1
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Kanai Y. Molecular pathological approach to cancer epigenomics and its clinical application. Pathol Int 2024; 74:167-186. [PMID: 38482965 DOI: 10.1111/pin.13418] [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] [Received: 01/09/2024] [Revised: 02/15/2024] [Accepted: 02/26/2024] [Indexed: 04/11/2024]
Abstract
Careful microscopic observation of histopathological specimens, accumulation of large numbers of high-quality tissue specimens, and analysis of molecular pathology in relation to morphological features are considered to yield realistic data on the nature of multistage carcinogenesis. Since the morphological hallmark of cancer is disruption of the normal histological structure maintained through cell-cell adhesiveness and cellular polarity, attempts have been made to investigate abnormalities of the cadherin-catenin cell adhesion system in human cancer cells. It has been shown that the CDH1 tumor suppressor gene encoding E-cadherin is silenced by DNA methylation, suggesting that a "double hit" involving DNA methylation and loss of heterozygosity leads to carcinogenesis. Therefore, in the 1990s, we focused on epigenomic mechanisms, which until then had not received much attention. In chronic hepatitis and liver cirrhosis associated with hepatitis virus infection, DNA methylation abnormalities were found to occur frequently, being one of the earliest indications that such abnormalities are present even in precancerous tissue. Aberrant expression and splicing of DNA methyltransferases, such as DNMT1 and DNMT3B, was found to underlie the mechanism of DNA methylation alterations in various organs. The CpG island methylator phenotype in renal cell carcinoma was identified for the first time, and its therapeutic targets were identified by multilayer omics analysis. Furthermore, the DNA methylation profile of nonalcoholic steatohepatitis (NASH)-related hepatocellular carcinoma was clarified in groundbreaking studies. Since then, we have developed diagnostic markers for carcinogenesis risk in NASH patients and noninvasive diagnostic markers for upper urinary tract cancer, as well as developing a new high-performance liquid chromatography-based diagnostic system for DNA methylation diagnosis. Research on the cancer epigenome has revealed that DNA methylation alterations occur from the precancerous stage as a result of exposure to carcinogenic factors such as inflammation, smoking, and viral infections, and continuously contribute to multistage carcinogenesis through aberrant expression of cancer-related genes and genomic instability. DNA methylation alterations at the precancerous stages are inherited by or strengthened in cancers themselves and determine the clinicopathological aggressiveness of cancers as well as patient outcome. DNA methylation alterations have applications as biomarkers, and are expected to contribute to diagnosis, as well as preventive and preemptive medicine.
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Affiliation(s)
- Yae Kanai
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
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2
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Watanabe A, Miyake K, Yamada Y, Sunamura EI, Yotani T, Kagami K, Kasai S, Tamai M, Harama D, Akahane K, Goi K, Sakaguchi K, Goto H, Kitahara S, Inukai T. Utility of ASNS gene methylation evaluated with the HPLC method as a pharmacogenomic biomarker to predict asparaginase sensitivity in BCP-ALL. Epigenetics 2023; 18:2268814. [PMID: 37839090 PMCID: PMC10578186 DOI: 10.1080/15592294.2023.2268814] [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] [Received: 06/12/2023] [Accepted: 10/01/2023] [Indexed: 10/17/2023] Open
Abstract
Asparaginase is an important agent for the treatment of acute lymphoblastic leukaemia (ALL), but it is occasionally associated with severe adverse events. Thus, for safer and more efficacious therapy, a clinical biomarker predicting asparaginase sensitivity is highly anticipated. Asparaginase depletes serum asparagine by deaminating asparagine into aspartic acid, and ALL cells are thought to be sensitive to asparaginase due to reduced asparagine synthetase (ASNS) activity. We have recently shown that allele-specific methylation of the ASNS gene is highly involved in asparaginase sensitivity in B-precursor ALL (BCP-ALL) by using next-generation sequence (NGS) analysis of bisulphite PCR products of the genomic DNA. Here, we sought to confirm the utility of methylation status of the ASNS gene evaluated with high-performance liquid chromatography (HPLC) analysis of bisulphite PCR products for future clinical applications. In the global methylation status of 23 CpG sites at the boundary region of promoter and exon 1 of the ASNS gene, a strong positive correlation was confirmed between the mean percent methylation evaluated with the HPLC method and that with the NGS method in 79 BCP-ALL cell lines (R2 = 0.85, p = 1.3 × 10-33) and in 63 BCP-ALL clinical samples (R2 = 0.84, p = 5.0 × 10-26). Moreover, methylation status of the ASNS gene evaluated with the HPLC method was significantly associated with in vitro asparaginase sensitivities as well as gene and protein expression levels of ASNS. These observations indicated that the ASNS gene methylation status evaluated with the HPLC method is a reliable biomarker for predicting the asparaginase sensitivity of BCP-ALL.
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Affiliation(s)
- Atsushi Watanabe
- Department of Pediatrics Environmental Medicine, School of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Kunio Miyake
- Department of Epidemiology and Environmental Medicine, School of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Yuriko Yamada
- Tsukuba Research Institute, Research and Development, Sekisui Medical Co, Ltd, Ibaraki, Japan
| | - Ei-Ichiro Sunamura
- Tsukuba Research Institute, Research and Development, Sekisui Medical Co, Ltd, Ibaraki, Japan
| | - Takuya Yotani
- Instrument System Development Center, Research and Development, Sekisui Medical Co, Ltd, Ibaraki, Japan
| | - Keiko Kagami
- Department of Pediatrics Environmental Medicine, School of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Shin Kasai
- Department of Pediatrics Environmental Medicine, School of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Minori Tamai
- Department of Pediatrics Environmental Medicine, School of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Daisuke Harama
- Department of Pediatrics Environmental Medicine, School of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Koshi Akahane
- Department of Pediatrics Environmental Medicine, School of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Kumiko Goi
- Department of Pediatrics Environmental Medicine, School of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Kimiyoshi Sakaguchi
- Department of Pediatrics, Hamamatsu University School of Medicine, Shizuoka, Japan
| | - Hiroaki Goto
- Hematology/Oncology, Kanagawa Children’s Medical Center, Kanagawa, Japan
| | - Shinichiro Kitahara
- R&D Management Department, Research and Development, Sekisui Medical Co, Ltd, Tokyo, Japan
| | - Takeshi Inukai
- Department of Pediatrics Environmental Medicine, School of Medicine, University of Yamanashi, Yamanashi, Japan
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3
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Lu D, Chen Y, Ke L, Wu W, Yuan L, Feng S, Huang Z, Lu Y, Wang J. Machine learning-assisted global DNA methylation fingerprint analysis for differentiating early-stage lung cancer from benign lung diseases. Biosens Bioelectron 2023; 235:115235. [PMID: 37178511 DOI: 10.1016/j.bios.2023.115235] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/10/2023] [Accepted: 03/14/2023] [Indexed: 03/17/2023]
Abstract
DNA methylation plays a critical role in the development of human tumors. However, routine characterization of DNA methylation can be time-consuming and labor-intensive. We herein describe a sensitive, simple surface-enhanced Raman spectroscopy (SERS) approach for identifying the DNA methylation pattern in early-stage lung cancer (LC) patients. By comparing SERS spectra of methylated DNA bases or sequences with their counterparts, we identified a reliable spectral marker of cytosine methylation. To move toward clinical applications, we applied our SERS strategy to detect the methylation patterns of genomic DNA (gDNA) extracted from cell line models as well as formalin-fixed paraffin-embedded tissues of early-stage LC and benign lung diseases (BLD) patients. In a clinical cohort of 106 individuals, our results showed distinct methylation patterns in gDNA between early-stage LC (n = 65) and BLD patients (n = 41), suggesting cancer-induced DNA methylation alterations. Combined with partial least square discriminant analysis, early-stage LC and BLD patients were differentiated with an area under the curve (AUC) value of 0.85. We believe that the SERS profiling of DNA methylation alterations, together with machine learning could potentially offer a promising new route toward the early detection of LC.
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Kuramoto J, Arai E, Fujimoto M, Tian Y, Yamada Y, Yotani T, Makiuchi S, Tsuda N, Ojima H, Fukai M, Seki Y, Kasama K, Funahashi N, Udagawa H, Nammo T, Yasuda K, Taketomi A, Kanto T, Kanai Y. Quantification of DNA methylation for carcinogenic risk estimation in patients with non-alcoholic steatohepatitis. Clin Epigenetics 2022; 14:168. [PMID: 36471401 PMCID: PMC9724255 DOI: 10.1186/s13148-022-01379-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 11/16/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND In recent years, non-alcoholic steatohepatitis (NASH) has become the main cause of hepatocellular carcinoma (HCC). As a means of improving the treatment of NASH-related HCCs based on early detection, this study investigated the feasibility of carcinogenic risk estimation in patients with NASH. RESULTS Normal liver tissue (NLT), non-cancerous liver tissue showing histological findings compatible with non-alcoholic fatty liver from patients without HCC (NAFL-O), non-cancerous liver tissue showing NASH from patients without HCC (NASH-O), non-cancerous liver tissue showing non-alcoholic fatty liver from patients with HCC (NAFL-W), non-cancerous liver tissue showing NASH from patients with HCC (NASH-W) and NASH-related HCC were analyzed. An initial cohort of 171 tissue samples and a validation cohort of 55 tissue samples were used. Genome-wide DNA methylation screening using the Infinium HumanMethylation450 BeadChip and DNA methylation quantification using high-performance liquid chromatography (HPLC) with a newly developed anion-exchange column were performed. Based on the Infinium assay, 4050 CpG sites showed alterations of DNA methylation in NASH-W samples relative to NLT samples. Such alterations at the precancerous NASH stage were inherited by or strengthened in HCC samples. Receiver operating characteristic curve analysis identified 415 CpG sites discriminating NASH-W from NLT samples with area under the curve values of more than 0.95. Among them, we focused on 21 CpG sites showing more than 85% specificity, even for discrimination of NASH-W from NASH-O samples. The DNA methylation status of these 21 CpG sites was able to predict the coincidence of HCC independently from histopathological findings such as ballooning and fibrosis stage. The methylation status of 5 candidate marker CpG sites was assessed using a HPLC-based system, and for 3 of them sufficient sensitivity and specificity were successfully validated in the validation cohort. By combining these 3 CpG sites including the ZC3H3 gene, NAFL-W and NASH-W samples from which HCCs had already arisen were confirmed to show carcinogenic risk with 95% sensitivity in the validation cohort. CONCLUSIONS After a further prospective validation study using a larger cohort, carcinogenic risk estimation in liver biopsy specimens of patients with NASH may become clinically applicable using this HPLC-based system for quantification of DNA methylation.
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Affiliation(s)
- Junko Kuramoto
- grid.26091.3c0000 0004 1936 9959Department of Pathology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582 Japan
| | - Eri Arai
- grid.26091.3c0000 0004 1936 9959Department of Pathology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582 Japan
| | - Mao Fujimoto
- grid.26091.3c0000 0004 1936 9959Department of Pathology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582 Japan
| | - Ying Tian
- grid.26091.3c0000 0004 1936 9959Department of Pathology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582 Japan
| | - Yuriko Yamada
- grid.471315.50000 0004 1770 184XTsukuba Research Institute, Research and Development Division, Sekisui Medical Co., Ltd., Ryugasaki, 301-0852 Japan
| | - Takuya Yotani
- grid.471315.50000 0004 1770 184XTsukuba Research Institute, Research and Development Division, Sekisui Medical Co., Ltd., Ryugasaki, 301-0852 Japan
| | - Satomi Makiuchi
- grid.26091.3c0000 0004 1936 9959Department of Pathology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582 Japan
| | - Noboru Tsuda
- grid.26091.3c0000 0004 1936 9959Department of Pathology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582 Japan
| | - Hidenori Ojima
- grid.26091.3c0000 0004 1936 9959Department of Pathology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582 Japan
| | - Moto Fukai
- grid.39158.360000 0001 2173 7691Department of Gastroenterological Surgery I, Graduate School of Medicine, Hokkaido University, Sapporo, 060-8638 Japan
| | - Yosuke Seki
- grid.505804.c0000 0004 1775 1986Weight Loss and Metabolic Surgery Center, Yotsuya Medical Cube, Tokyo, 102-0084 Japan
| | - Kazunori Kasama
- grid.505804.c0000 0004 1775 1986Weight Loss and Metabolic Surgery Center, Yotsuya Medical Cube, Tokyo, 102-0084 Japan
| | - Nobuaki Funahashi
- grid.32197.3e0000 0001 2179 2105Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501 Japan
| | - Haruhide Udagawa
- grid.411205.30000 0000 9340 2869Department of Biochemistry, Kyorin University School of Medicine, Tokyo, 181-8611 Japan
| | - Takao Nammo
- grid.136593.b0000 0004 0373 3971Department of Metabolic Medicine and Department of Diabetes Care Medicine, Graduate School of Medicine, Osaka University, Suita, 565-0871 Japan
| | - Kazuki Yasuda
- grid.411205.30000 0000 9340 2869Department of Diabetes, Endocrinology and Metabolism, Kyorin University School of Medicine, Tokyo, 181-8611 Japan ,grid.45203.300000 0004 0489 0290Diabetes Research Center, National Center for Global Health and Medicine, Tokyo, 162-8655 Japan
| | - Akinobu Taketomi
- grid.39158.360000 0001 2173 7691Department of Gastroenterological Surgery I, Graduate School of Medicine, Hokkaido University, Sapporo, 060-8638 Japan
| | - Tatsuya Kanto
- grid.45203.300000 0004 0489 0290The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Ichikawa, 272-8516 Japan
| | - Yae Kanai
- grid.26091.3c0000 0004 1936 9959Department of Pathology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582 Japan
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Hirano T, Arai E, Fujimoto M, Nakayama Y, Tian Y, Ito N, Makabe T, Yamagami W, Susumu N, Aoki D, Kanai Y. Prognostication of early-onset endometrioid endometrial cancer based on genome-wide DNA methylation profiles. J Gynecol Oncol 2022; 33:e74. [PMID: 36047377 DOI: 10.3802/jgo.2022.33.e74] [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: 01/05/2022] [Revised: 07/01/2022] [Accepted: 07/10/2022] [Indexed: 11/30/2022] Open
Abstract
OBJECTIVE The aim of this study was to establish criteria that would indicate whether fertility preservation therapy would likely be safe for patients aged 40 years or less with endometrioid endometrial cancer based on their DNA methylation profile. METHODS Forty-nine fresh-frozen tissue samples from patients with endometrial cancer from an initial cohort and 31 formalin-fixed paraffin-embedded tissue samples from a second cohort were subjected to genome-wide DNA methylation analysis using the Infinium MethylationEPIC BeadChip. RESULTS Epigenomic clustering of early-onset endometrial cancer was correlated with the widely used recurrence risk classification. Genes showing differences in DNA methylation levels between the low-recurrence-risk category and intermediate- and high-risk categories were accumulated in pathways related to fibroblast growth factor and nuclear factor-κB signaling. DNA hypomethylation and overexpression of ZBTB38 were frequently observed in the low-risk category. Eight hundred thirty-one marker CpG probes showed area under the curve values of >0.7 on the receiver operating characteristic curve for discrimination of patients belonging to the low-risk category. By combining marker CpG sites, seven panels for placing patients into the low-risk category with 91.3% or more sensitivity and specificity in both the initial and second cohorts were established. CONCLUSIONS DNA methylation diagnostics criteria using up to 6 of 8 CpG sites for LPP, FOXO1, RNF4, EXOC6B, CCPG1, RREB1 and ZBTB38 may be applicable to recurrence risk estimation for patients aged 40 years or less with endometrial cancer, regardless of tumor cell content, even if formalin-fixed paraffin-embedded biopsy or curettage materials are used.
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Affiliation(s)
- Takuro Hirano
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan.,Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo, Japan
| | - Eri Arai
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan.
| | - Mao Fujimoto
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Yuji Nakayama
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Ying Tian
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Nanako Ito
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Takeshi Makabe
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan.,Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo, Japan
| | - Wataru Yamagami
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo, Japan
| | - Nobuyuki Susumu
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo, Japan.,Department of Obstetrics and Gynecology, International University of Health and Welfare School of Medicine, Chiba, Japan
| | - Daisuke Aoki
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo, Japan
| | - Yae Kanai
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
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Irfan J, Febrianto MR, Sharma A, Rose T, Mahmudzade Y, Di Giovanni S, Nagy I, Torres-Perez JV. DNA Methylation and Non-Coding RNAs during Tissue-Injury Associated Pain. Int J Mol Sci 2022; 23:ijms23020752. [PMID: 35054943 PMCID: PMC8775747 DOI: 10.3390/ijms23020752] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/04/2022] [Accepted: 01/07/2022] [Indexed: 02/01/2023] Open
Abstract
While about half of the population experience persistent pain associated with tissue damages during their lifetime, current symptom-based approaches often fail to reduce such pain to a satisfactory level. To provide better patient care, mechanism-based analgesic approaches must be developed, which necessitates a comprehensive understanding of the nociceptive mechanism leading to tissue injury-associated persistent pain. Epigenetic events leading the altered transcription in the nervous system are pivotal in the maintenance of pain in tissue injury. However, the mechanisms through which those events contribute to the persistence of pain are not fully understood. This review provides a summary and critical evaluation of two epigenetic mechanisms, DNA methylation and non-coding RNA expression, on transcriptional modulation in nociceptive pathways during the development of tissue injury-associated pain. We assess the pre-clinical data and their translational implication and evaluate the potential of controlling DNA methylation and non-coding RNA expression as novel analgesic approaches and/or biomarkers of persistent pain.
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Affiliation(s)
- Jahanzaib Irfan
- Nociception Group, Department of Surgery and Cancer, Division of Anaesthetics, Pain Medicine and Intensive Care, Chelsea and Westminster Hospital Campus, Imperial College London, 369 Fulham Road, London SW10 9FJ, UK; (J.I.); (M.R.F.); (A.S.); (T.R.); (Y.M.)
| | - Muhammad Rizki Febrianto
- Nociception Group, Department of Surgery and Cancer, Division of Anaesthetics, Pain Medicine and Intensive Care, Chelsea and Westminster Hospital Campus, Imperial College London, 369 Fulham Road, London SW10 9FJ, UK; (J.I.); (M.R.F.); (A.S.); (T.R.); (Y.M.)
| | - Anju Sharma
- Nociception Group, Department of Surgery and Cancer, Division of Anaesthetics, Pain Medicine and Intensive Care, Chelsea and Westminster Hospital Campus, Imperial College London, 369 Fulham Road, London SW10 9FJ, UK; (J.I.); (M.R.F.); (A.S.); (T.R.); (Y.M.)
| | - Thomas Rose
- Nociception Group, Department of Surgery and Cancer, Division of Anaesthetics, Pain Medicine and Intensive Care, Chelsea and Westminster Hospital Campus, Imperial College London, 369 Fulham Road, London SW10 9FJ, UK; (J.I.); (M.R.F.); (A.S.); (T.R.); (Y.M.)
| | - Yasamin Mahmudzade
- Nociception Group, Department of Surgery and Cancer, Division of Anaesthetics, Pain Medicine and Intensive Care, Chelsea and Westminster Hospital Campus, Imperial College London, 369 Fulham Road, London SW10 9FJ, UK; (J.I.); (M.R.F.); (A.S.); (T.R.); (Y.M.)
| | - Simone Di Giovanni
- Department of Brain Sciences, Division of Neuroscience, Imperial College London, E505, Burlington Danes, Du Cane Road, London W12 ONN, UK;
| | - Istvan Nagy
- Nociception Group, Department of Surgery and Cancer, Division of Anaesthetics, Pain Medicine and Intensive Care, Chelsea and Westminster Hospital Campus, Imperial College London, 369 Fulham Road, London SW10 9FJ, UK; (J.I.); (M.R.F.); (A.S.); (T.R.); (Y.M.)
- Correspondence: (I.N.); (J.V.T.-P.)
| | - Jose Vicente Torres-Perez
- Department of Brain Sciences, Dementia Research Institute, Imperial College London, 86 Wood Ln, London W12 0BZ, UK
- Departament de Biologia Cellular, Biologia Funcional i Antropologia Física, Facultat de Ciències Biològiques, Universitat de València, C/Dr. Moliner 50, 46100 Burjassot, Spain
- Correspondence: (I.N.); (J.V.T.-P.)
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Endo Y, Fujimoto M, Ito N, Takahashi Y, Kitago M, Gotoh M, Hiraoka N, Yoshida T, Kitagawa Y, Kanai Y, Arai E. Clinicopathological impacts of DNA methylation alterations on pancreatic ductal adenocarcinoma: prediction of early recurrence based on genome-wide DNA methylation profiling. J Cancer Res Clin Oncol 2021; 147:1341-1354. [PMID: 33635431 PMCID: PMC8021514 DOI: 10.1007/s00432-021-03541-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 01/19/2021] [Indexed: 12/21/2022]
Abstract
PURPOSE The present study was conducted to clarify the clinicopathological impacts of DNA methylation alterations on pancreatic ductal adenocarcinoma (PDAC). METHODS Genome-wide DNA methylation screening was performed using the Infinium HumanMethylation450 BeadChip, and DNA methylation quantification was verified using pyrosequencing. We analyzed fresh-frozen tissues from an initial cohort (17 samples of normal control pancreatic tissue [C] from 17 patients without PDAC, and 34 samples of non-cancerous pancreatic tissue [N] and 82 samples of cancerous tissue [T] both obtained from 82 PDAC patients) and formalin-fixed paraffin-embedded T samples from 34 patients in a validation cohort. RESULTS The DNA methylation profiles of N samples tended to differ from those of C samples, and 91,907 probes showed significant differences in DNA methylation levels between C and T samples. Epigenetic clustering of T samples was significantly correlated with a larger tumor diameter and early recurrence (ER), defined as relapse within 6 months after surgery. Three marker CpG sites, applicable to formalin-fixed paraffin-embedded surgically resected materials regardless of their tumor cell content, were identified for prediction of ER. The sensitivity and specificity for detection of patients belonging to the ER group using a panel combining these three marker CpG sites, including a CpG site in the CDK14 gene, were 81.8% and 71.7% and 88.9% and 70.4% in the initial and validation cohorts, respectively. CONCLUSION These findings indicate that DNA methylation alterations may have a clinicopathological impact on PDAC. Application of our criteria will ultimately allow prediction of ER after surgery to improve the outcome of PDAC patients.
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Affiliation(s)
- Yutaka Endo
- Department of Pathology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
- Department of Surgery, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Mao Fujimoto
- Department of Pathology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Nanako Ito
- Department of Pathology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Yoriko Takahashi
- Bioscience Department, Solution Knowledge Center, Mitsui Knowledge Industry Co., Ltd., Tokyo, 105-6215, Japan
| | - Minoru Kitago
- Department of Surgery, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Masahiro Gotoh
- Fundamental Innovative Oncology Core Center, National Cancer Center Research Institute, Tokyo, 104-0045, Japan
| | - Nobuyoshi Hiraoka
- Department of Pathology and Clinical Laboratory, National Cancer Center Hospital, Tokyo, 104-0045, Japan
| | - Teruhiko Yoshida
- Fundamental Innovative Oncology Core Center, National Cancer Center Research Institute, Tokyo, 104-0045, Japan
| | - Yuko Kitagawa
- Department of Surgery, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Yae Kanai
- Department of Pathology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Eri Arai
- Department of Pathology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan.
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Genome-wide DNA methylation analysis of breast cancer MCF-7 / Taxol cells with MeDIP-Seq. PLoS One 2020; 15:e0241515. [PMID: 33306680 PMCID: PMC7732127 DOI: 10.1371/journal.pone.0241515] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 09/16/2020] [Indexed: 11/19/2022] Open
Abstract
Breast cancer (BC) is the most frequently diagnosed tumor in women worldwide. Although the combination of surgery and Taxol chemotherapy can achieve a certain therapeutic effect, patients often develop drug-resistance, resulting in a poor prognosis. Therefore, it is significative to seek the molecular mechanism of chemotherapy resistance. Recent studies have found that abnormal epigenetic regulation in breast cells changes the expression of key genes, which can lead to the occurrence, development, and maintenance of cancer, even related to the development of drug-resistance. Therefore, in this study, we performed methylated DNA immunoprecipitation-sequencing (MeDIP-seq) to reveal the difference in methylation between breast cancer drug-resistant cells and sensitive cells. A total of 55076 differentially methylated genes (DMGs) were detected, including 21061 hypermethylated DMGs and 34015 hypomethylated DMGs. Moreover, Gene Ontology (GO) analysis and KEGG pathway analysis reveal the function and pathway of screening genes. These results indicate that DNA methylation may be involved in regulating the occurrence and development of breast cancer.
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9
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Hanihara M, Miyake K, Watanabe A, Yamada Y, Oishi N, Kawataki T, Inukai T, Kondo T, Kinouchi H. Assessment of MGMT methylation status using high-performance liquid chromatography in newly diagnosed glioblastoma. Clin Epigenetics 2020; 12:174. [PMID: 33203454 PMCID: PMC7672949 DOI: 10.1186/s13148-020-00968-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 11/03/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The utility of O6-methylguanine-DNA methyltransferase (MGMT) gene promoter methylation status as a prognostic marker in patients with glioblastoma (GBM) has been established. However, the number of CpG sites that must be methylated to cause transcriptional silencing remains unclear, and no significant consensus exists on the optimal method of assessing MGMT methylation. We developed a new high-performance liquid chromatography (HPLC) method that enables accurate analysis of DNA methylation levels using long PCR products. In the present study, we analyzed the MGMT methylation status of 28 isocitrate dehydrogenase-wild-type GBMs treated with temozolomide using ion-exchange HPLC and set the optimal cutoff values. RESULTS We designed three primers for separate regions (regions 1-3) that had 21 to 38 CpGs for PCR and validated the MGMT promoter methylation status using frozen samples. There was a strong correlation between HPLC and bisulfite sequencing results (R = 0.794). The optimal cutoff values for MGMT methylation in HPLC were determined to allow differentiation of patient prognosis by receiver operating characteristic curve analysis. The cutoff values were 34.15% for region 1, 8.84% for region 2, and 36.72% for region 3. Kaplan-Meyer curve analysis estimated that the most differentiated prognosis was enabled in the setting of 8.84% methylation of MGMT in region 2. Progression-free survival and overall survival were significantly longer for patients in this setting of region 2 methylation (p = 0.00365 and p = 0.00258, respectively). CONCLUSIONS The combination of our HPLC method and the original primer setting provides a new standard method for determination of MGMT methylation status in patients with GBM and is useful for refining MGMT-based drug selection.
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Affiliation(s)
- Mitsuto Hanihara
- Departments of Neurosurgery, University of Yamanashi, Chuo, Yamanashi, Japan
| | - Kunio Miyake
- Department of Health Sciences, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi, 409-3898, Japan.
| | - Atsushi Watanabe
- Department of Pediatrics, University of Yamanashi, Chuo, Yamanashi, Japan
| | - Yuriko Yamada
- Tsukuba Research Institute, Research and Development Division, Sekisui Medical Co., Ltd., Ryugasaki, Japan
| | - Naoki Oishi
- Department of Pathology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Chuo, Yamanashi, Japan
| | - Tomoyuki Kawataki
- Departments of Neurosurgery, University of Yamanashi, Chuo, Yamanashi, Japan
| | - Takeshi Inukai
- Tsukuba Research Institute, Research and Development Division, Sekisui Medical Co., Ltd., Ryugasaki, Japan
| | - Tetsuo Kondo
- Department of Pathology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Chuo, Yamanashi, Japan
| | - Hiroyuki Kinouchi
- Departments of Neurosurgery, University of Yamanashi, Chuo, Yamanashi, Japan
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10
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Sheng Q, Wang C, Li X, Qin H, Ye M, Xiong Y, Wang X, Li X, Lan M, Li J, Ke Y, Qing G, Liang X. Highly Efficient Separation of Methylated Peptides Utilizing Selective Complexation between Lysine and 18-Crown-6. Anal Chem 2020; 92:15663-15670. [PMID: 33169968 DOI: 10.1021/acs.analchem.0c04158] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Protein methylation is one of the most common and important post-translational modifications, and it plays vital roles in epigenetic regulation, signal transduction, and chromatin metabolism. However, due to the diversity of methylation forms, slight difference between methylated sites and nonmodified ones, and ultralow abundance, it is extraordinarily challenging to capture and separate methylated peptides from biological samples. Here, we introduce a simple and highly efficient method to separate methylated and nonmethylated peptides using 18-crown-6 as a mobile phase additive in high-performance liquid chromatography. Selective complexation between lysine and 18-crown-6 remarkably increases the retention of the peptides on a C18 stationary phase, leading to an excellent baseline separation between the lysine methylated and nonmethylated peptides. A possible binding mechanism is verified by nuclear magnetic resonance titration, biolayer interferometry technology, and quantum chemistry calculation. Through establishment of a simple enrichment methodology, a good selectivity is achieved and four methylated peptides with greatly improved signal-to-noise (S/N) ratios are successfully separated from a complex peptide sample containing 10-fold bovine serum albumin tryptic digests. By selecting rLys N as an enzyme to digest histone, methylation information in the histone could be well identified based on our enrichment method. This study will open an avenue and provide a novel insight for selective enrichment of lysine methylated peptides in post-translational modification proteomics.
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Affiliation(s)
- Qianying Sheng
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Cunli Wang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Xiaopei Li
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Hongqiang Qin
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Mingliang Ye
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Yuting Xiong
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Xue Wang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Xiuling Li
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Minbo Lan
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Junyan Li
- Engineering Research Center of Pharmaceutical Process Chemistry, Ministry of Education, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Yanxiong Ke
- Engineering Research Center of Pharmaceutical Process Chemistry, Ministry of Education, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Guangyan Qing
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Xinmiao Liang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China.,Engineering Research Center of Pharmaceutical Process Chemistry, Ministry of Education, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, P. R. China
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11
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Fujimoto M, Arai E, Tsumura K, Yotani T, Yamada Y, Takahashi Y, Maeshima AM, Fujimoto H, Yoshida T, Kanai Y. Establishment of diagnostic criteria for upper urinary tract urothelial carcinoma based on genome-wide DNA methylation analysis. Epigenetics 2020; 15:1289-1301. [PMID: 32498593 PMCID: PMC7678936 DOI: 10.1080/15592294.2020.1767374] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The aim of this study was to develop a less invasive and accurate diagnostic system for upper urinary tract urothelial carcinoma (UTUC) based on genome-wide DNA methylation profiling. Genome-wide DNA methylation screening was performed using the Infinium HumanMethylation450 BeadChip, and DNA methylation quantification was verified using pyrosequencing. We analysed 26 samples of normal control urothelial tissue (C), an initial cohort of 62 samples (31 samples of non-cancerous urothelium [N] from UTUC patients and 31 samples of the corresponding UTUCs), a validation cohort of 82 samples (41 N and 41 UTUC samples), and 14 samples of urinary bladder urothelial carcinoma (BUC). In the initial cohort, we identified 2,448 CpG sites showing significant differences in DNA methylation levels between both C and UTUC and N and UTUC, but not showing differences between C and N. Among these CpG sites, 10 were located within CpG islands or their shores and shelves included in genomic domains where DNA methylation levels are stably controlled, allowing discrimination of UTUC even from BUC. Receiver operating characteristic curve analysis for discrimination of UTUC from N in these 10 CpG and neighbouring sites (37 diagnostic panels in total) yielded area under the curve values of 0.959-1.000, with a sensitivity and specificity of 86.6-100% and 93.5-100%, respectively. The diagnostic impact was successfully confirmed in the validation cohort. Our criteria were useful for diagnosis of UTUC, regardless of its clinicopathological features. Application of our criteria to voided urine samples will ultimately allow non-invasive DNA methylation diagnosis of UTUC.
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Affiliation(s)
- Mao Fujimoto
- Department of Pathology, Keio University School of Medicine , Tokyo, Japan
| | - Eri Arai
- Department of Pathology, Keio University School of Medicine , Tokyo, Japan
| | - Koji Tsumura
- Department of Urology, Graduate School of Medicine, the University of Tokyo , Tokyo, Japan
| | - Takuya Yotani
- Tsukuba Research Institute, Research and Development Division, Sekisui Medical Co., Ltd ., Ryugasaki, Japan
| | - Yuriko Yamada
- Tsukuba Research Institute, Research and Development Division, Sekisui Medical Co., Ltd ., Ryugasaki, Japan
| | - Yoriko Takahashi
- Bioscience Department, Solution Knowledge Center, Mitsui Knowledge Industry Co., Ltd ., Tokyo, Japan
| | - Akiko Miyagi Maeshima
- Department of Pathology and Clinical Laboratories, National Cancer Center Hospital , Tokyo, Japan
| | - Hiroyuki Fujimoto
- Department of Urology, National Cancer Center Hospital , Tokyo, Japan
| | - Teruhiko Yoshida
- Fundamental Innovative Oncology Core Center, National Cancer Center Research Institute , Tokyo, Japan
| | - Yae Kanai
- Department of Pathology, Keio University School of Medicine , Tokyo, Japan
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12
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Tsumura K, Arai E, Tian Y, Shibuya A, Nishihara H, Yotani T, Yamada Y, Takahashi Y, Maeshima AM, Fujimoto H, Nakagawa T, Kume H, Homma Y, Yoshida T, Kanai Y. Establishment of permutation for cancer risk estimation in the urothelium based on genome-wide DNA methylation analysis. Carcinogenesis 2020; 40:1308-1319. [PMID: 31241739 DOI: 10.1093/carcin/bgz112] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 05/25/2019] [Accepted: 06/22/2019] [Indexed: 02/02/2023] Open
Abstract
The aim of this study was to establish permutation for cancer risk estimation in the urothelium. Twenty-six samples of normal control urothelium obtained from patients without urothelial carcinomas (C), 47 samples of non-cancerous urothelium without noticeable morphological changes obtained from patients with urothelial carcinomas (N), and 46 samples of the corresponding cancerous tissue (T) in the learning cohort and 64 N samples in the validation cohort, i.e. 183 tissue samples in total, were analyzed. Genome-wide DNA methylation analysis was performed using the Infinium HumanMethylation 450K BeadChip, and DNA methylation levels were verified using pyrosequencing and MassARRAY. Amplicon sequencing was performed using the GeneRead DNAseq Targeted Panels V2. Although N samples rarely showed genetic mutations or copy number alterations, they showed DNA methylation alterations at 2502 CpG sites compared to C samples, and such alterations were inherited by or strengthened in T samples, indicating that DNA methylation alterations may participate in field cancerization in the urothelium. Receiver operating characteristic curve analysis confirmed the feasibility of cancer risk estimation to identify urothelium at the precancerous stage by DNA methylation quantification. Cancer risk estimation permutation was established using a combination of two marker CpG loci on the HOXC4, TENM3 and TLR1 genes (sensitivity and specificity 96-100%). Among them, the diagnostic impact of 10 patterns of permutation was successfully validated in the validation cohort (sensitivity and specificity 94-98%). These data suggest that cancer risk estimation using procedures such as urine tests during health checkups might become applicable for clinical use.
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Affiliation(s)
- Koji Tsumura
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Eri Arai
- Department of Pathology, Keio University School of Medicine, Shinanomachi, Shinjuku-ku, Tokyo, Japan
| | - Ying Tian
- Department of Pathology, Keio University School of Medicine, Shinanomachi, Shinjuku-ku, Tokyo, Japan
| | - Ayako Shibuya
- Department of Pathology, Keio University School of Medicine, Shinanomachi, Shinjuku-ku, Tokyo, Japan
| | - Hiroshi Nishihara
- Genomics Unit, Keio Cancer Center, Keio University School of Medicine, Tokyo, Japan
| | - Takuya Yotani
- Tsukuba Research Institute, Research and Development Division, Sekisui Medical Co., Ltd, Ryugasaki, Japan
| | - Yuriko Yamada
- Tsukuba Research Institute, Research and Development Division, Sekisui Medical Co., Ltd, Ryugasaki, Japan
| | - Yoriko Takahashi
- Biomedical Department, Cloud Service Division, IT Infrastructure Services Unit, Mitsui Knowledge Industry Co., Ltd., Tokyo, Japan
| | - Akiko Miyagi Maeshima
- Department of Pathology and Clinical Laboratories, National Cancer Center Hospital, Tokyo, Japan
| | - Hiroyuki Fujimoto
- Department of Urology, National Cancer Center Hospital, Tokyo, Japan
| | - Tohru Nakagawa
- Department of Urology, Teikyo University School of Medicine, Tokyo, Japan
| | - Haruki Kume
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yukio Homma
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Teruhiko Yoshida
- Fundamental Innovative Oncology Core Center, National Cancer Center Research Institute, Tokyo, Japan
| | - Yae Kanai
- Department of Pathology, Keio University School of Medicine, Shinanomachi, Shinjuku-ku, Tokyo, Japan
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13
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Zhang S, Huang J, Lu J, Liu M, Li Y, Fang L, Huang H, Huang J, Mo F, Zheng J. A novel fluorescent biosensor based on dendritic DNA nanostructure in combination with ligase reaction for ultrasensitive detection of DNA methylation. J Nanobiotechnology 2019; 17:121. [PMID: 31812164 PMCID: PMC6898925 DOI: 10.1186/s12951-019-0552-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 11/25/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND DNA methylation detection is indispensable for the diagnosis and prognosis of various diseases including malignancies. Hence, it is crucial to develop a simple, sensitive, and specific detection strategy. METHODS A novel fluorescent biosensor was developed based on a simple dual signal amplification strategy using functional dendritic DNA nanostructure and signal-enriching polystyrene microbeads in combination with ligase detection reaction (LDR). Dendritic DNA self-assembled from Y-DNA and X-DNA through enzyme-free DNA catalysis of a hairpin structure, which was prevented from unwinding at high temperature by adding psoralen. Then dendritic DNA polymer labeled with fluorescent dye Cy5 was ligated with reporter probe into a conjugate. Avidin-labeled polystyrene microbeads were specifically bound to biotin-labeled capture probe, and hybridized with target sequence and dendritic DNA. LDR was triggered by adding Taq ligase. When methylated cytosine existed, the capture probe and reporter probe labeled with fluorescent dye perfectly matched the target sequence, forming a stable duplex to generate a fluorescence signal. However, after bisulfite treatment, unmethylated cytosine was converted into uracil, resulting in a single base mismatch. No fluorescence signal was detected due to the absence of duplex. RESULTS The obtained dendritic DNA polymer had a large volume. This method was time-saving and low-cost. Under the optimal experimental conditions using avidin-labeled polystyrene microbeads, the fluorescence signal was amplified more obviously, and DNA methylation was quantified ultrasensitively and selectively. The detection range of this sensor was 10-15 to 10-7 M, and the limit of detection reached as low as 0.4 fM. The constructed biosensor was also successfully used to analyze actual samples. CONCLUSION This strategy has ultrasensitivity and high specificity for DNA methylation quantification, without requiring complex processes such as PCR and enzymatic digestion, which is thus of great value in tumor diagnosis and biomedical research.
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Affiliation(s)
- Shu Zhang
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, China.,Department of Basic Clinical Laboratory Medicine, School of Clinical Laboratory Science, Guizhou Medical University, Guiyang, 550004, China.,Center for Clinical Laboratories, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Jian Huang
- Center for Clinical Laboratories, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Jingrun Lu
- Center for Clinical Laboratories, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Min Liu
- Center for Clinical Laboratories, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Yan Li
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, China
| | - Lichao Fang
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, China
| | - Hui Huang
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, China
| | - Jianjun Huang
- Department of Breast Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Fei Mo
- Department of Basic Clinical Laboratory Medicine, School of Clinical Laboratory Science, Guizhou Medical University, Guiyang, 550004, China. .,Center for Clinical Laboratories, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China.
| | - Junsong Zheng
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, China.
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14
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Wang Z, Hu S, Li F, Fan Q, Jia Y. Study of porphyrin-modified liquid exfoliated graphene field-effect transistors for evaluating DNA methylation degree. Analyst 2019; 144:4787-4794. [PMID: 31305809 DOI: 10.1039/c9an00993k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The applications of graphene field-effect transistors (FETs) for monitoring DNA hybridization have been widely accepted; however, for evaluating DNA methylation degree, an emerging requirement of epigenetic research, no work has been found due to the difficulties in detecting 5-methylcytosine (5mC) sites along the genomic sequence as well as counting their amount (NmC). Herein, to achieve this, a strategy for exploiting a liquid exfoliated graphene (LEG)-based FET (LEG-FET) as a sensing platform was proposed. First, LEG-FETs were prepared and activated by tetra-4-aminophenyl-porphyrin (TAPP) for anchoring single-strand DNAs (ssDNAs). Second, the 5mC sites in ssDNA were recognized by the specifically absorbed 5mC antibody (5mCab) and transduced to the changed currents (ΔIDS) by LEG-FET according to the integration of the methylation-immuno sensing principle and FET's working mechanism. Briefly, more 5mCab molecules could be captured by more 5mC sites, resulting in larger ΔIDS. The TAPP effects on LEG-FET were analyzed by SEM, Raman, AFM, and XPS characterizations as well as electronic measurements. The validity of this LEG-FET sensing platform for evaluating DNA methylation degree was proven step by step; this included the examinations of the synthesized ssDNAs with the known NmC and real ssDNA samples, whose methylation degrees were pre-determined by the gold-standard method, which is based on tedious bisulphite sequence operations and expensive mass spectrometry technology. Moreover, theoretical explanations were also provided for the sensing mechanism in the proposed DNA methylation analytical components. In conclusion, the positive and linear relations of IDS changing ratio vs. NmC as well as the detection limit of one 5mC site indicate that TAPP-modified LEG-FET can provide an alternative analytical tool to realize fast and economical DNA methylation evaluation.
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Affiliation(s)
- Zhongrong Wang
- College of Electronic Information and Optical Engineering, Nankai University, Tianjin, China.
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15
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Jia Y, Li F, Jia T, Wang Z. Meso-tetra(4-carboxyphenyl)porphine-Enhanced DNA Methylation Sensing Interface on a Light-Addressable Potentiometric Sensor. ACS OMEGA 2019; 4:12567-12574. [PMID: 31460377 PMCID: PMC6682126 DOI: 10.1021/acsomega.9b00980] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 07/12/2019] [Indexed: 05/05/2023]
Abstract
DNA methylation (DNAm) sensors are an emerging branch in the discipline of sensors. It is believed to be able to promote the next generation of epigenetics-based diagnostic technology. Differing from the traditional biochemical sensors that aimed at individual molecules, the challenge in DNAm sensors is how to determine the amount of 5-methylcytosine (5mC) in a continuous nucleotide sequence. Here, we report a comparative study about meso-tetra(4-carboxyphenyl)porphine (TCPP)-based DNAm sensing interfaces on a light-addressable potentiometric sensor (LAPS), depending on TCPP's postures that are flat in the π-conjugated TCPP layer on reduced-graphene-oxide-decorated LAPS (#1) and stand-up in the covalently anchored TCPP on glutaraldehyde (GA)-treated LAPS (#2), along with the blank one (only GA-treated LAPS, #3). These DNAm sensing interfaces are also distinct from the traditional biosensing interface on LAPS, that is: it is not functionalized by the sensing indicator (5mC antibody, in this case) but by the target nucleotide sequence. The surface characterization techniques such as Raman spectra, scanning electron microscopy, and X-ray photoelectron spectroscopy are conducted to prove the decorations, as well as the anchored nucleotides. It is found that, though all of them can detect as low as one 5mC in the target sequence, the enhanced DNAm sensitivity is obtained by #2, which is evidenced by the higher output-voltage changing ratio for the 5mC site of #2 than those of #1 and #3. Furthermore, the underlying causes for the improved sensitivity in #2 are proposed, according to the conformational and electronic properties of TCPP molecules. Conclusively, TCPP's synergetic function, including the molecular configuration and the activate (carboxyl) groups on its peripheral substituents, to improve the DNAm sensing interface on LAPS is investigated and demonstrated. This can shed light on a new approach for DNA methylation detection, with the merits of low cost, independence on bisulfite conversion, and polymerase chain reaction.
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16
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Chen W, Zhuang J, Wang PP, Jiang J, Lin C, Zeng P, Liang Y, Zhang X, Dai Y, Diao H. DNA methylation-based classification and identification of renal cell carcinoma prognosis-subgroups. Cancer Cell Int 2019; 19:185. [PMID: 31346320 PMCID: PMC6636124 DOI: 10.1186/s12935-019-0900-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 07/04/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Renal cell carcinoma (RCC) is the most common kidney cancer and includes several molecular and histological subtypes with different clinical characteristics. The combination of DNA methylation and gene expression data can improve the classification of tumor heterogeneity, by incorporating differences at the epigenetic level and clinical features. METHODS In this study, we identified the prognostic methylation and constructed specific prognosis-subgroups based on the DNA methylation spectrum of RCC from the TCGA database. RESULTS Significant differences in DNA methylation profiles among the seven subgroups were revealed by consistent clustering using 3389 CpGs that indicated that were significant differences in prognosis. The specific DNA methylation patterns reflected differentially in the clinical index, including TNM classification, pathological grade, clinical stage, and age. In addition, 437 CpGs corresponding to 477 genes of 151 samples were identified as specific hyper/hypomethylation sites for each specific subgroup. A total of 277 and 212 genes corresponding to DNA methylation at promoter sites were enriched in transcription factor of GKLF and RREB-1, respectively. Finally, Bayesian network classifier with specific methylation sites was constructed and was used to verify the test set of prognoses into DNA methylation subgroups, which was found to be consistent with the classification results of the train set. DNA methylation-based classification can be used to identify the distinct subtypes of renal cell carcinoma. CONCLUSIONS This study shows that DNA methylation-based classification is highly relevant for future diagnosis and treatment of renal cell carcinoma as it identifies the prognostic value of each epigenetic subtype.
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Affiliation(s)
- Wenbiao Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 Qing Chun Road, Hangzhou, China
| | - Jia Zhuang
- Department of Urinary Surgery, Puning People’s Hospital, Puning People’s Hospital Affiliated To Southern Medical University, 30 Liusha Avenue, Jieyang, Guangdong China
| | - Peizhong Peter Wang
- Division of Community Health and Humanities, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Newfoundland Canada
| | - Jingjing Jiang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 Qing Chun Road, Hangzhou, China
| | - Chenhong Lin
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 Qing Chun Road, Hangzhou, China
| | - Ping Zeng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 Qing Chun Road, Hangzhou, China
| | - Yan Liang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 Qing Chun Road, Hangzhou, China
| | - Xujun Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 Qing Chun Road, Hangzhou, China
| | - Yong Dai
- Clinical Medical Research Center, Shenzhen People’s Hospital, The Second Clinical Medical College of Jinan University, 1017 Dongmen North Road, Luohu District, Shenzhen, Guangdong China
| | - Hongyan Diao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 Qing Chun Road, Hangzhou, China
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17
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Yotani T, Yamada Y, Arai E, Tian Y, Gotoh M, Komiyama M, Fujimoto H, Sakamoto M, Kanai Y. Novel method for DNA methylation analysis using high-performance liquid chromatography and its clinical application. Cancer Sci 2018; 109:1690-1700. [PMID: 29520901 PMCID: PMC5980336 DOI: 10.1111/cas.13566] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 02/17/2018] [Accepted: 02/25/2018] [Indexed: 12/21/2022] Open
Abstract
The aim of this study was to develop a new methodology that is suitable for DNA methylation diagnostics and to demonstrate its clinical applicability. We developed a new anion-exchange column for high-performance liquid chromatography (HPLC) with electrostatic and hydrophobic properties. Both cytosine and thymine, corresponding to methylated and unmethylated cytosine after bisulfite modification, respectively, are captured by electrostatic interaction and then discriminated from each other by their hydrophobic interactions. The DNA methylation levels of synthetic DNA were quantified accurately and reproducibly within 10 minutes without time-consuming pretreatment of PCR products, and the measured values were unaffected by the distribution of methylated CpG within the synthetic DNA fragments. When the DNA methylation status of the FAM150A gene, a marker of the CpG island methylator phenotype specific to clear cell renal cell carcinoma (ccRCC), was examined in 98 patients with ccRCC, bulk specimens of tumorous tissue including cancer cells showing DNA methylation of the FAM150A gene were easily identifiable by simply viewing the differentiated chromatograms, even when the cancer cell content was low. Sixteen ccRCC showing DNA methylation more frequently exhibited clinicopathological parameters reflecting tumor aggressiveness (ie, a larger diameter, higher histological grade, vascular involvement, renal vein tumor thrombi, infiltrating growth, tumor necrosis, renal pelvis invasion and higher pathological TNM stage), and had significantly lower recurrence-free and overall survival rates. These data indicate that HPLC analysis using this newly developed anion-exchange column could be a powerful tool for DNA methylation diagnostics, including prognostication of patients with cancers, in a clinical setting.
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Affiliation(s)
- Takuya Yotani
- Department of PathologyKeio University School of MedicineTokyoJapan
- Tsukuba Research InstituteResearch and Development DivisionSekisui Medical Co., Ltd.RyugasakiJapan
- Division of Molecular PathologyNational Cancer Center Research InstituteTokyoJapan
| | - Yuriko Yamada
- Tsukuba Research InstituteResearch and Development DivisionSekisui Medical Co., Ltd.RyugasakiJapan
- Division of Molecular PathologyNational Cancer Center Research InstituteTokyoJapan
| | - Eri Arai
- Department of PathologyKeio University School of MedicineTokyoJapan
- Division of Molecular PathologyNational Cancer Center Research InstituteTokyoJapan
| | - Ying Tian
- Department of PathologyKeio University School of MedicineTokyoJapan
| | - Masahiro Gotoh
- Division of Molecular PathologyNational Cancer Center Research InstituteTokyoJapan
| | | | | | - Michiie Sakamoto
- Department of PathologyKeio University School of MedicineTokyoJapan
| | - Yae Kanai
- Department of PathologyKeio University School of MedicineTokyoJapan
- Division of Molecular PathologyNational Cancer Center Research InstituteTokyoJapan
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