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Tsumura K, Fujimoto M, Tian Y, Kawahara T, Fujimoto H, Maeshima AM, Nakagawa T, Kume H, Yoshida T, Kanai Y, Arai E. Aberrant cell adhesiveness due to DNA hypermethylation of KLF11 in papillary urothelial carcinomas. Exp Mol Pathol 2024; 137:104908. [PMID: 38824688 DOI: 10.1016/j.yexmp.2024.104908] [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: 12/12/2023] [Revised: 05/15/2024] [Accepted: 05/24/2024] [Indexed: 06/04/2024]
Abstract
PURPOSE The aim of this study was to clarify DNA methylation profiles determining the clinicopathological diversity of urothelial carcinomas. METHODS Genome-wide DNA methylation analysis was performed using the Infinium HumanMethylation450 BeadChip in 46 paired samples of non-cancerous urothelium (N) and corresponding cancerous tissue (T), and 26 samples of normal control urothelium obtained from patients without urothelial carcinomas (C). For genes of interest, correlation between DNA methylation and mRNA expression was examined using the Cancer Genome Atlas database. In addition, the role of a selected target for cancer-relevant endpoints was further examined in urothelial carcinoma cell lines. RESULTS The genes showing significant differences in DNA methylation levels between papillary carcinomas and more aggressive non-papillary (nodular) carcinomas were accumulated in signaling pathways participating in cell adhesion and cytoskeletal remodeling. Five hundred ninety-six methylation sites showed differences in DNA methylation levels between papillary and nodular carcinomas. Of those sites, that were located in CpG-islands around transcription start site, 5'-untranslated region or 1st exon, 16 genes exhibited inverse correlations between DNA methylation and mRNA expression levels. Among the latter, only the KLF11 gene showed papillary T sample-specific DNA hypermethylation in comparison to C and N samples. The DNA methylation levels of KLF11 were not significantly different between T samples and N samples or T samples and C samples for patients with papillo-nodular or nodular carcinomas. Knockdown experiments using the urothelial carcinoma cell lines HT1376 and 5637, which are considered models for papillary carcinoma, revealed that KLF11 participates in altering the adhesiveness of cells to laminin-coated dishes, although cell growth was not affected. CONCLUSION These data indicate that DNA hypermethylation of KLF11 may participate in the generation of papillary urothelial carcinomas through induction of aberrant cancer cell adhesion to the basement membrane.
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Affiliation(s)
- Koji Tsumura
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8654, Japan
| | - Mao Fujimoto
- Department of Pathology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Ying Tian
- Department of Pathology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Toru Kawahara
- Department of Pathology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Hiroyuki Fujimoto
- Department of Urology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Akiko Miyagi Maeshima
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Tohru Nakagawa
- Department of Urology, Teikyo University School of Medicine, Tokyo 173-8605, Japan
| | - Haruki Kume
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8654, Japan
| | - Teruhiko Yoshida
- Fundamental Innovative Oncology Core Center, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Yae Kanai
- Department of Pathology, Keio University School of Medicine, Tokyo 160-8582, Japan.
| | - Eri Arai
- Department of Pathology, Keio University School of Medicine, Tokyo 160-8582, Japan.
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Nishimura N, Miyake M, Miyamoto T, Shimizu T, Fujii T, Morizawa Y, Hori S, Gotoh D, Nakai Y, Torimoto K, Tanaka N, Fujimoto K. Routine Surveillance of Upper Urinary Tract Imaging for Diagnosing Upper Urinary Tract Urothelial Cancer Recurrence in Patients with Nonmuscle Invasive Bladder Cancer. Adv Urol 2024; 2024:5894288. [PMID: 38807901 PMCID: PMC11132829 DOI: 10.1155/2024/5894288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/18/2024] [Accepted: 04/26/2024] [Indexed: 05/30/2024] Open
Abstract
Background Although routine surveillance imaging to examine upper urinary tract urothelial cancer recurrence during follow-up of nonmuscle invasive bladder cancer is recommended, its necessity remains invalidated. A single-institute long-term follow-up cohort study to evaluate the clinical impact of routine surveillance imaging and identify risk factors for upper urinary tract urothelial cancer recurrence after nonmuscle invasive bladder cancer treatment was conducted. Methods and Materials A retrospective chart review of 864 patients with primary nonmuscle invasive bladder cancer who underwent initial transurethral resection of bladder tumor between 1980 and 2020 was conducted. The opportunities to diagnose its recurrence were examined. Moreover, oncological outcomes included upper urinary tract urothelial cancer recurrence-free survival and overall survival. Results Of 864 patients, 19 (2.2%) experienced upper urinary tract urothelial cancer recurrence. Among 19 patients, recurrence was detected through routine imaging in 12 (63.2%), cystoscopy in 2 (10.5%), urine cytology in 2 (10.5%), and presence of gross hematuria in 1 (5.3%). All patients had high- or highest-risk NMIBC at diagnosis of primary nonmuscle invasive bladder cancer. On multivariate Fine-Gray proportional regression analyses, a tumor size of ≥30 mm and carcinoma in situ were independently associated with short upper urinary tract urothelial cancer recurrence-free survival (P=0.040 and 0.0089, respectively). Conclusion Most patients experiencing upper urinary tract urothelial cancer recurrence were diagnosed by routine surveillance imaging, suggesting its clinical importance, especially for patients with nonmuscle invasive bladder cancer accompanied by a tumor size of ≥30 mm and carcinoma in situ.
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Affiliation(s)
- Nobutaka Nishimura
- Department of Urology, Nara Medical University, 840 Shijo-cho, Kashihara, Nara 634-8522, Japan
| | - Makito Miyake
- Department of Urology, Nara Medical University, 840 Shijo-cho, Kashihara, Nara 634-8522, Japan
| | - Tatsuki Miyamoto
- Department of Urology, Nara Medical University, 840 Shijo-cho, Kashihara, Nara 634-8522, Japan
| | - Takuto Shimizu
- Department of Urology, Nara Medical University, 840 Shijo-cho, Kashihara, Nara 634-8522, Japan
| | - Tomomi Fujii
- Department of Diagnostic Pathology, Nara Medical University, 840 Shijo-cho, Kashihara, Nara 634-8522, Japan
| | - Yosuke Morizawa
- Department of Urology, Nara Medical University, 840 Shijo-cho, Kashihara, Nara 634-8522, Japan
| | - Shunta Hori
- Department of Urology, Nara Medical University, 840 Shijo-cho, Kashihara, Nara 634-8522, Japan
| | - Daisuke Gotoh
- Department of Urology, Nara Medical University, 840 Shijo-cho, Kashihara, Nara 634-8522, Japan
| | - Yasushi Nakai
- Department of Urology, Nara Medical University, 840 Shijo-cho, Kashihara, Nara 634-8522, Japan
| | - Kazumasa Torimoto
- Department of Urology, Nara Medical University, 840 Shijo-cho, Kashihara, Nara 634-8522, Japan
| | - Nobumichi Tanaka
- Department of Urology, Nara Medical University, 840 Shijo-cho, Kashihara, Nara 634-8522, Japan
- Department of Prostate Brachytherapy, Nara Medical University, 840 Shijo-cho, Kashihara, Nara 634-8522, Japan
| | - Kiyohide Fujimoto
- Department of Urology, Nara Medical University, 840 Shijo-cho, Kashihara, Nara 634-8522, Japan
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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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Makiuchi S, Tian Y, Fujimoto M, Kuramoto J, Tsuda N, Ojima H, Gotoh M, Hiraoka N, Yoshida T, Kanai Y, Arai E. DNA methylation alterations of ADCY5, MICAL2, and PLEKHG2 during the developmental stage of cryptogenic hepatocellular carcinoma. Hepatol Res 2024; 54:284-299. [PMID: 37906571 DOI: 10.1111/hepr.13984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 10/22/2023] [Accepted: 10/27/2023] [Indexed: 11/02/2023]
Abstract
AIM The aim of this study was to clarify the significance of DNA methylation alterations of cryptogenic hepatocellular carcinomas (HCCs). METHODS Using the Infinium assay, we performed genome-wide DNA methylation analysis of 250 liver tissue samples, including noncancerous liver tissue (U-N) and corresponding cancerous tissue (U-T) from patients with cryptogenic HCC without a history of excessive alcohol use and hepatitis virus infection, and whose U-N samples showed no remarkable histological features (no microscopic evidence of simple steatosis, any form of hepatitis including nonalcoholic steatohepatitis, or liver cirrhosis). RESULTS We identified 3272 probes that showed significant differences of DNA methylation levels between U-N and normal liver tissue samples from patients without HCC, indicating that a distinct DNA methylation profile had already been established at the precancerous U-N stage. U-Ns have a DNA methylation profile differing from that of noncancerous liver tissue of patients with nonalcoholic steatohepatitis-related, viral hepatitis-related, and alcoholic liver disease-related HCCs. Such DNA methylation alterations in U-Ns were inherited by U-Ts. The U-Ns showed DNA methylation alteration of ADCY5, resulting in alteration of its mRNA expression, whereas noncancerous liver tissue of patients with nonalcoholic steatohepatitis-, viral hepatitis-, or alcoholic liver disease-related HCCs did not. DNA methylation levels of MICAL2 and PLEKHG2 in U-Ts were correlated with larger tumor diameter and portal vein involvement, respectively. CONCLUSIONS U-N-specific DNA hypermethylation of ADCY5 may have significance, even from the precancerous stage in liver showing no remarkable histological features. DNA hypomethylation of MICAL2 and PLEKHG2 may determine the clinicopathological features of cryptogenic HCC.
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Affiliation(s)
- Satomi Makiuchi
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Ying Tian
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Mao Fujimoto
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Junko Kuramoto
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Noboru Tsuda
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Hidenori Ojima
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Masahiro Gotoh
- Fundamental Innovative Oncology Core Center, National Cancer Center Research Institute, Tokyo, Japan
| | - Nobuyoshi Hiraoka
- Department of Diagnostic Pathology, 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
| | - Eri Arai
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
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5
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Lin Y, Lin L, Yang Y, Li M, Jiang X, Fu T, Long Y, Guo Q, He H, Chen Z, Du L, Liao G, Liao B, Huang J. DNA Methylation Architecture Provides Insight into the Pathogenesis of Upper Tract Urothelial Carcinoma: A Systematic Review and Meta-Analysis. Clin Genitourin Cancer 2023; 21:32-42. [PMID: 36376170 DOI: 10.1016/j.clgc.2022.10.008] [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: 03/22/2022] [Revised: 10/12/2022] [Accepted: 10/15/2022] [Indexed: 02/01/2023]
Abstract
PURPOSE Numerous studies suggested methylation modifications play an important role in upper tract urothelial carcinoma (UTUC), but few have depicted DNA methylation architecture on the pathological process of UTUC. We aimed to better understand the pathogenesis of UTUC and provide precision medicine references when managing UTUC patients. METHODS PubMed, Cochrane Library, EMBASE, and Scopus were searched for UTUC until December 31, 2020. Methodological quality assessment was conducted according to NIH recommendations. Meta-analysis was conducted to assess the prognostic effect of methylated genes. Kaplan-Meier survival analyses were performed to validate methylated genes and cytosine-phosphate-guanine (CpG) sites. RESULTS Eleven studies (3619 patients) were eligible to investigate 12 methylated genes and 10 CpGs. The quality of all the studies was fair to good. Meta-analysis found the pooled effect of eligible methylated genes had a low risk of tumor recurrence (HR = 0·67; 95% CI: 0·51-0·87; P = ·003), but a high risk of tumor progression (HR = 1·60; 95% CI: 1·17-2·18; P = ·003) and cancer-specific mortality (HR = 1·35; 95% CI: 1·06-1·72; P = ·01). For individual methylation status of GDF15, HSPA2, RASSF1A, TMEFF2, and VIM, the pooled effect of each gene was found pleiotropic on both diagnosis and prognosis. Survival analysis suggested higher methylation of SPARCL1 had a better disease-specific survival (P = ·048). CONCLUSION We combined meta-analysis and Kaplan-Meier survival analysis using the most updated evidence on the methylation of UTUC. Candidate biomarkers with essential diagnosis and prognosis function might provide precision medicine references for personalized therapies.
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Affiliation(s)
- Yifei Lin
- West China Hospital, Sichuan University, Chengdu, PR China
| | - Ling Lin
- Medical Device Regulatory Research and Evaluation Centre, West China Hospital, Sichuan University, Chengdu, PR China
| | - Yong Yang
- Medical Device Regulatory Research and Evaluation Centre, West China Hospital, Sichuan University, Chengdu, PR China
| | - Mei Li
- Medical Equipment Innovation Research Center, West China School of Medicine, Med+X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R.China
| | - Xin Jiang
- Medical Equipment Innovation Research Center, West China School of Medicine, Med+X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R.China
| | - Tingting Fu
- Medical Device Regulatory Research and Evaluation Centre, West China Hospital, Sichuan University, Chengdu, PR China; Medical Device Regulatory Research and Evaluation Center, Frontiers Science Center for Disease-related Molecular Network, West China Hospital/West China School of Medicine, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education,College of Life Sciences, Sichuan University, Chengdu, Sichuan, P.R.China
| | - Youlin Long
- Medical Device Regulatory Research and Evaluation Centre, West China Hospital, Sichuan University, Chengdu, PR China; Chinese Evidence-Based Medicine Centre, West China Hospital, Sichuan University, Chengdu, PR China
| | - Qiong Guo
- Medical Device Regulatory Research and Evaluation Centre, West China Hospital, Sichuan University, Chengdu, PR China
| | - He He
- Department of laboratory medicine, West China Hospital, Sichuan University, Chengdu, PR China
| | - Zhenglong Chen
- Medical Device Regulatory Research and Evaluation Centre, West China Hospital, Sichuan University, Chengdu, PR China
| | - Liang Du
- Medical Device Regulatory Research and Evaluation Centre, West China Hospital, Sichuan University, Chengdu, PR China
| | - Ga Liao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China
| | - Banghua Liao
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, Chengdu, PR China.
| | - Jin Huang
- Medical Device Regulatory Research and Evaluation Centre, West China Hospital, Sichuan University, Chengdu, PR China; Medical Equipment Innovation Research Center, West China School of Medicine, Med+X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R.China.
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6
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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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7
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DNA methylation status of the SPHK1 and LTB genes underlies the clinicopathological diversity of non-alcoholic steatohepatitis-related hepatocellular carcinomas. J Cancer Res Clin Oncol 2022:10.1007/s00432-022-04445-9. [DOI: 10.1007/s00432-022-04445-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/19/2022] [Indexed: 11/09/2022]
Abstract
Abstract
Purpose
This study was performed to identify the DNA methylation profiles underlying the clinicopathological diversity of non-alcoholic steatohepatitis (NASH)-related hepatocellular carcinomas (HCCs).
Methods
Genome-wide DNA methylation analysis of 88 liver tissue samples was performed using the Infinium assay.
Results
Principal component analysis revealed that distinct DNA methylation profiles differing from such profiles in normal control liver tissue had already been established in non-cancerous liver tissue showing NASH, which is considered to be a precancerous condition. Hierarchical clustering separated 26 NASH-related HCCs into Cluster I (n = 8) and Cluster II (n = 18). Such epigenetic clustering was significantly correlated with histopathological diversity, i.e. poorer tumor differentiation, tumor steatosis and development of a scirrhous HCC component. Significant differences in DNA methylation levels between the two clusters were accumulated in molecular pathways participating in cell adhesion and cytoskeletal remodeling, as well as cell proliferation and apoptosis. Among tumor-related genes characterizing Clusters I and II, differences in the levels of DNA methylation and mRNA expression for the SPHK1, INHBA, LTB and PDE3B genes were correlated with poorer tumor differentiation. 5-Aza-2′-deoxycytidine treatment of HCC cells revealed epigenetic regulation of the SPHK1 and LTB genes. Knockdown experiments showed that SPHK1 promotes cell proliferation, represses apoptosis and enhances migration, whereas LTB enhances migration of HCC cells. DNA hypomethylation resulting in increased expression of SPHK1 and LTB in poorly differentiated HCCs may underlie the aggressive phenotype of such HCCs.
Conclusion
These data indicate that DNA methylation profiles may determine the clinicopathological heterogeneity of NASH-related HCCs via alterations of tumor-related gene expression.
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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: 4] [Impact Index Per Article: 2.0] [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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9
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Molecular intricacies of upper tract urothelial carcinoma and their relevance for therapy considerations. Curr Opin Urol 2022; 32:48-53. [PMID: 34772864 DOI: 10.1097/mou.0000000000000943] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
PURPOSE OF REVIEW The aim of this study was to give an overview of molecular alterations in upper tract urothelial carcinomas (UTUCs) and to discuss them in the context of current and prospective systemic therapies. RECENT FINDINGS UTUCs not only share a similar molecular landscape with urothelial carcinoma of the bladder (UCB), but also have distinct molecular features that can have an impact on therapy selection. FGFR3 alterations occur with a significant higher frequency in UTUC, with up to 40% of tumours harbouring FGFR3 driver mutations compared with 20% in UCB. In addition, a substantial number of high-grade UTUC show an immune-depleted phenotype and a luminal papillary expression subtype, thus predisposing them for FGFR inhibitor treatment. Approximately 20% of UTUC tumours have acquired mutations in TP53 and demonstrate a significant degree of genomic instability, which makes them candidates for systemic chemotherapy or immunotherapy. Whereas microsatellite instability (MSI) is rare in sporadic UTUC, 5-10% of UTUC patients have germline mutations in DNA mismatch repair genes, which leads to high MSI with enriched neoantigen load and presumably better response rates to immunotherapy. SUMMARY Treatment decisions in UTUC should take molecular tumour characteristics into account. The currently most therapy-relevant molecular alterations in UTUC comprise FGFR3 mutational status and mutations in DNA mismatch repair genes with concomitant microsatellite instability.
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10
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Yang YF, Chuang HW, Kuo WT, Lin BS, Chang YC. Current Development and Application of Anaerobic Glycolytic Enzymes in Urothelial Cancer. Int J Mol Sci 2021; 22:ijms221910612. [PMID: 34638949 PMCID: PMC8508954 DOI: 10.3390/ijms221910612] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 09/27/2021] [Accepted: 09/27/2021] [Indexed: 12/23/2022] Open
Abstract
Urothelial cancer is a malignant tumor with metastatic ability and high mortality. Malignant tumors of the urinary system include upper tract urothelial cancer and bladder cancer. In addition to typical genetic alterations and epigenetic modifications, metabolism-related events also occur in urothelial cancer. This metabolic reprogramming includes aberrant expression levels of genes, metabolites, and associated networks and pathways. In this review, we summarize the dysfunctions of glycolytic enzymes in urothelial cancer and discuss the relevant phenotype and signal transduction. Moreover, we describe potential prognostic factors and risks to the survival of clinical cancer patients. More importantly, based on several available databases, we explore relationships between glycolytic enzymes and genetic changes or drug responses in urothelial cancer cells. Current advances in glycolysis-based inhibitors and their combinations are also discussed. Combining all of the evidence, we indicate their potential value for further research in basic science and clinical applications.
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Affiliation(s)
- Yi-Fang Yang
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung 81362, Taiwan;
| | - Hao-Wen Chuang
- Department of Pathology and Laboratory Medicine, Kaohsiung Veterans General Hospital, Kaohsiung 81362, Taiwan;
- Institute of Oral Biology, School of Dentistry, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Wei-Ting Kuo
- Division of Urology, Department of Surgery, Kaohsiung Veterans General Hospital, Kaohsiung 81362, Taiwan;
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Bo-Syuan Lin
- Department of Biomedical Imaging and Radiological Sciences, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan;
| | - Yu-Chan Chang
- Department of Biomedical Imaging and Radiological Sciences, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan;
- Correspondence: ; Tel.: +886-2-2826-7064
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11
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Hamada K, Tian Y, Fujimoto M, Takahashi Y, Kohno T, Tsuta K, Watanabe SI, Yoshida T, Asamura H, Kanai Y, Arai E. DNA hypermethylation of the ZNF132 gene participates in the clinicopathological aggressiveness of 'pan-negative'-type lung adenocarcinomas. Carcinogenesis 2021; 42:169-179. [PMID: 33152763 PMCID: PMC7905838 DOI: 10.1093/carcin/bgaa115] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 10/12/2020] [Accepted: 10/29/2020] [Indexed: 11/26/2022] Open
Abstract
Although some previous studies have examined epigenomic alterations in lung adenocarcinomas, correlations between epigenomic events and genomic driver mutations have not been fully elucidated. Single-CpG resolution genome-wide DNA methylation analysis with the Infinium HumanMethylation27 BeadChip was performed using 162 paired samples of adjacent normal lung tissue (N) and the corresponding tumorous tissue (T) from patients with lung adenocarcinomas. Correlations between DNA methylation data on the one hand and clinicopathological parameters and genomic driver mutations, i.e. mutations of EGFR, KRAS, BRAF and HER2 and fusions involving ALK, RET and ROS1, were examined. DNA methylation levels in 12 629 probes from N samples were significantly correlated with recurrence-free survival. Principal component analysis revealed that distinct DNA methylation profiles at the precancerous N stage tended not to induce specific genomic driver aberrations. Most of the genes showing significant DNA methylation alterations during transition from N to T were shared by two or more driver aberration groups. After small interfering RNA knockdown of ZNF132, which showed DNA hypermethylation only in the pan-negative group and was correlated with vascular invasion, the proliferation, apoptosis and migration of cancer cell lines were examined. ZNF132 knockdown led to increased cell migration ability, rather than increased cell growth or reduced apoptosis. We concluded that DNA hypermethylation of the ZNF132 gene participates in the clinicopathological aggressiveness of ‘pan-negative’ lung adenocarcinomas. In addition, DNA methylation alterations at the precancerous stage may determine tumor aggressiveness, and such alterations that accumulate after driver mutation may additionally modify clinicopathological features through alterations of gene expression.
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Affiliation(s)
- Kenichi Hamada
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
- Division of Thoracic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Ying Tian
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Mao Fujimoto
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Yoriko Takahashi
- Bioscience Department, Solution Knowledge Center, Mitsui Knowledge Industry Co., Ltd., Tokyo, Japan
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Koji Tsuta
- Department of Pathology & Laboratory Medicine, Kansai Medical University, Osaka, Japan
| | - Shun-ichi Watanabe
- Department of Thoracic Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Teruhiko Yoshida
- Fundamental Innovative Oncology Core Center, National Cancer Center Research Institute, Tokyo, Japan
| | - Hisao Asamura
- Division of Thoracic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Yae Kanai
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Eri Arai
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
- To whom correspondence should be addressed. Tel: +81 3 3353 1211; Fax: +81 3 3353 3290;
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