pancreatic juice samples from 45 patients with various pancreatic lesions. The results were compared with final diagnosis of the pancreatic lesions including IHC of mucin expression in the paired pancreatic tissues. The results indicated that the DNA methylation status of MUC1, MUC2 and MUC4 in pancreatic juice matched with the mucin expression in tissue. Analyses of the DNA methylation status of MUC1, MUC2 and MUC4 were useful for differential diagnosis of human pancreatic neoplasms, with specificity and sensitivity of 87% and 80% for PDAC; 100% and 88% for intestinal-type IPMN; and 88% and 77% for gastric-type IPMN, respectively. In conclusion, MSE analysis of human pancreatic juice may provide useful information for selection of treatment for pancreatic neoplasms.
Collapse
Affiliation(s)
- Seiya Yokoyama
- Department of Human Pathology, Field of Oncology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Kagoshima, Japan
| | - Sho Kitamoto
- Department of Human Pathology, Field of Oncology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Kagoshima, Japan
| | - Michiyo Higashi
- Department of Human Pathology, Field of Oncology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Kagoshima, Japan
| | - Yuko Goto
- Department of Human Pathology, Field of Oncology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Kagoshima, Japan
| | - Taro Hara
- Division of Endoscopy, Chiba Cancer Center, Chiba, Chiba, Japan
| | - Dai Ikebe
- Division of Surgical Pathology, Chiba Cancer Center, Chiba, Chiba, Japan
| | - Taketo Yamaguchi
- Division of Gastroenterology, Chiba Cancer Center, Chiba, Chiba, Japan
| | - Yoshifumi Arisaka
- Department of Gastroenterology, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Toru Niihara
- Division of Gastroenterology, Nanpuh Hospital, Kagoshima, Kagoshima, Japan
| | - Hiroto Nishimata
- Division of Gastroenterology, Nanpuh Hospital, Kagoshima, Kagoshima, Japan
| | - Sadao Tanaka
- Division of Surgical Pathology, Nanpuh Hospital, Kagoshima, Kagoshima, Japan
| | - Kyoichi Takaori
- Division of Hepato-Biliary-Pancreatic Surgery and Transplantation, Department of Surgery, Kyoto University Graduate School of Medicine, Kyoto, Kyoto, Japan
| | - Surinder K. Batra
- Department of Biochemistry and Molecular Biology, Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Suguru Yonezawa
- Department of Human Pathology, Field of Oncology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Kagoshima, Japan
| |
Collapse
|
13
|
Guang W, Czinn SJ, Blanchard TG, Kim KC, Lillehoj EP. Genetic regulation of MUC1 expression by Helicobacter pylori in gastric cancer cells. Biochem Biophys Res Commun 2014; 445:145-50. [PMID: 24491543 DOI: 10.1016/j.bbrc.2014.01.142] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 01/26/2014] [Indexed: 02/08/2023]
Abstract
Helicobacter pylori infection of the stomach is associated with the development of gastritis, peptic ulcers, and gastric adenocarcinomas, but the mechanisms are unknown. MUC1 is aberrantly overexpressed by more than 50% of stomach cancers, but its role in carcinogenesis remains to be defined. The current studies were undertaken to identify the genetic mechanisms regulating H. pylori-dependent MUC1 expression by gastric epithelial cells. Treatment of AGS cells with H. pylori increased MUC1 mRNA and protein levels, and augmented MUC1 gene promoter activity, compared with untreated cells. H. pylori increased binding of STAT3 and MUC1 itself to the MUC1 gene promoter within a region containing a STAT3 binding site, and decreased CpG methylation of the MUC1 promoter proximal to the STAT3 binding site, compared with untreated cells. These results suggest that H. pylori upregulates MUC1 expression in gastric cancer cells through STAT3 and CpG hypomethylation.
Collapse
Affiliation(s)
- Wei Guang
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Steven J Czinn
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Thomas G Blanchard
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD, United States
| | - K Chul Kim
- Department of Physiology, Temple University School of Medicine, Philadelphia, PA, United States
| | - Erik P Lillehoj
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD, United States.
| |
Collapse
|
14
|
Hinton J, Callan R, Bodine C, Glasgow W, Brower S, Jiang SW, Li J. Potential epigenetic biomarkers for the diagnosis and prognosis of pancreatic ductal adenocarcinomas. Expert Rev Mol Diagn 2014; 13:431-43. [DOI: 10.1586/erm.13.38] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
15
|
Expression of MUC4 mucin is observed mainly in the intestinal type of intraductal papillary mucinous neoplasm of the pancreas. Pancreas 2013; 42:1120-8. [PMID: 23921963 PMCID: PMC3779537 DOI: 10.1097/mpa.0b013e3182965915] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
OBJECTIVES This study aimed to examine expression profile of MUC4 in intraductal papillary mucinous neoplasm of the pancreas (IPMN). METHODS We performed immunohistochemistry (IHC) of MUC4 in 142 IPMNs, with evaluation of the specificity of 2 anti-MUC4 monoclonal antibodies, 8G7 and 1G8, in cancer cell lines. RESULTS Monoclonal antibody 8G7 showed a clear immunoreactivity, whereas MAb 1G8 did not show any immunoreactivity, in the Western blotting and IHC for human pancreatic carcinoma cell lines expressing MUC4 messenger RNA. However, IHC signals detected by both monoclonal antibodies were observed in the tissue specimens. The expression rates of MUC4/8G7 detected by MAb 8G7 and MUC4/1G8 detected by MAb 1G8 in the intestinal-type IPMNs were significantly higher than those in the gastric-type IPMNs. In the intestinal-type IPMNs, MUC4/8G7 was expressed mainly in the cytoplasm of the neoplastic cells, whereas MUC4/1G8 was expressed mainly at the cell apexes. Even in the gastric-type IPMNs with rare MUC4 expression in the low-grade dysplasia, both MUC4 expression rates increased when dysplasia advanced. CONCLUSIONS A significantly higher expression of MUC4 in intestinal-type IPMNs than in gastric-type IPMNs will be one of the biomarkers to discriminate between the intestinal-type IPMNs with high malignancy potential from gastric-type IPMNs with low malignancy potential.
Collapse
|
16
|
Sipos F, Mũzes G, Patai AV, Fũri I, Péterfia B, Hollósi P, Molnár B, Tulassay Z. Genome-wide screening for understanding the role of DNA methylation in colorectal cancer. Epigenomics 2013; 5:569-81. [PMID: 24059802 DOI: 10.2217/epi.13.52] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
DNA methylation analysis methods have undergone an impressive revolution over the past 15 years. Regarding colorectal cancer (CRC), the localization and distribution of several differently methylated genes have been determined by genome-wide DNA methylation assays. These genes do not just influence the pathogenesis of CRC, but can be used further as diagnostic or prognostic markers. Moreover, the identified four DNA methylation-based subgroups of CRC have important clinical and therapeutic merit. Since genome-wide DNA methylation analyzes result in a large amount of data, there is a need for complex bioinformatic and pathway analysis. Future challenges in epigenetic alterations of CRC include the demand for comprehensive identification and experimental validation of gene abnormalities. By introduction of genome-wide DNA methylation profiling into clinical practice not only the patients' risk stratification but development of targeted therapies will also be possible.
Collapse
Affiliation(s)
- Ferenc Sipos
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | | | | | | | | | | | | | | |
Collapse
|
17
|
Kitamoto S, Yokoyama S, Higashi M, Yamada N, Matsubara S, Takao S, Batra SK, Yonezawa S. Expression of MUC17 is regulated by HIF1α-mediated hypoxic responses and requires a methylation-free hypoxia responsible element in pancreatic cancer. PLoS One 2012; 7:e44108. [PMID: 22970168 PMCID: PMC3438193 DOI: 10.1371/journal.pone.0044108] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Accepted: 07/30/2012] [Indexed: 12/13/2022] Open
Abstract
MUC17 is a type 1 membrane-bound glycoprotein that is mainly expressed in the digestive tract. Recent studies have demonstrated that the aberrant overexpression of MUC17 is correlated with the malignant potential of pancreatic ductal adenocarcinomas (PDACs); however, the exact regulatory mechanism of MUC17 expression has yet to be identified. Here, we provide the first report of the MUC17 regulatory mechanism under hypoxia, an essential feature of the tumor microenvironment and a driving force of cancer progression. Our data revealed that MUC17 was significantly induced by hypoxic stimulation through a hypoxia-inducible factor 1α (HIF1α)-dependent pathway in some pancreatic cancer cells (e.g., AsPC1), whereas other pancreatic cancer cells (e.g., BxPC3) exhibited little response to hypoxia. Interestingly, these low-responsive cells have highly methylated CpG motifs within the hypoxia responsive element (HRE, 5'-RCGTG-3'), a binding site for HIF1α. Thus, we investigated the demethylation effects of CpG at HRE on the hypoxic induction of MUC17. Treatment of low-responsive cells with 5-aza-2'-deoxycytidine followed by additional hypoxic incubation resulted in the restoration of hypoxic MUC17 induction. Furthermore, DNA methylation of HRE in pancreatic tissues from patients with PDACs showed higher hypomethylation status as compared to those from non-cancerous tissues, and hypomethylation was also correlated with MUC17 mRNA expression. Taken together, these findings suggested that the HIF1α-mediated hypoxic signal pathway contributes to MUC17 expression, and DNA methylation of HRE could be a determinant of the hypoxic inducibility of MUC17 in pancreatic cancer cells.
Collapse
Affiliation(s)
- Sho Kitamoto
- Department of Human Pathology, Field of Oncology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Seiya Yokoyama
- Department of Human Pathology, Field of Oncology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Michiyo Higashi
- Department of Human Pathology, Field of Oncology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Norishige Yamada
- Department of Human Pathology, Field of Oncology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | | | - Sonshin Takao
- Frontier Science Research Center, Kagoshima University, Kagoshima, Japan
| | - Surinder K. Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Suguru Yonezawa
- Department of Human Pathology, Field of Oncology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
- * E-mail:
| |
Collapse
|
18
|
Joshi K, Bhat S, Deshpande P, Sule M, Satyamoorthy K. Epigenetics mechanisms and degenerative diseases. ACTA ACUST UNITED AC 2012. [DOI: 10.4236/ojgen.2012.24023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|