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Wang H, Wang Z, Wang Z, Li X, Li Y, Yan N, Wu L, Liang Y, Wu J, Song H, Qu Q, Huang J, Chang C, Shen K, Chen X, Lu M. Decitabine induces IRF7-mediated immune responses in p53-mutated triple-negative breast cancer: a clinical and translational study. Front Med 2024; 18:357-374. [PMID: 38157193 DOI: 10.1007/s11684-023-1016-8] [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: 12/20/2022] [Accepted: 06/24/2023] [Indexed: 01/03/2024]
Abstract
p53 is mutated in half of cancer cases. However, no p53-targeting drugs have been approved. Here, we reposition decitabine for triple-negative breast cancer (TNBC), a subtype with frequent p53 mutations and extremely poor prognosis. In a retrospective study on tissue microarrays with 132 TNBC cases, DNMT1 overexpression was associated with p53 mutations (P = 0.037) and poor overall survival (OS) (P = 0.010). In a prospective DEciTabinE and Carboplatin in TNBC (DETECT) trial (NCT03295552), decitabine with carboplatin produced an objective response rate (ORR) of 42% in 12 patients with stage IV TNBC. Among the 9 trialed patients with available TP53 sequencing results, the 6 patients with p53 mutations had higher ORR (3/6 vs. 0/3) and better OS (16.0 vs. 4.0 months) than the patients with wild-type p53. In a mechanistic study, isogenic TNBC cell lines harboring DETECT-derived p53 mutations exhibited higher DNMT1 expression and decitabine sensitivity than the cell line with wild-type p53. In the DETECT trial, decitabine induced strong immune responses featuring the striking upregulation of the innate immune player IRF7 in the p53-mutated TNBC cell line (upregulation by 16-fold) and the most responsive patient with TNBC. Our integrative studies reveal the potential of repurposing decitabine for the treatment of p53-mutated TNBC and suggest IRF7 as a potential biomarker for decitabine-based treatments.
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Affiliation(s)
- Haoyu Wang
- Department of General Surgery, Comprehensive Breast Health Center, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Zhengyuan Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine (Shanghai), Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Zheng Wang
- Department of General Surgery, Comprehensive Breast Health Center, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xiaoyang Li
- Department of Hematology, Shanghai Institute of Hematology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yuntong Li
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine (Shanghai), Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ni Yan
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine (Shanghai), Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Lili Wu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine (Shanghai), Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ying Liang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine (Shanghai), Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jiale Wu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine (Shanghai), Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Huaxin Song
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine (Shanghai), Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Qing Qu
- Department of General Surgery, Comprehensive Breast Health Center, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jiahui Huang
- Department of General Surgery, Comprehensive Breast Health Center, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Chunkang Chang
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200025, China
| | - Kunwei Shen
- Department of General Surgery, Comprehensive Breast Health Center, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Xiaosong Chen
- Department of General Surgery, Comprehensive Breast Health Center, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Min Lu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine (Shanghai), Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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Yan Q, Tang Y, He F, Xue J, Zhou R, Zhang X, Luo H, Zhou D, Wang X. Global analysis of DNA methylation in hepatocellular carcinoma via a whole-genome bisulfite sequencing approach. Genomics 2021; 113:3618-3634. [PMID: 34461228 DOI: 10.1016/j.ygeno.2021.08.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 05/01/2021] [Accepted: 08/25/2021] [Indexed: 01/04/2023]
Abstract
Alterations in DNA methylation patterns are considered early events in hepatocellular carcinoma (HCC). However, their mechanism and significance remain to be elucidated. We studied the genome-wide DNA methylation landscape of HCC by applying whole-genome bisulfite sequencing (WGBS) techonlogy. Overall, HCC exhibits a genome-wide hypomethylation pattern. After further annotation, we obtained 590 differentially hypermethylated genes (hyper-DMGs) and 977 differentially hypomethylated genes (hypo-DMGs) from three groups. Hyper-DMGs were mainly involved in ascorbate and alternate metabolism pathways, while hypo-DMGs were mainly involved in focal adhesion. By integrating the DMGs with HCC-related differentially expressed genes (DEGs) and DMGs from the TCGA database, we constructed prognostic model based on thirteen aberrantly methylated DEGs, and verified our prognostic model in GSE14520 dataset. This study compares the patterns of global epigenomic DNA methylation during the development of HCC, focusing on the role of DNA methylation in the early occurrence and development of HCC, providing a direction for future research on its epigenetic mechanism.
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Affiliation(s)
- Qian Yan
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China; Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Ying Tang
- Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou, China; Institute of Tumor, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Fan He
- The First Affiliated Hospital of Guizhou University of Chinese Medicine, Guizhou, China
| | - Jiao Xue
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Ruisheng Zhou
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiaoying Zhang
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Huiyan Luo
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Daihan Zhou
- Institute of Tumor, Guangzhou University of Chinese Medicine, Guangzhou, China; Department of Oncology, The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China.
| | - Xiongwen Wang
- Department of Oncology, The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China.
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Mungamuri SK, Nagasuryaprasad K. Epigenetic mechanisms of hepatocellular carcinoma progression: Potential therapeutic opportunities. EPIGENETICS AND METABOLOMICS 2021:279-296. [DOI: 10.1016/b978-0-323-85652-2.00008-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
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Liu HH, Fang Y, Wang JW, Yuan XD, Fan YC, Gao S, Han LY, Wang K. Hypomethylation of the cyclin D1 promoter in hepatitis B virus-associated hepatocellular carcinoma. Medicine (Baltimore) 2020; 99:e20326. [PMID: 32443384 PMCID: PMC7253776 DOI: 10.1097/md.0000000000020326] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The hypomethylation of the Cyclin D1 (CCND1) promoter induced by excess oxidative stress likely promotes the development of hepatitis B virus-associated hepatocellular carcinoma (HBV-HCC). We aimed to evaluate methylation status of the CCND1 promoter as a new plasma marker for the detection of HBV-HCC.We consecutively recruited 191 participants, including 105 patients with HBV-HCC, 54 patients with chronic hepatitis B (CHB), and 32 healthy controls (HCs). Using methylation-specific polymerase chain reaction, we identified the methylation status of the CCND1 promoter in plasma samples. We analyzed the expression levels of the CCND1 mRNA in peripheral blood mononuclear cells by using quantitative real-time PCR. We assessed the plasma levels of superoxide dismutase, 8-hydroxydeoxyguanosine and malondialdehyde by using enzyme-linked immunosorbent assays.Patients with HBV-HCC (23.81%) presented a reduced methylation frequency compared with patients with CHB (64.81%) or HCs (78.13%) (P < .001). When receiver operating characteristic curves were plotted for patients with HBV-HCC versus CHB, the methylation status of the CCND1 promoter yielded diagnostic parameter values for the area under the curve of 0.705, sensitivity of 76.19%, and specificity of 64.81%, thus outperforming serum alpha-fetoprotein (AFP), which had an area under the curve of 0.531, sensitivity of 36.19%, and specificity of 90.74%. Methylation of the CCND1 promoter represents a prospective diagnostic marker for patients with AFP-negative HBV-HCC and AFP-positive CHB. The expression levels of CCND1 mRNA was increased in patients with HBV-HCC compared with patients with CHB (Z = -4.946, P < .001) and HCs (Z = -6.819, P < .001). Both the extent of oxidative injury and antioxidant capacity indicated by the superoxide dismutase, 8-hydroxydeoxyguanosine and malondialdehyde levels were increased in patients with HBV-HCC. Clinical follow up of patients with HBV-HCC revealed a worse overall survival (P = .012, log-rank test) and a decreased progression-free survival (HR = 0.109, 95%CI: 0.031-0.384) for the unmethylated CCND1 group than methylated CCND1 group.Our study confirms that oxidative stress appears to correlate with plasma levels of CCND1 promoter methylation, and the methylation status of the CCND1 promoter represents a prospective biomarker with better diagnostic performance than serum AFP levels.
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Affiliation(s)
- Hui-Hui Liu
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan
| | - Yu Fang
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan
| | - Jing-Wen Wang
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan
| | - Xiao-Dong Yuan
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan
| | - Yu-Chen Fan
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan
- Shenzhen Research Institute of Shandong University, Shenzhen
- Institute of Hepatology, Shandong University, Jinan, China
| | - Shuai Gao
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan
- Institute of Hepatology, Shandong University, Jinan, China
| | - Li-Yan Han
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan
- Institute of Hepatology, Shandong University, Jinan, China
| | - Kai Wang
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan
- Shenzhen Research Institute of Shandong University, Shenzhen
- Institute of Hepatology, Shandong University, Jinan, China
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Kanazawa T, Misawa K, Shinmura K, Misawa Y, Kusaka G, Maruta M, Sasaki T, Watanabe Y, Carey TE. Promoter methylation of galanin receptors as epigenetic biomarkers for head and neck squamous cell carcinomas. Expert Rev Mol Diagn 2019; 19:137-148. [PMID: 30640567 DOI: 10.1080/14737159.2019.1567334] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
INTRODUCTION While remarkable progress has been made in standard treatments for head and neck squamous cell carcinomas (HNSCCs), the long-term survival remains at an unsatisfactory 40-50%. To improve the survival rate, biomarkers for optimal treatment selection and prognostic prediction, as well as novel, low-toxicity treatment strategies, are required. Galanin receptor (GALR) 1 and GALR2 are well-studied tumor suppressors in HNSCCs. Compared with other clinicopathological factors, the epigenetic variants of GALRs have been found to be the most powerful markers to predict the prognosis of HNSCC patients. Areas covered: This review outlines the functions and signaling pathways of GALRs and explains the potential of GALR promoter methylation as a biomarker for HNSCC prognosis. We also summarize recent developments in promoter methylation studies in HNSCC and indicate future directions for GALR promoter methylation studies. Expert commentary: GALR studies have highlighted two major aspects with implications in HNSCC - that G-protein coupled receptors (GPCRs) act as tumor suppressor genes and that GALR promoter methylation is significantly related to the carcinogenesis of HNSCC. The findings of GALR studies can be applied to studies on other GPCRs and further in-depth DNA methylation studies. Deeper insights into GPCR epigenetics are expected to markedly improve HNSCC treatment.
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Affiliation(s)
- Takeharu Kanazawa
- a Department of Otolaryngology-Head and Neck Surgery , International University of Health and Welfare , Tokyo , Japan.,b Department of Otolaryngology-Head and Neck Surgery , Jichi Medical University , Shimotsuke , Japan
| | - Kiyoshi Misawa
- c Department of Otolaryngology/Head and Neck Surgery , Hamamatsu University School of Medicine , Hamamatsu , Japan
| | - Kazuya Shinmura
- d Department of Tumor Pathology , Hamamatsu University School of Medicine , Hamamatsu , Japan
| | - Yuki Misawa
- c Department of Otolaryngology/Head and Neck Surgery , Hamamatsu University School of Medicine , Hamamatsu , Japan
| | - Gen Kusaka
- e Department of Neurosurgery , Jichi Medical University Saitama Medical Center , Saitama , Saitama , Japan
| | - Mikiko Maruta
- b Department of Otolaryngology-Head and Neck Surgery , Jichi Medical University , Shimotsuke , Japan
| | - Toru Sasaki
- b Department of Otolaryngology-Head and Neck Surgery , Jichi Medical University , Shimotsuke , Japan
| | - Yusuke Watanabe
- a Department of Otolaryngology-Head and Neck Surgery , International University of Health and Welfare , Tokyo , Japan
| | - Thomas E Carey
- f Laboratory of Head and Neck Center Biology, Department of Otolaryngology, Head and Neck Surgery , The University of Michigan , Ann Arbor , MI , USA
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Kanazawa T, Misawa K, Fukushima H, Misawa Y, Sato Y, Maruta M, Imayoshi S, Kusaka G, Kawabata K, Mineta H, Carey TE, Nishino H. Epigenetic inactivation of galanin receptors in salivary duct carcinoma of the parotid gland: Potential utility as biomarkers for prognosis. Oncol Lett 2018; 15:9043-9050. [PMID: 29805635 PMCID: PMC5958682 DOI: 10.3892/ol.2018.8525] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 02/23/2018] [Indexed: 01/21/2023] Open
Abstract
Salivary duct carcinoma (SDC) constitutes one of the most aggressive cancers in the salivary gland and is associated with a poor prognosis; however, no established systemic therapy options are available. SDC exhibits biological similarity to prostate and breast cancers, therefore anti-hormone therapy and molecular target therapies are available, however with limited beneficial effects. Galanin and galanin receptors (GALRs) are well established as molecular biomarkers to predict the survival rate and risk of recurrence of head and neck squamous cell carcinoma. The present study investigated the clinicopathological features of patients with SDC and the methylation status of their galanin and GALR genes to demonstrate the prognostic value for this disease. The median overall survival (OS) was 37.2 months. T-stage, N-stage, disease stage, tumor size, and preoperative facial paralysis were significantly associated with OS, whereas human epidermal growth factor receptor 2 (HER2) overexpression was not. GALR1 and GALR2 methylation rates in tumor tissues were significantly increased compared with normal tissues with 9.85- and 4.49-fold increase, respectively. p27kip1 and p57kip2 expression significantly inversely correlated with the methylation rate of GALR1 and GALR2. In addition, the observed GALR1 and/or GALR2 methylation rates were significantly correlated with a decrease in OS. These results suggest that GALR1 and GALR2 may serve as potential prognostic factors and therapeutic targets in SDC.
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Affiliation(s)
- Takeharu Kanazawa
- Department of Otolaryngology/Head and Neck Surgery, Jichi Medical University, Shimotsuke, Tochigi 329-0498, Japan.,Department of Otolaryngology/Head and Neck Surgery, Jichi Medical University, Saitama Medical Center, Saitama 330-8503, Japan
| | - Kiyoshi Misawa
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
| | - Hirofumi Fukushima
- Division of Head and Neck, Cancer Institute, Japanese Foundation of Cancer Research, Tokyo 135-8550, Japan
| | - Yuki Misawa
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
| | - Yukiko Sato
- Department of Pathology, Cancer Institute, Japanese Foundation of Cancer Research, Tokyo 135-8550, Japan
| | - Mikiko Maruta
- Department of Otolaryngology/Head and Neck Surgery, Jichi Medical University, Saitama Medical Center, Saitama 330-8503, Japan
| | - Shoichiro Imayoshi
- Department of Otolaryngology/Head and Neck Surgery, Jichi Medical University, Shimotsuke, Tochigi 329-0498, Japan
| | - Gen Kusaka
- Department of Neurosurgery, Jichi Medical University, Saitama Medical Center, Saitama 330-8503, Japan
| | - Kazuyoshi Kawabata
- Division of Head and Neck, Cancer Institute, Japanese Foundation of Cancer Research, Tokyo 135-8550, Japan
| | - Hiroyuki Mineta
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
| | - Thomas E Carey
- Laboratory of Head and Neck Cancer Biology, Department of Otolaryngology/Head and Neck Surgery, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hiroshi Nishino
- Department of Otolaryngology/Head and Neck Surgery, Jichi Medical University, Shimotsuke, Tochigi 329-0498, Japan
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Zhou G, Ye J, Fang Y, Zhang Z, Zhang J, Sun L, Feng J. Identification of DBCCR1 as a suppressor in the development of lung cancer that is associated with increased DNA methyltransferase 1. Oncotarget 2018; 8:32821-32832. [PMID: 28427182 PMCID: PMC5464830 DOI: 10.18632/oncotarget.15826] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 02/08/2017] [Indexed: 12/13/2022] Open
Abstract
Accumulating evidence has pointed to a role of the CpG island hypermethylation in the regulation of cancer-related genes in tumor progression. However, the biological impacts in cancer pathogenesis associated with down-regulation of such gene targets remains elusive. Here we focused on a potential target of hypermethylation, DBCCR1 (deleted in bladder cancer chromosome region 1), a gene encoding a candidate tumor suppressor. We found that the expression of DBCCR1 is significantly lower in the lung cancer tissues compared with adjacent non-tumor tissues of patients. Importantly, the decreased DBCCR1 was found correlated with more advanced stages of cancer, and with a significantly shorter survival of patients. Genetic silencing DBCCR1 in human lung cancer cell line A549 resulted in an enhanced proliferation, migration, and invasion capacity. Conversely, restoring DBCCR1 expression blocked the growth and inhibited the ability of cancer cell in migration and invasion. Interestingly, DBCCR1 attenuates the expression of DNMT1 (DNA methyltransferase 1), suggesting a reciprocal regulation between genetic silencing of cancer suppressor genes and activating DNA methylation. Our data thus implicates DBCCR1 downregulation as a potential module in the pathogenesis of lung cancer through DNA methylation.
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Affiliation(s)
- Guoren Zhou
- Department of Chemotherapy, Jiangsu Cancer Hospital Affiliated to Nanjing Medical University, Nanjing 210000, Jiangsu, China
| | - Jinjun Ye
- Department of Radiotherapy, Jiangsu Cancer Hospital Affiliated to Nanjing Medical University, Nanjing 210000, Jiangsu, China
| | - Ying Fang
- Department of Chemotherapy, Jiangsu Cancer Hospital Affiliated to Nanjing Medical University, Nanjing 210000, Jiangsu, China
| | - Zhi Zhang
- Department of Thoracic Surgery, Jiangsu Cancer Hospital Affiliated to Nanjing Medical University, Nanjing 210000, Jiangsu, China
| | - Jingyuan Zhang
- Department of Pathology, Jiangsu Cancer Hospital Affiliated to Nanjing Medical University, Nanjing 210000, Jiangsu, China
| | - Lei Sun
- Department of Medical Iconography, Jiangsu Cancer Hospital Affiliated to Nanjing Medical University, Nanjing 210000, Jiangsu, China
| | - Jifeng Feng
- Department of Chemotherapy, Jiangsu Cancer Hospital Affiliated to Nanjing Medical University, Nanjing 210000, Jiangsu, China
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Zhang C, Li J, Huang T, Duan S, Dai D, Jiang D, Sui X, Li D, Chen Y, Ding F, Huang C, Chen G, Wang K. Meta-analysis of DNA methylation biomarkers in hepatocellular carcinoma. Oncotarget 2018; 7:81255-81267. [PMID: 27835605 PMCID: PMC5348390 DOI: 10.18632/oncotarget.13221] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 11/01/2016] [Indexed: 12/14/2022] Open
Abstract
DNA methylation is an epigenetic mechanism in the pathogenesis of hepatocellular carcinoma (HCC). Here, we conducted a systematic meta-analysis to evaluate the contribution of DNA methylation to the risk of HCC. A total of 2109 publications were initially retrieved from PubMed, Web of Science, Cochrane Library, Embase, CNKI and Wanfang literature database. After a four-step filtration, we harvested 144 case-control articles in the meta-analysis. Our results revealed that 24 genes (carcinoma tissues vs adjacent tissues), 17 genes (carcinoma tissues vs normal tissues) and six genes (carcinoma serums vs normal serums) were significantly hypermethylated in HCC. Subgroup meta-analysis by geographical populations showed that six genes (carcinoma tissues vs adjacent tissues) and four genes (carcinoma tissues vs normal tissues) were significantly hypermethylated in HCC. Our meta-analysis identified the correlations between a number of aberrant methylated genes (p16, RASSF1A, GSTP1, p14, CDH1, APC, RUNX3, SOCS1, p15, MGMT, SFRP1, WIF1, PRDM2, DAPK1, RARβ, hMLH1, p73, DLC1, p53, SPINT2, OPCML and WT1) and HCC. Aberrant DNA methylation might become useful biomarkers for the prediction and diagnosis of HCC.
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Affiliation(s)
- Cheng Zhang
- Department of Medical Oncology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Jinyun Li
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Tao Huang
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Shiwei Duan
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Dongjun Dai
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Danjie Jiang
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Xinbing Sui
- Department of Medical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang, China
| | - Da Li
- Department of Medical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yidan Chen
- Department of Medical Oncology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Fei Ding
- Department of Medical Oncology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Changxin Huang
- Department of Medical Oncology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Gongying Chen
- Department of Medical Oncology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Kaifeng Wang
- Department of Medical Oncology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang, China
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Wang LL, Chen ZS, Zhou WD, Shu J, Wang XH, Jin R, Zhuang LL, Hoda MA, Zhang H, Zhou GP. Down-regulated GATA-1 up-regulates interferon regulatory factor 3 in lung adenocarcinoma. Sci Rep 2017; 7:2551. [PMID: 28566697 PMCID: PMC5451405 DOI: 10.1038/s41598-017-02700-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 04/19/2017] [Indexed: 12/18/2022] Open
Abstract
Interferon regulatory factor 3 (IRF-3) is widely known for its prompt response against viral infection by activating the interferon system. We previously reported that E2F1, Sp1 and Sp3 regulated transcriptional activity of IRF-3. Recently, different expression patterns of IRF-3 were found in lung cancer, leading to the alternation of the immunomodulatory function in tumorigenesis. However, the mechanism of transcriptional regulation of IRF-3 in lung cancer has not been extensively studied. Here, we investigated the characterization of IRF-3 promoter and found that GATA-1 bound to a specific domain of IRF-3 promoter in vitro and in vivo. We found elevated IRF-3 and decreased GATA-1 gene expression in lung adenocarcinoma in Oncomine database. Additionally, higher IRF-3 gene expression was observed in human lung adenocarcinoma, accompanied by aberrant GATA-1 protein expression. We further analyzed the relationship of GATA-1 and IRF-3 expression in lung adenocarcinoma cell lines and found that inhibition of GATA-1 by siRNA increased the promoter activity, mRNA and protein levels of IRF-3, while over-expression of GATA-1 down-regulated IRF-3 gene expression. Taken together, we conclude that reduced GATA-1 could be responsible for the upregulation of IRF-3 in lung adenocarcinoma cells through binding with a specific domain of IRF-3 promoter.
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Affiliation(s)
- Lu-Lu Wang
- Dpartment of Pediatrics, The First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Zheng-Sen Chen
- Department of Urology, The Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Wen-Di Zhou
- Dpartment of Pediatrics, Huai'an First People's Hospital, Nanjing Medical University, Huai'an, Jiangsu Province, China
| | - Jin Shu
- Department of Pediatric Respiration, Affiliated Wuxi People's Hospital, Nanjing Medical University, Wuxi, Jiangsu Province, China
| | - Xiao-Hua Wang
- Dpartment of Pediatrics, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Rui Jin
- Dpartment of Pediatrics, The First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Li-Li Zhuang
- Dpartment of Pediatrics, The First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Mir Alireza Hoda
- Translational Thoracic Oncology Laboratory, Division of Thoracic Surgery, Department of Surgery, Comprehensive Cancer Center, Medical University Vienna, Vienna, Austria
| | - Hao Zhang
- Department of Thoracic and Cardiovascular Surgery, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu Province, China.
| | - Guo-Ping Zhou
- Dpartment of Pediatrics, The First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, China.
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10
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Site-specific methylation patterns of theGALandGALR1/2genes in head and neck cancer: Potential utility as biomarkers for prognosis. Mol Carcinog 2016; 56:1107-1116. [DOI: 10.1002/mc.22577] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 09/12/2016] [Accepted: 09/23/2016] [Indexed: 01/21/2023]
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Kanazawa T, Misawa K, Misawa Y, Uehara T, Fukushima H, Kusaka G, Maruta M, Carey TE. G-Protein-Coupled Receptors: Next Generation Therapeutic Targets in Head and Neck Cancer? Toxins (Basel) 2015; 7:2959-84. [PMID: 26251921 PMCID: PMC4549734 DOI: 10.3390/toxins7082959] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 06/22/2015] [Accepted: 07/20/2015] [Indexed: 01/28/2023] Open
Abstract
Therapeutic outcome in head and neck squamous cell carcinoma (HNSCC) is poor in most advanced cases. To improve therapeutic efficiency, novel therapeutic targets and prognostic factors must be discovered. Our studies have identified several G protein-coupled receptors (GPCRs) as promising candidates. Significant epigenetic silencing of GPCR expression occurs in HNSCC compared with normal tissue, and is significantly correlated with clinical behavior. Together with the finding that GPCR activity can suppress tumor cell growth, this indicates that GPCR expression has potential utility as a prognostic factor. In this review, we discuss the roles that galanin receptor type 1 (GALR1) and type 2 (GALR2), tachykinin receptor type 1 (TACR1), and somatostatin receptor type 1 (SST1) play in HNSCC. GALR1 inhibits proliferation of HNSCC cells though ERK1/2-mediated effects on cell cycle control proteins such as p27, p57, and cyclin D1, whereas GALR2 inhibits cell proliferation and induces apoptosis in HNSCC cells. Hypermethylation of GALR1, GALR2, TACR1, and SST1 is associated with significantly reduced disease-free survival and a higher recurrence rate. Although their overall activities varies, each of these GPCRs has value as both a prognostic factor and a therapeutic target. These data indicate that further study of GPCRs is a promising strategy that will enrich pharmacogenomics and prognostic research in HNSCC.
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Affiliation(s)
- Takeharu Kanazawa
- Department of Otolaryngology-Head and Neck Surgery, Jichi Medical University, Shimotsuke 329-0498, Japan.
- Laboratory of Head and Neck Center Biology, Department of Otolaryngology, Head and Neck Surgery, the University of Michigan, Ann Arbor, MI 48109, USA.
| | - Kiyoshi Misawa
- Laboratory of Head and Neck Center Biology, Department of Otolaryngology, Head and Neck Surgery, the University of Michigan, Ann Arbor, MI 48109, USA.
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu 431-319, Japan.
| | - Yuki Misawa
- Laboratory of Head and Neck Center Biology, Department of Otolaryngology, Head and Neck Surgery, the University of Michigan, Ann Arbor, MI 48109, USA.
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu 431-319, Japan.
| | - Takayuki Uehara
- Department of Otorhinolaryngology, Head and Neck Surgery, Graduate School of Medicine, University of the Ryukyus, Nishihara 903-0215, Japan.
| | - Hirofumi Fukushima
- Department of Head and Neck, Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan.
| | - Gen Kusaka
- Department of Neurosurgery, Jichi Medical University Saitama Medical Center, Saitama 330-8503, Japan.
| | - Mikiko Maruta
- Department of Otolaryngology-Head and Neck Surgery, Jichi Medical University, Shimotsuke 329-0498, Japan.
| | - Thomas E Carey
- Laboratory of Head and Neck Center Biology, Department of Otolaryngology, Head and Neck Surgery, the University of Michigan, Ann Arbor, MI 48109, USA.
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Gnoni A, Santini D, Scartozzi M, Russo A, Licchetta A, Palmieri V, Lupo L, Faloppi L, Palasciano G, Memeo V, Angarano G, Brunetti O, Guarini A, Pisconti S, Lorusso V, Silvestris N. Hepatocellular carcinoma treatment over sorafenib: epigenetics, microRNAs and microenvironment. Is there a light at the end of the tunnel? Expert Opin Ther Targets 2015. [PMID: 26212068 DOI: 10.1517/14728222.2015.1071354] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Sorafenib is currently the only approved therapy in hepatocellular carcinoma (HCC). Alternative first- and second-line treatments are a significant unmet medical need, and several biologic agents have been tested in recent years, with poor results. Therefore, angiogenic pathways and the cytokine cascade remain possible targets in HCC. Recent studies suggest a role of epigenetic processes, associated with the initiation and development of HCC. In this field, DNA methylation, micro-RNAs (miRNAs) and tumor microenvironment cells became a possible new target for HCC treatment. AREAS COVERED This review explains the possible role of DNA methylation and histone deacetylase inhibitors as predictive biomarkers and target therapy, the extensive world of the promising miRNA blockade strategy, and the recent strong evidence of correlation between HCC tumors and peritumoral stroma cells. The literature and preclinic/clinic data were obtained through an electronic search. EXPERT OPINION Future research should aim to understand how best to identify patient groups that would benefit most from the prescribed therapy. To overcome the 'therapeutic stranding' of HCC, a possible way out from the current therapeutic tunnel might be to evaluate the major epigenetic and genetic processes involved in HCC carcinogenesis, not underestimating the tumor microenvironment and its 'actors' (angiogenesis, immune system, platelets). We are only at the start of a long journey towards the elucidation of HCC molecular pathways as therapeutic targets. Yet, currently this path appears to be the only one to cast some light at the end of the tunnel.
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Affiliation(s)
- Antonio Gnoni
- a 1 Hospital of Taranto, Medical Oncology Unit , Taranto, Italy
| | - Daniele Santini
- b 2 University Campus Biomedico, Medical Oncology Unit , Rome, Italy
| | - Mario Scartozzi
- c 3 University of Cagliari, Medical Oncology Unit , Cagliari, Italy
| | - Antonio Russo
- d 4 University of Palermo, Medical Oncology Unit , Palermo, Italy
| | | | - Vincenzo Palmieri
- e 5 University of Bari, Department of Biomedical Sciences and Human Oncology, Clinica Medica "A. Murri" , Bari, Italy
| | - Luigi Lupo
- f 6 University of Bari, Institute of General Surgery and Liver Transplantation, Department of Emergency and Organ Transplantation , Bari, Italy
| | - Luca Faloppi
- g 7 Polytechnic University of the Marche, Medical Oncology Unit , Ancona, Italy
| | - Giuseppe Palasciano
- e 5 University of Bari, Department of Biomedical Sciences and Human Oncology, Clinica Medica "A. Murri" , Bari, Italy
| | - Vincenzo Memeo
- f 6 University of Bari, Institute of General Surgery and Liver Transplantation, Department of Emergency and Organ Transplantation , Bari, Italy
| | | | - Oronzo Brunetti
- i 9 National Cancer Research Centre "Giovanni Paolo II", Medical Oncology Unit , Viale Orazio Flacco, 65, 70124 Bari, Italy +39 080 555 5419 ; +39 080 555 5419 ;
| | - Attilio Guarini
- j 10 National Cancer Research Centre "Giovanni Paolo II", Medical Ematology Unit , Bari, Italy
| | | | - Vito Lorusso
- i 9 National Cancer Research Centre "Giovanni Paolo II", Medical Oncology Unit , Viale Orazio Flacco, 65, 70124 Bari, Italy +39 080 555 5419 ; +39 080 555 5419 ;
| | - Nicola Silvestris
- i 9 National Cancer Research Centre "Giovanni Paolo II", Medical Oncology Unit , Viale Orazio Flacco, 65, 70124 Bari, Italy +39 080 555 5419 ; +39 080 555 5419 ;
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Kuo CC, Lin CY, Shih YL, Hsieh CB, Lin PY, Guan SB, Hsieh MS, Lai HC, Chen CJ, Lin YW. Frequent methylation of HOXA9 gene in tumor tissues and plasma samples from human hepatocellular carcinomas. Clin Chem Lab Med 2015; 52:1235-45. [PMID: 24681432 DOI: 10.1515/cclm-2013-0780] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 02/11/2014] [Indexed: 12/13/2022]
Abstract
BACKGROUND Aberrant DNA methylation is associated with the development of hepatocellular carcinoma (HCC), suggesting that gene methylation could be a potential biomarker for detection of HCC. The aim of this study is to identify potential biomarkers in HCC. METHODS We used the Infinium methylation array and a DNA-pooling strategy to analyze the genome-wide methylation profile in HCC. Quantitative methylation-specific PCR (Q-MSP) was used to validate homeobox A9 (HOXA9) methylation in 29 normal controls, 100 HCC samples and adjacent non-tumor tissues and in 74 plasma samples, including 40 patients with HCC. RESULTS Ten genes (HOXA9, NEUROG1, TNFRSF10C, IRAK3, GFPT2, ZNF177, DPYSL4, ELOVL4, FSD1, and CACNA1G) showed differences in methylation between controls and HCCs. Of these, HOXA9 was significantly hypermethylated in HCCs (76.7%; 23/30) compared with controls (3.4%; 1/29). In addition, combination analysis of two- and three-gene sets for HCC detection showed greater sensitivity (90%-96.7%) and comparable specificity (93.1%-96.6%) to each individual gene (33.3%-76.7% and 55.2%-100.0%). HOXA9 methylation was further validated by Q-MSP in two independent set of clinical samples including 100 HCC and paired non-tumor tissues. Further, HOXA9 methylation could be detected in plasma from HCC patients (n=40) but not in normal plasma (n=34) (p<0.0005). Combined testing (either parameter positive) for α-fetoprotein (AFP, a plasma protein biomarker) and HOXA9 methylation showed greater sensitivity (94.6%) for detection of HCC than AFP alone (75.7%). CONCLUSIONS These data suggest that methylation of HOXA9 could be a helpful biomarker to assist in HCC detection.
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Correlation of CCNA1 promoter methylation with malignant tumors: a meta-analysis introduction. BIOMED RESEARCH INTERNATIONAL 2015; 2015:134027. [PMID: 25654082 PMCID: PMC4310450 DOI: 10.1155/2015/134027] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Revised: 10/23/2014] [Accepted: 11/07/2014] [Indexed: 01/09/2023]
Abstract
Epigenetic silencing of tumor suppressor genes by promoter methylation plays vital roles in the process of carcinogenesis. The purpose of this meta-analysis was to determine whether the aberrant methylation of cyclin A1 (CCNA1) may be of great significance to human malignant tumors. By searching both English and Chinese language-based electronic databases carefully, we tabulated and analyzed parameters from each study. All human-associated case-control studies were included providing available data for CCNA1 methylation and reporting the adjusted odds ratios (ORs) and 95% confidence intervals (CI) conducted with the use of Version 12.0 STATA software. A total of 10 case-control studies (619 patients with cancers and 292 healthy controls) were included for the following statistical analysis. Pooled OR values from all articles revealed that the frequency of CCNA1 methylation in cancer tissues was significantly higher than those of normal tissues (P < 0.001). Further ethnicity indicated that the frequency of CCNA1 methylation was correlated with the development of malignant tumors among all those included experimental subgroups (all P < 0.05). These data from results indicated a significant connection of CCNA1 methylation with poor progression in human malignant tumors among both Caucasian and Asian populations.
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Abstract
Cancer is a genetic and epigenetic disease. Multiple genetic and epigenetic changes have been studied in cervical cancer; however, such changes are selected for during tumorigenesis and tumor aggression is not yet clear. Cervical cancer is a multistep process with accumulation of genetic and epigenetic alterations in regulatory genes, leading to activation of oncogenes and inactivation or loss of tumor suppressor genes. In cervical cancer, epigenetic alterations can affect the expression of papillomaviral as well as host genes in relation to stages representing the multistep process of carcinogenesis.
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Zhao Y, Xue F, Sun J, Guo S, Zhang H, Qiu B, Geng J, Gu J, Zhou X, Wang W, Zhang Z, Tang N, He Y, Yu J, Xia Q. Genome-wide methylation profiling of the different stages of hepatitis B virus-related hepatocellular carcinoma development in plasma cell-free DNA reveals potential biomarkers for early detection and high-risk monitoring of hepatocellular carcinoma. Clin Epigenetics 2014; 6:30. [PMID: 25859288 PMCID: PMC4391300 DOI: 10.1186/1868-7083-6-30] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 11/14/2014] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND An important model of hepatocellular carcinoma (HCC) that has been described in southeast Asia includes the transition from chronic hepatitis B infection (CHB) to liver cirrhosis (LC) and, finally, to HCC. The genome-wide methylation profiling of plasma cell-free DNA (cfDNA) has not previously been used to assess HCC development. Using MethylCap-seq, we analyzed the genome-wide cfDNA methylation profiles by separately pooling healthy control (HC), CHB, LC and HCC samples and independently validating the library data for the tissue DNA and cfDNA by MSP, qMSP and Multiplex-BSP-seq. RESULTS The dynamic features of cfDNA methylation coincided with the natural course of HCC development. Data mining revealed the presence of 240, 272 and 286 differentially methylated genes (DMGs) corresponding to the early, middle and late stages of HCC progression, respectively. The validation of the DNA and cfDNA results in independent tissues identified three DMGs, including ZNF300, SLC22A20 and SHISA7, with the potential for distinguishing between CHB and LC as well as between LC and HCC. The area under the curve (AUC) ranged from 0.65 to 0.80, and the odds ratio (OR) values ranged from 5.18 to 14.2. CONCLUSIONS Our data revealed highly dynamic cfDNA methylation profiles in support of HBV-related HCC development. We have identified a panel of DMGs that are predictive for the early, middle and late stages of HCC development, and these are potential markers for the early detection of HCC as well as the screening of high-risk populations.
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Affiliation(s)
- Yangxing Zhao
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, LN 2200/25,Xietu Road, Shanghai, 200032 China
| | - Feng Xue
- Department of Liver Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127 China
| | - Jinfeng Sun
- Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032 China
| | - Shicheng Guo
- Ministry of Education Key Laboratory of Contemporary Anthropology School of Life Sciences, Fudan University, 220 Handan Road, Shanghai, 200433 China
| | - Hongyu Zhang
- Shanghai Cancer Institute,Renji Hospital, Shanghai Jiao Tong University School of Medicine, LN 2200/25,Xietu Road, Shanghai, 200032 China
| | - Bijun Qiu
- Department of Liver Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127 China
| | - Junfeng Geng
- Department of General Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, 241 West Huaihai Road, Shanghai, 200030 China
| | - Jun Gu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, LN 2200/25,Xietu Road, Shanghai, 200032 China
| | - Xiaoyu Zhou
- Key Laboratory of Contraceptive Drugs and Devices of NPFPC, Shanghai Institute of Planned Parenthood Research, 2140 Xietu Road, Shanghai, 200032 China
| | - Wei Wang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, LN 2200/25,Xietu Road, Shanghai, 200032 China
| | - Zhenfeng Zhang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, LN 2200/25,Xietu Road, Shanghai, 200032 China
| | - Ning Tang
- Shanghai Cancer Institute,Renji Hospital, Shanghai Jiao Tong University School of Medicine, LN 2200/25,Xietu Road, Shanghai, 200032 China
| | - Yinghua He
- Shanghai Cancer Institute,Renji Hospital, Shanghai Jiao Tong University School of Medicine, LN 2200/25,Xietu Road, Shanghai, 200032 China
| | - Jian Yu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, LN 2200/25,Xietu Road, Shanghai, 200032 China
| | - Qiang Xia
- Department of Liver Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127 China
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Lee KJ, Ye JS, Choe H, Nam YR, Kim N, Lee U, Joo CH. Serine cluster phosphorylation liberates the C-terminal helix of IFN regulatory factor 7 to bind histone acetyltransferase p300. THE JOURNAL OF IMMUNOLOGY 2014; 193:4137-48. [PMID: 25225665 DOI: 10.4049/jimmunol.1401290] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
IFN regulatory factor 7 (IRF7) is a major regulator of type I (αβ) IFN secretion. A growing body of evidence shows that IRF7 is involved in a wide variety of pathologic conditions in addition to infections; however, the detailed mechanism of IRF7 transactivation remains elusive. Our current knowledge of IRF7 transactivation is based on studies of IRF3, another major regulator of IFN-β secretion. IRF3 and IRF7 are closely related homologs with high sequence similarity in their C-terminal regions, and both proteins are activated by phosphorylation of a specific serine cluster (SC). Nevertheless, the functional domains of the two proteins are arranged in an inverted manner. We generated a model structure of the IRF7 C-terminal region using homology modeling and used it to guide subsequent functional domain studies. The model structure led to the identification of a tripod-helix structure containing the SC. Based on the model and experimental data, we hypothesized that phosphorylation-mediated IRF7 transactivation is controlled by a tripod-helix structure. Inducible IκB kinase binds a tripod-helix structure. Serial phosphorylation of the SC by the kinase liberates C-terminal helix from an inhibitory hydrophobic pocket. A histone acetyltransferase P300 binds the liberated helix. The difference in the P300 binding sites explains why the domain arrangement of IRF7 is inverted relative to that of IRF3.
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Affiliation(s)
- Kyoung Jin Lee
- Department of Microbiology, University of Ulsan College of Medicine, Seoul 138-736, Korea
| | - Jung Sook Ye
- Department of Microbiology, University of Ulsan College of Medicine, Seoul 138-736, Korea
| | - Han Choe
- Bio-Medical Institute of Technology, University of Ulsan College of Medicine, Seoul 138-736, Korea; Department of Physiology, University of Ulsan College of Medicine, Seoul 138-736, Korea; and
| | - Young Ran Nam
- Department of Microbiology, University of Ulsan College of Medicine, Seoul 138-736, Korea
| | - Nari Kim
- Department of Microbiology, University of Ulsan College of Medicine, Seoul 138-736, Korea
| | - Uk Lee
- Department of Microbiology, University of Ulsan College of Medicine, Seoul 138-736, Korea
| | - Chul Hyun Joo
- Department of Microbiology, University of Ulsan College of Medicine, Seoul 138-736, Korea; Cell Dysfunction Research Center, University of Ulsan College of Medicine, Seoul 138-736, Korea
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Abstract
LKB1 is commonly thought of as a tumor suppressor gene because its hereditary mutation is responsible for a cancer syndrome, and somatic inactivation of LKB1 is found in non-small cell lung cancer, melanoma, and cervical cancers. However, unlike other tumor suppressors whose main function is to either suppress cell proliferation or promote cell death, one of the functions of LKB1-regulated AMPK signaling is to suppress cell proliferation in order to promote cell survival under energetic stress conditions. This unique, pro-survival function of LKB1 has led to the discovery of reagents, such as phenformin, that specifically exploit the vulnerability of LKB1-null cells in their defect in sensing energetic stress. Such targeted agents represent a novel treatment strategy because they induce cell killing when LKB1 is absent. This review article summarizes various vulnerabilities of LKB1-mutant cells that have been reported in the literature and discusses the potential of using existing or developing novel reagents to target cancer cells with defective LKB1.
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Affiliation(s)
- Wei Zhou
- Corresponding author. Departments of Hematology and Medical Oncology, Emory University School of Medicine, 1365 Clifton Road, NE, Suite C4084, Atlanta 30322, Georgia. Tel.: +995 404 778 2134; fax: +995 404 778 5530.
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Li CC, Yu Z, Cui LH, Piao JM, Liu M. Role of P14 and MGMT Gene Methylation in Hepatocellular Carcinomas: a Meta-analysis. Asian Pac J Cancer Prev 2014; 15:6591-6. [DOI: 10.7314/apjcp.2014.15.16.6591] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Mah WC, Thurnherr T, Chow PKH, Chung AYF, Ooi LLPJ, Toh HC, Teh BT, Saunthararajah Y, Lee CGL. Methylation profiles reveal distinct subgroup of hepatocellular carcinoma patients with poor prognosis. PLoS One 2014; 9:e104158. [PMID: 25093504 PMCID: PMC4122406 DOI: 10.1371/journal.pone.0104158] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 07/05/2014] [Indexed: 12/12/2022] Open
Abstract
Hepatocellular Carcinoma (HCC) is one of the leading causes of cancer-associated mortality worldwide. However, the role of epigenetic changes such as aberrant DNA methylation in hepatocarcinogenesis remains largely unclear. In this study, we examined the methylation profiles of 59 HCC patients. Using consensus hierarchical clustering with feature selection, we identified three tumor subgroups based on their methylation profiles and correlated these subgroups with clinicopathological parameters. Interestingly, one tumor subgroup is different from the other 2 subgroups and the methylation profile of this subgroup is the most distinctly different from the non-tumorous liver tissues. Significantly, this subgroup of patients was found to be associated with poor overall as well as disease-free survival. To further understand the pathways modulated by the deregulation of methylation in HCC patients, we integrated data from both the methylation as well as the gene expression profiles of these 59 HCC patients. In these patients, while 4416 CpG sites were differentially methylated between the tumors compared to the adjacent non-tumorous tissues, only 536 of these CpG sites were associated with differences in the expression of their associated genes. Pathway analysis revealed that forty-four percent of the most significant upstream regulators of these 536 genes were involved in inflammation-related NFκB pathway. These data suggest that inflammation via the NFκB pathway play an important role in modulating gene expression of HCC patients through methylation. Overall, our analysis provides an understanding on aberrant methylation profile in HCC patients.
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Affiliation(s)
- Way-Champ Mah
- Division of Medical Sciences, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Singapore, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, Singapore
| | - Thomas Thurnherr
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, Singapore
- Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Pierce K. H. Chow
- Duke-NUS Graduate Medical School, Singapore, Singapore
- Department of Surgery, Singapore General Hospital, Singapore, Singapore
| | | | - London L. P. J. Ooi
- Department of Surgery, Singapore General Hospital, Singapore, Singapore
- Department of Surgical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Han Chong Toh
- Department of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Bin Tean Teh
- Division of Medical Sciences, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Graduate Medical School, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Yogen Saunthararajah
- Department of Hematologic Oncology and Blood Disorders, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Caroline G. L. Lee
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Division of Medical Sciences, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Singapore, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, Singapore
- Duke-NUS Graduate Medical School, Singapore, Singapore
- * E-mail:
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DNA methylation: potential biomarker in Hepatocellular Carcinoma. Biomark Res 2014; 2:5. [PMID: 24635883 PMCID: PMC4022334 DOI: 10.1186/2050-7771-2-5] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Accepted: 03/07/2014] [Indexed: 12/12/2022] Open
Abstract
Hepatocellular Carcinoma (HCC) is one of the most common cancers in the world and it is often associated with poor prognosis. Liver transplantation and resection are two currently available curative therapies. However, most patients cannot be treated with such therapies due to late diagnosis. This underscores the urgent need to identify potential markers that ensure early diagnosis of HCC. As more evidences are suggesting that epigenetic changes contribute hepatocarcinogenesis, DNA methylation was poised as one promising biomarker. Indeed, genome wide profiling reveals that aberrant methylation is frequent event in HCC. Many studies showed that differentially methylated genes and CpG island methylator phenotype (CIMP) status in HCC were associated with clinicopathological data. Some commonly studied hypermethylated genes include p16, SOCS1, GSTP1 and CDH1. In addition, studies have also revealed that methylation markers could be detected in patient blood samples and associated with poor prognosis of the disease. Undeniably, increasing number of methylation markers are being discovered through high throughput genome wide data in recent years. Proper and systematic validation of these candidate markers in prospective cohort is required so that their actual prognostication and surveillance value could be accurately determined. It is hope that in near future, methylation marker could be translate into clinical use, where patients at risk could be diagnosed early and that the progression of disease could be more correctly assessed.
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DNA methylation and regulation of the CD8A after duck hepatitis virus type 1 infection. PLoS One 2014; 9:e88023. [PMID: 24505360 PMCID: PMC3913717 DOI: 10.1371/journal.pone.0088023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 01/02/2014] [Indexed: 11/19/2022] Open
Abstract
Background Cluster of differentiation 8 (CD8) is expressed in cytotoxic T cells, where it functions as a co-receptor for the T-cell receptor by binding to major histocompatibility complex class I (MHCI) proteins, which present peptides on the cell surface. CD8A is critical for cell-mediated immune defense and T-cell development. CD8A transcription is controlled by several cis-acting elements and trans-acting elements and is also regulated by DNA methylation. However, the epigenetic regulation of CD8A in the duck and its relationship with virus infection are still unclear. Results We investigated the epigenetic transcriptional regulatory mechanisms, such as DNA methylation, for the expression of the CD8A and further evaluated the contribution of such epigenetic regulatory mechanisms to DHV-I infection in the duck. Real-time quantitative polymerase chain reaction (RT-qPCR) revealed the highest level of CD8A expression to be in the thymus, followed by the lungs, spleen, and liver, and the levels of CD8A expression were very low in the kidney, cerebrum, cerebellum, and muscle in the duck. RT-qPCR also demonstrated that the CD8A mRNA was down-regulated significantly in morbid ducklings treated with DHV-1 and up-regulated significantly in non-morbid ducklings in all the tissues tested. In addition, hypermethylation of CD8A was detected in the morbid ducklings, whereas relatively low methylation of CD8A was evident in the non-morbid ducklings. The CD8A mRNA level was negatively associated with the CpG methylation level of CD8A and global methylation status. Conclusions We concluded that the mRNA level of the CD8A was negatively associated with the CpG methylation level of CD8A and global methylation status in the duck, suggesting that the hypermethylation of CD8A may be associated with DHV-1 infection. The first two CpG sites of the CD8A promoter region could be considered as epigenetic biomarkers for resistance breeding against duckling hepatitis disease in the duck.
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Promoter methylation of SFRP3 is frequent in hepatocellular carcinoma. DISEASE MARKERS 2014; 2014:351863. [PMID: 24591760 PMCID: PMC3925610 DOI: 10.1155/2014/351863] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Revised: 10/01/2013] [Accepted: 10/22/2013] [Indexed: 12/30/2022]
Abstract
Oncogenic activation of the Wnt/β-catenin signaling pathway is common in human cancers. The secreted frizzled-related proteins (SFRPs) function as negative regulators of Wnt signaling and have important implications in carcinogenesis. Because there have been no reports about the role of SFRP3 in hepatocellular carcinoma (HCC), we investigated the level of methylation and transcription of SFRP3. Four HCC cell lines, 60 HCCs, 23 cirrhosis livers, 37 chronic hepatitis livers, and 30 control livers were prescreened for SFRP3 promoter methylation by methylation-specific polymerase chain reaction (MS-PCR) and bisulfite sequencing. SFRP3 promoter methylation was observed in 100%, 60%, 39.1%, 16.2%, and 0% in HCC cell lines, primary HCCs, cirrhosis livers, chronic hepatitis livers, and control livers, respectively. Demethylation treatment with 5-aza-2′-deoxycytidine in HCC cells restored or increased the SFRP3 mRNA expression. We next used quantitative MS-PCR (QMSP) to analyze the methylation level of SFRP3 in 60 HCCs and their corresponding nontumor tissues. Methylation of SFRP3 promoter region in HCCs increased significantly compared with control tissues. There is a positive correlation between promoter hypermethylation and SFRP3 mRNA downregulation. Our data suggest that promoter hypermethylation of SFRP3 is a common event in HCCs and plays an important role in regulation of SFRP3 mRNA expression.
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Hou X, Peng JX, Hao XY, Cai JP, Liang LJ, Zhai JM, Zhang KS, Lai JM, Yin XY. DNA methylation profiling identifies EYA4 gene as a prognostic molecular marker in hepatocellular carcinoma. Ann Surg Oncol 2013; 21:3891-9. [PMID: 24306662 DOI: 10.1245/s10434-013-3401-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Indexed: 12/17/2022]
Abstract
BACKGROUND DNA hypermethylation plays important roles in carcinogenesis by silencing key genes. This study aims to identify pivotal genes in hepatocellular carcinoma (HCC) by DNA methylation microarray and to assess their prognostic values. MATERIALS AND METHODS DNA methylation microarray was performed in 45 pairs of HCC and adjacent nontumorous tissues and six normal liver tissues to identify hypermethylated genes in HCC. Potential prognosis-related genes were selected among hypermethylated genes by analyzing influences of methylation levels on disease-free survival (DFS) and overall survival (OS) in 45 patients. Their prognostic values were validated in 154 patients with HCC (including the initial 45 patients) to determine the independent prognostic gene. RESULTS Altogether, 54 CpG islands in 44 genes were hypermethylated in HCC compared with liver tissues. Among them, methylation levels of ERG and HOXA11 were inversely associated with DFS (both P < 0.050), and methylation levels of EYA4 were inversely related to DFS and OS (both P < 0.050). EYA4 expression was inversely related to tumor size (P < 0.050). Lower EYA4 expression and larger tumor size were independent predictors of both shorter DFS and OS, and higher Barcelona Clinic Liver Cancer (BCLC) staging was an independent predictor of shorter OS (all P < 0.050). CONCLUSIONS EYA4 functions as a prognostic molecular marker in HCC. Its aberrant hypermethylation and subsequent down-regulation may promote tumor progression.
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Affiliation(s)
- Xun Hou
- Departments of Hepatobiliary Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, People's Republic of China
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Murphy SK, Yang H, Moylan CA, Pang H, Dellinger A, Abdelmalek MF, Garrett ME, Ashley-Koch A, Suzuki A, Tillmann HL, Hauser MA, Mae Diehl A. Relationship between methylome and transcriptome in patients with nonalcoholic fatty liver disease. Gastroenterology 2013; 145:1076-87. [PMID: 23916847 PMCID: PMC3805742 DOI: 10.1053/j.gastro.2013.07.047] [Citation(s) in RCA: 277] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 07/25/2013] [Accepted: 07/26/2013] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Cirrhosis and liver cancer are potential outcomes of advanced nonalcoholic fatty liver disease (NAFLD). It is not clear what factors determine whether patients will develop advanced or mild NAFLD, limiting noninvasive diagnosis and treatment before clinical sequelae emerge. We investigated whether DNA methylation profiles can distinguish patients with mild disease from those with advanced NAFLD, and how these patterns are functionally related to hepatic gene expression. METHODS We collected frozen liver biopsies and clinical data from patients with biopsy-proven NAFLD (56 in the discovery cohort and 34 in the replication cohort). Samples were divided into groups based on histologic severity of fibrosis: F0-1 (mild) and F3-4 (advanced). DNA methylation profiles were determined and coupled with gene expression data from the same biopsies; differential methylation was validated in subsets of the discovery and replication cohorts. We then analyzed interactions between the methylome and transcriptome. RESULTS Clinical features did not differ between patients known to have mild or advanced fibrosis based on biopsy analysis. There were 69,247 differentially methylated CpG sites (76% hypomethylated, 24% hypermethylated) in patients with advanced vs mild NAFLD (P < .05). Methylation at fibroblast growth factor receptor 2, methionine adenosyl methyltransferase 1A, and caspase 1 was validated by bisulfite pyrosequencing and the findings were reproduced in the replication cohort. Methylation correlated with gene transcript levels for 7% of differentially methylated CpG sites, indicating that differential methylation contributes to differences in expression. In samples with advanced NAFLD, many tissue repair genes were hypomethylated and overexpressed, and genes in certain metabolic pathways, including 1-carbon metabolism, were hypermethylated and underexpressed. CONCLUSIONS Functionally relevant differences in methylation can distinguish patients with advanced vs mild NAFLD. Altered methylation of genes that regulate processes such as steatohepatitis, fibrosis, and carcinogenesis indicate the role of DNA methylation in progression of NAFLD.
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Affiliation(s)
- Susan K. Murphy
- Department of Obstetrics and Gynecology, Duke University, Durham, NC
| | - Hyuna Yang
- Department of Bioinformatics and Biostatistics, Duke University, Durham, NC
| | - Cynthia A. Moylan
- Division of Gastroenterology and Hepatology, Duke University, Durham, NC
| | - Herbert Pang
- Department of Bioinformatics and Biostatistics, Duke University, Durham, NC
| | - Andrew Dellinger
- Department of Bioinformatics and Biostatistics, Duke University, Durham, NC
| | | | | | | | - Ayako Suzuki
- Division of Gastroenterology and Hepatology, Duke University, Durham, NC
| | - Hans L. Tillmann
- Section of Medical Genetics, Department of Medicine, Duke University, Durham, NC
| | | | - Anna Mae Diehl
- Division of Gastroenterology and Hepatology, Duke University, Durham, NC
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Misawa Y, Misawa K, Kanazawa T, Uehara T, Endo S, Mochizuki D, Yamatodani T, Carey TE, Mineta H. Tumor suppressor activity and inactivation of galanin receptor type 2 by aberrant promoter methylation in head and neck cancer. Cancer 2013; 120:205-13. [DOI: 10.1002/cncr.28411] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 09/07/2013] [Accepted: 09/11/2013] [Indexed: 01/28/2023]
Affiliation(s)
- Yuki Misawa
- Department of Otolaryngology/Head and Neck Surgery; Hamamatsu University School of Medicine; Shizuoka Japan
| | - Kiyoshi Misawa
- Department of Otolaryngology/Head and Neck Surgery; Hamamatsu University School of Medicine; Shizuoka Japan
| | - Takeharu Kanazawa
- Department of Otolaryngology/Head and Neck Surgery; Jichi Medical University; Tochigi Japan
| | - Takayuki Uehara
- Department of Otolaryngology/Head and Neck Surgery; Jichi Medical University; Tochigi Japan
| | - Shori Endo
- Department of Otolaryngology/Head and Neck Surgery; Hamamatsu University School of Medicine; Shizuoka Japan
| | - Daiki Mochizuki
- Department of Otolaryngology/Head and Neck Surgery; Hamamatsu University School of Medicine; Shizuoka Japan
| | - Takashi Yamatodani
- Department of Otolaryngology/Head and Neck Surgery; Hamamatsu University School of Medicine; Shizuoka Japan
| | - Thomas E. Carey
- Laboratory of Head and Neck Cancer Biology, Department of Otolaryngology/Head and Neck Surgery; University of Michigan; Ann Arbor Michigan
| | - Hiroyuki Mineta
- Department of Otolaryngology/Head and Neck Surgery; Hamamatsu University School of Medicine; Shizuoka Japan
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Cao J, Song Y, Bi N, Shen J, Liu W, Fan J, Sun G, Tong T, He J, Shi Y, Zhang X, Lu N, He Y, Zhang H, Ma K, Luo X, Lv L, Deng H, Cheng J, Zhu J, Wang L, Zhan Q. DNA methylation-mediated repression of miR-886-3p predicts poor outcome of human small cell lung cancer. Cancer Res 2013; 73:3326-35. [PMID: 23592755 DOI: 10.1158/0008-5472.can-12-3055] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Small cell lung cancer (SCLC) is one of the most aggressive types of cancer, yet the pathologic mechanisms underlying its devastating clinical outcome remain elusive. In this report, we surveyed 924 miRNA (miR) for their expressions in the formalin-fixed paraffin-embedded specimens from 42 patients with SCLC, and found that the downregulated miR-886-3p is closely correlated with the shorter survival of SCLC. This correlation was validated with another 40 cases. It was further discovered that loss of miR-886-3p expression was mediated by DNA hypermethylation of its promoter in both cultured SCLC cells and tumor samples. Moreover, miR-886-3p potently repressed cell proliferation, migration, and invasion of NCI-H446 cell in cell culture via suppression of the expression of its target genes: PLK1 and TGF-β1 at posttranscription levels. Forced upregulation of miR-886-3p greatly inhibited in vivo tumor growth, bone/muscle invasion, and lung metastasis of NCI-H446 cells. This newly identified miR-886-3p-PLK1/TGF-β1 nexus that modulates SCLC aggression suggests that both loss of miR-886-3p expression and hypermethylation of the miR-886 promoter are the promising indicators for poor outcome of as well as new therapeutic targets for SCLC.
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Affiliation(s)
- Jianzhong Cao
- The State Key Laboratory of Molecular Oncology, Cancer Hospital and Cancer Institute, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, China
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Mohana Devi S, Balachandar V, Arun M, Suresh Kumar S, Balamurali Krishnan B, Sasikala K. Analysis of genetic damage and gene polymorphism in hepatocellular carcinoma (HCC) patients in a South Indian population. Dig Dis Sci 2013; 58:759-67. [PMID: 23053887 DOI: 10.1007/s10620-012-2409-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Accepted: 09/06/2012] [Indexed: 01/15/2023]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is the second leading cause of cancer death in many regions of Asia and the etiology of human HCC is clearly multi-factorial. The development of effective markers for the detection of HCC could have an impact on cancer mortality and significant health implications worldwide. The subjects presented here were recruited based on the serum alpha-fetoprotein level, which is an effective marker for HCC. Further, the chromosomal alterations were elucidated using trypsin G-banding. HCCs with p53 mutations have high malignant potential and are used as an indicator for the biological behavior of recurrent HCCs. The functional polymorphism in the XRCC1 gene, which participates in the base-excision repair of oxidative DNA damage, was associated with increased risk of early onset HCC. Thus, in this investigation, the p53 and XRCC1 gene polymorphisms using the standard protocols were also assessed to find out whether these genes may be associated with HCC susceptibility. METHODS Blood samples from HCC patients (n = 93) were collected from oncology clinics in South India. Control subjects (n = 93) who had no history of tumors were selected and they were matched to cases on sex, age, and race. Peripheral blood was analyzed for chromosomal aberrations (CAs) and micronuclei (MN) formation. p53 and XRCC1 genotypes were detected using a PCR-RFLP technique. RESULTS Specific biomarkers on cytogenetic endpoints might help in diagnosis and treatment measures. The frequencies of genotypes between groups were calculated by χ(2) test. A statistically significant (p < 0.05) increase in CA was observed in HCC patients compared to their controls as confirmed by ANOVA and MN shows insignificant results. The study on p53 Arg72Pro and XRCC1 Arg399Gln polymorphism in HCC patients demonstrated differences in allele frequencies compared to their controls. CONCLUSIONS The present study indicates that chromosomal alterations and the genetic variations of p53 and XRCC1 may contribute to inter-individual susceptibility to HCC. A very limited role of genetic polymorphism was investigated in modulating the HCC risk, but the combined effect of these variants may interact to increase the risk of HCC in the South Indian population.
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Affiliation(s)
- Subramaniam Mohana Devi
- Human Genetics Laboratory, School of Life Sciences, Bharathiar University, Coimbatore, Tamil Nadu, India.
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Shih YL, Hsieh CB, Yan MD, Tsao CM, Hsieh TY, Liu CH, Lin YW. Frequent concomitant epigenetic silencing of SOX1 and secreted frizzled-related proteins (SFRPs) in human hepatocellular carcinoma. J Gastroenterol Hepatol 2013; 28:551-9. [PMID: 23215838 DOI: 10.1111/jgh.12078] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/24/2012] [Indexed: 01/16/2023]
Abstract
BACKGROUND AND AIM Except for genetic mutations, epigenetic changes are also involved in the development of human cancers. Recently, we have identified SOX1, SRY (sex determining region Y)-box 1, is hypermethylated in cervical cancer and ovarian cancer. Therefore, we investigated whether promoter hypermethylation of SOX1 is common in hepatocellular carcinoma (HCC). METHODS We used methylation-specific polymerase chain reaction (MS-PCR) and bisulfite sequencing to analyze the methyaltion level of the SOX1 promoter in seven HCC cell lines, 54 clinical HCCs, 42 cirrhotic livers, 21 livers with chronic hepatitis, and 15 control livers. Then, we employed quantitative MS-PCR (QMSP) to validate in an independent set of samples (60 paired HCCs and 30 control livers). Finally, we used luciferase reporter and colony formation assay to check the effect of SOX1 in HCC. RESULTS Promoter methylation of SOX1 was significantly frequent in HCC cell lines and clinical HCCs, cirrhotic livers, but not in control livers (P < 0.0001). There is a significant correlation between downregulation of SOX1 expression and promoter methylation. QMSP results confirmed that promoter hypermethylation of SOX1 is significantly more frequent in HCCs than control livers (P < 0.0001). The frequency of SOX1 methylation in patients with secreted frizzled-related proteins (SFRPs) methylation is significantly higher than in patients without SFRPs methylation (P < 0.0001). Furthermore, ectopic expression of SOX1 could suppress T-cell factor-dependent transcriptional activity and colony formation number in HCCs. CONCLUSIONS Concomitant epigenetic silencing of SOX1 and SFRPs through promoter hypermethylation is frequent in HCCs, and this might contribute to abnormal activation of canonical Wnt signal pathway.
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Affiliation(s)
- Yu-Lueng Shih
- Division of Gastroenterology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taiwan
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Wang J, Zhu Z, Ma H. Label-Free Real-Time Detection of DNA Methylation Based on Quartz Crystal Microbalance Measurement. Anal Chem 2013; 85:2096-101. [DOI: 10.1021/ac3026724] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Jie Wang
- Division of
Nanobiomedicine,
Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, Jiangsu 215123, People’s
Republic of China
- Institute
of Biophysics, Chinese Academy of Sciences, Beijing, 100101, People’s
Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People’s
Republic of China
| | - Zhiqiang Zhu
- Division of
Nanobiomedicine,
Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, Jiangsu 215123, People’s
Republic of China
| | - Hongwei Ma
- Division of
Nanobiomedicine,
Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, Jiangsu 215123, People’s
Republic of China
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Zhao Y, Guo S, Sun J, Huang Z, Zhu T, Zhang H, Gu J, He Y, Wang W, Ma K, Wang J, Yu J. Methylcap-seq reveals novel DNA methylation markers for the diagnosis and recurrence prediction of bladder cancer in a Chinese population. PLoS One 2012; 7:e35175. [PMID: 22529986 PMCID: PMC3328468 DOI: 10.1371/journal.pone.0035175] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Accepted: 03/09/2012] [Indexed: 12/21/2022] Open
Abstract
PURPOSE There is a need to supplement or supplant the conventional diagnostic tools, namely, cystoscopy and B-type ultrasound, for bladder cancer (BC). We aimed to identify novel DNA methylation markers for BC through genome-wide profiling of BC cell lines and subsequent methylation-specific PCR (MSP) screening of clinical urine samples. EXPERIMENTAL DESIGN The methyl-DNA binding domain (MBD) capture technique, methylCap/seq, was performed to screen for specific hypermethylated CpG islands in two BC cell lines (5637 and T24). The top one hundred hypermethylated targets were sequentially screened by MSP in urine samples to gradually narrow the target number and optimize the composition of the diagnostic panel. The diagnostic performance of the obtained panel was evaluated in different clinical scenarios. RESULTS A total of 1,627 hypermethylated promoter targets in the BC cell lines was identified by Illumina sequencing. The top 104 hypermethylated targets were reduced to eight genes (VAX1, KCNV1, ECEL1, TMEM26, TAL1, PROX1, SLC6A20, and LMX1A) after the urine DNA screening in a small sample size of 8 normal control and 18 BC subjects. Validation in an independent sample of 212 BC patients enabled the optimization of five methylation targets, including VAX1, KCNV1, TAL1, PPOX1, and CFTR, which was obtained in our previous study, for BC diagnosis with a sensitivity and specificity of 88.68% and 87.25%, respectively. In addition, the methylation of VAX1 and LMX1A was found to be associated with BC recurrence. CONCLUSIONS We identified a promising diagnostic marker panel for early non-invasive detection and subsequent BC surveillance.
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Affiliation(s)
- Yangxing Zhao
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shicheng Guo
- Ministry of Education's Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Jinfeng Sun
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhaohui Huang
- Oncology Institute of Wuxi, The Fourth Affiliated Hospital of Suzhou University, Wuxi, China
| | - Tongyu Zhu
- Department of Urology, Shanghai Key Laboratory of Organ Transplantation, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Hongyu Zhang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jun Gu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yinghua He
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Wang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kelong Ma
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jina Wang
- Department of Urology, Shanghai Key Laboratory of Organ Transplantation, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jian Yu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Geng J, Sun J, Lin Q, Gu J, Zhao Y, Zhang H, Feng X, He Y, Wang W, Zhou X, Yu J. Methylation status of NEUROG2 and NID2 improves the diagnosis of stage I NSCLC. Oncol Lett 2012; 3:901-906. [PMID: 22741015 DOI: 10.3892/ol.2012.587] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Accepted: 01/26/2012] [Indexed: 01/09/2023] Open
Abstract
In our previous study, we attempted to develop a tool for the early diagnosis of non-small cell lung cancer (NSCLC) using DNA methylation biomarkers. With the aim of improving the diagnostic potential by optimizing the composition of the target set, in this study, 13 candidate genes (ACTA1, AIDH1A2, CBX8, CDH8, EVX1, MGC16275, NEUROG1, NEUROG2, NID2, OTX2OS1, PGAM2, PHOX2B and TOX) were analyzed by methylation-specific PCR to determine the methylation status of each gene in 5 NSCLC cell lines and in lung tissue samples from 15 healthy volunteers, 103 stage I NSCLC patients and 26 non-cancerous control patients. Results showed that NEUROG2 and NID2 were hypermethylated in stage I NSCLC tissues (31.07 and 46.60%, respectively) and unmethylated in normal lung tissues (0/15) and non-cancerous tissues (0/26). Following recombination, an optimized 5-gene panel (NEUROG2, NID2, RASSF1A, APC and HOXC9) achieved a sensitivity of 91.26% with a specificity of 84.62% in the detection of stage I NSCLC. The optimized 5-gene panel greatly improved the diagnostic power for stage I NSCLC.
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Affiliation(s)
- Junfeng Geng
- Department of General Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, P.R. China
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Epigenetic silencing of IRF7 and/or IRF5 in lung cancer cells leads to increased sensitivity to oncolytic viruses. PLoS One 2011; 6:e28683. [PMID: 22194884 PMCID: PMC3237484 DOI: 10.1371/journal.pone.0028683] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Accepted: 11/13/2011] [Indexed: 01/28/2023] Open
Abstract
Defective IFN signaling results in loss of innate immunity and sensitizes cells to enhanced cytolytic killing after Vesticular Stomatitis Virus (VSV) infection. Examination of the innate immunity status of normal human bronchial epithelial cells Beas2B and 7 lung cancer cells revealed that the abrogation of IFN signaling in cancer cells is associated with greater sensitivity to VSV infection. The disruption of the IFN pathway in lung cancer cell lines and primary tumor tissues is caused by epigenetic silencing of critical interferon responsive transcription factors IRF7 and/or IRF5. Although 5-aza-2′-deoxycytidine treatment fails to reactivate IRF7 and IRF5 expression or protect cells from VSV infection, manipulating IFN signaling by altering IRF expression changes the viral susceptibility of these cells. Lung cancer cells can be partially protected from viral killing using IRF5+IRF7 overexpression, whereas IFN pathway disruption by transfection of siRNAs to IRF5+IRF7 increases cells' vulnerability to viral infection. Therefore, IRF5 and IRF7 are key transcription factors in IFN pathway that determine viral sensitivity of lung cancer cells; the epigenetically impaired IFN pathway in lung cancer tissues provides potential biomarkers for successful selective killing of cancer cells by oncolytic viral therapy.
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Aberrant CpG island hypermethylation and down-regulation of Oct-6 mRNA expression in human hepatocellular carcinoma. Dig Dis Sci 2011; 56:3072-7. [PMID: 21448695 DOI: 10.1007/s10620-011-1686-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Accepted: 03/15/2011] [Indexed: 01/31/2023]
Abstract
BACKGROUND Aberrant CpG island hypermethylation is a major epigenetic mechanism that can inactivate the transcription of cancer-related genes. PURPOSE This study aimed to investigate whether Oct-6 transcription was regulated by CpG island methylation in hepatocellular carcinoma (HCC). METHODS Quantitative real-time PCR and the MassARRAY platform (Sequenom) were employed in 38 HCC tissues samples and four cell lines. RESULTS The levels of Oct-6 mRNA were decreased by more than twofold in 31 of 38 tumor tissues compared to that of adjacent non-cancerous tissues. Among the 31 tumor tissues with lower levels of Oct-6 mRNA, 17 tumor tissues also had higher methylation levels in Oct-6 CpG island. Based on these results, we hypothesized that CpG island hypermethylation may down-regulate Oct-6 mRNA expression in HCC. To confirm this hypothesis, we also analyzed the changes in Oct-6 mRNA expression and CpG island methylation in four HCC cell lines (Huh7, Bel-7402, HepG2 and SMMC-7721) after treatment with 0.1, 0.5 and 2.5 μM 5-Aza-2-deoxycytidine (5-Aza-CdR), a demethylating agent. The results demonstrated that the CpG island methylation levels decreased and Oct-6 mRNA levels increased in a dose-dependent manner in both Huh7 and Bel7402 cells, but there were only slight changes in HepG2 cell. Interestingly, there were no significant alterations of Oct-6 mRNA levels observed in SMMC7721 cell; although lower levels of CpG island methylation were detected after treatment with 5-Aza-CdR. CONCLUSIONS Our study shows that CpG island hypermethylation contributes to down-regulation of Oct-6 mRNA expression in HCC.
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Zang JJ, Xie F, Xu JF, Qin YY, Shen RX, Yang JM, He J. P16 gene hypermethylation and hepatocellular carcinoma: A systematic review and meta-analysis. World J Gastroenterol 2011; 17:3043-8. [PMID: 21799651 PMCID: PMC3132256 DOI: 10.3748/wjg.v17.i25.3043] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Revised: 03/17/2011] [Accepted: 03/24/2011] [Indexed: 02/06/2023] Open
Abstract
AIM: To quantitatively investigate the effect of p16 hypermethylation on hepatocellular carcinoma (HCC) and hepatocirrhosis using a meta-analysis of available case-control studies.
METHODS: Previous studies have primarily evaluated the incidence of p16 hypermethylation in HCC and corresponding control groups, and compared the incidence of p16 hypermethylation in tumor tissues, pericancer liver tissues, normal liver tissues and non-tumor liver tissues with that in other diseases. Data regarding publication information, study characteristics, and incidence of p16 hypermethylation in both groups were collected from these studies and summarized.
RESULTS: Fifteen studies, including 744 cases of HCC and 645 non-tumor cases, were identified for meta-analysis. Statistically significant odds ratios (ORs) of p16 hypermethylation were obtained from tumor tissues and non-tumorous liver tissues of HCC patients (OR 7.04, 95% CI: 3.87%-12.78%, P < 0.0001), tumor tissues of HCC patients and healthy liver tissues of patients with other diseases (OR 12.17, 95% CI: 6.64%-22.31%, P < 0.0001), tumor tissues of HCC patients and liver tissues of patients with non-tumorous liver diseases (OR 6.82, 95% CI: 4.31%-10.79%, P < 0.0001), and cirrhotic liver tissues and non-cirrhotic liver tissues (OR 4.96, 95% CI: 1.45%-16.96%, P = 0.01). The pooled analysis showed significantly increased ORs of p16 hypermethylation (OR 6.98, 95% CI: 4.64%-10.49%, P < 0.001) from HCC tissues and cirrhotic tissues.
CONCLUSION: P16 hypermethylation induces the inactivation of p16 gene, plays an important role in hepatocarcinogenesis, and is associated with an increased risk of HCC and liver cirrhosis.
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Starker LF, Svedlund J, Udelsman R, Dralle H, Akerström G, Westin G, Lifton RP, Björklund P, Carling T. The DNA methylome of benign and malignant parathyroid tumors. Genes Chromosomes Cancer 2011; 50:735-45. [PMID: 21638518 PMCID: PMC3134609 DOI: 10.1002/gcc.20895] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Accepted: 04/29/2011] [Indexed: 11/09/2022] Open
Abstract
The role of DNA methylation of CpG islands in parathyroid tumorigenesis has not been analyzed in an unbiased, systematic fashion. DNA was isolated from normal and pathologic parathyroid tissues, bisulphite modified and analyzed using the Infinium HumanMethylation27 BeadChip. Distinct hierarchical clustering of genes with altered DNA methylation profiles in normal and pathologic parathyroid tissue was evident. Comparing normal parathyroid tissue with parathyroid adenomas, 367 genes were significantly altered, while 175 genes significantly differed when comparing parathyroid carcinomas and normal parathyroid tissues. A comparison between parathyroid adenomas and parathyroid carcinomas identified 263 genes with significantly distinct methylation levels. Results were confirmed for certain genes in a validation cohort of 40 parathyroid adenomas by methylation-specific PCR. Genes of known or putative importance in the development of parathyroid tumors showed significant and frequent hypermethylation. DNA hypermethylation of CDKN2B, CDKN2A, WT1, SFRP1, SFRP2, and SFRP4 was associated with reduced gene expression in both benign and malignant parathyroid tumors. Treatment with 5-aza-2'-deoxycytidine of primary cell cultures restores expression of hypermethylated genes in benign and malignant parathyroid tumors. In conclusion, the unbiased, genome-wide study of the parathyroid tumor DNA methylome identified a number of genes with altered DNA methylation patterns of putative importance to benign and malignant parathyroid tumorigenesis.
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Affiliation(s)
- Lee F Starker
- Department of Surgery, Yale University , New Haven, CT; Yale Endocrine Neoplasia Laboratory, 333 Cedar Street, New Haven, CT 06520, USA
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Hua D, Hu Y, Wu YY, Cheng ZH, Yu J, Du X, Huang ZH. Quantitative methylation analysis of multiple genes using methylation-sensitive restriction enzyme-based quantitative PCR for the detection of hepatocellular carcinoma. Exp Mol Pathol 2011; 91:455-60. [PMID: 21600201 DOI: 10.1016/j.yexmp.2011.05.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Revised: 04/30/2011] [Accepted: 05/02/2011] [Indexed: 01/16/2023]
Abstract
DNA methylation is a promising biomarker for cancer. This study was aimed at investigating the methylation levels of multiple genes in hepatocellular carcinoma (HCC) and to identify a combination of methylation markers that would be useful for the diagnosis of HCC. The methylation status of a panel of nine tumor-associated genes (APC, GSTP1, RASSF1A, CDKN2A, SFRP1, RUNX3, SOCS1, Hint1, and HIC-1) in 8 normal liver tissues and 47 paired HCCs and non-tumorous tissues (NTs) was determined using a modified methylation-sensitive, restriction enzyme-based quantitative PCR (MSRE-qPCR) method. The methylation levels of six genes (APC, CDKN2A, GSTP1, RASSF1A, SFRP1 and RUNX3) were significantly higher in HCCs than in adjacent NTs (P<0.05). Although the AUC (area under the curve) for each individual gene was low to moderate (range: 0.576 to 0.835) according to receiver operator characteristic (ROC) curve analysis, the combination analysis of these six genes resulted in an increase of AUC of 0.954 with 85.1% sensitivity, 89.4% specificity, 88.9% positive predictive value, and 85.7% negative predictive value in discriminating HCC tissues from NT tissues. These results indicate that the analysis of a combination of these six methylated genes may be a promising method for the risk assessment and diagnosis of HCC.
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Affiliation(s)
- Dong Hua
- Oncology institute, The Fourth Affiliated Hospital of Suzhou University, Wuxi 214062, China
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38
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Su H, Hu N, Yang HH, Wang C, Takikita M, Wang QH, Giffen C, Clifford R, Hewitt SM, Shou JZ, Goldstein AM, Lee MP, Taylor PR, Kaempgen E, Van Gool SW, Helms W, Keegan P, Pazdur R. Global gene expression profiling and validation in esophageal squamous cell carcinoma and its association with clinical phenotypes. Clin Cancer Res 2011. [PMID: 29950348 DOI: 10.1158/1078-0432] [Citation(s) in RCA: 402] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
PURPOSE Esophageal squamous cell carcinoma (ESCC) is an aggressive tumor with poor prognosis. Understanding molecular changes in ESCC will enable identification of molecular subtypes and provide potential targets for early detection and therapy. EXPERIMENTAL DESIGN We followed up a previous array study with additional discovery and confirmatory studies in new ESCC cases by using alternative methods. We profiled global gene expression for discovery and confirmation, and validated selected dysregulated genes with additional RNA and protein studies. RESULTS A total of 159 genes showed differences with extreme statistical significance (P < E-15) and 2-fold differences or more in magnitude (tumor/normal RNA expression ratio, N = 53 cases), including 116 upregulated and 43 downregulated genes. Of 41 genes dysregulated in our prior array study, all but one showed the same fold change directional pattern in new array studies, including 29 with 2-fold changes or more. Alternative RNA expression methods validated array results: more than two thirds of 51 new cases examined by real-time PCR (RT-PCR) showed 2-fold differences or more for all seven genes assessed. Immunohistochemical protein expression results in 275 cases which were concordant with RNA for five of six genes. CONCLUSION We identified an expanded panel of genes dysregulated in ESCC and confirmed previously identified differentially expressed genes. Microarray-based gene expression results were confirmed by RT-PCR and protein expression studies. These dysregulated genes will facilitate molecular categorization of tumor subtypes and identification of their risk factors, and serve as potential targets for early detection, outcome prediction, and therapy.
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Affiliation(s)
- Hua Su
- Genetic Epidemiology Branch, DCEG, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Whitney Helms
- Office of Hematology and Oncology Products, Office of New Drugs, U.S. Food and Drug Administration, Silver Spring, Maryland
| | - Patricia Keegan
- Office of Hematology and Oncology Products, Office of New Drugs, U.S. Food and Drug Administration, Silver Spring, Maryland
| | - Richard Pazdur
- Office of Biostatistics, Office of Translational Sciences, U.S. Food and Drug Administration, Silver Spring, Maryland
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Murray PG, Fan Y, Davies G, Ying J, Geng H, Ng KM, Li H, Gao Z, Wei W, Bose S, Anderton J, Kapatai G, Reynolds G, Ito A, Marafioti T, Woodman CB, Ambinder R, Tao Q. Epigenetic silencing of a proapoptotic cell adhesion molecule, the immunoglobulin superfamily member IGSF4, by promoter CpG methylation protects Hodgkin lymphoma cells from apoptosis. THE AMERICAN JOURNAL OF PATHOLOGY 2010; 177:1480-90. [PMID: 20709797 DOI: 10.2353/ajpath.2010.100052] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The malignant Hodgkin/Reed-Sternberg (HRS) cells of Hodgkin lymphoma (HL) are believed to derive from germinal center (GC) B cells, but lack expression of a functional B cell receptor. As apoptosis is the normal fate of B-cell receptor-negative GC B cells, mechanisms that abrogate apoptosis are thus critical in HL development, such as epigenetic disruption of certain pro-apoptotic cancer genes including tumor suppressor genes. Identifying methylated genes elucidates oncogenic mechanisms and provides valuable biomarkers; therefore, we performed a chemical epigenetic screening for methylated genes in HL through pharmacological demethylation and expression profiling. IGSF4/CADM1/TSLC1, a pro-apoptotic cell adhesion molecule of the immunoglobulin superfamily, was identified together with other methylated targets. In contrast to its expression in normal GC B cells, IGSF4 was down-regulated and methylated in HL cell lines, most primary HL, and microdissected HRS cells of 3/5 cases, but not in normal peripheral blood mononuclear cells and seldom in normal lymph nodes. We also detected IGSF4 methylation in sera of 14/18 (78%) HL patients but seldom in normal sera. Ectopic IGSF4 expression decreased HL cells survival and increased their sensitivity to apoptosis. IGSF4 induction that normally follows heat shock stress treatment was also abrogated in methylated lymphoma cells. Thus, our data demonstrate that IGSF4 silencing by CpG methylation provides an anti-apoptotic signal to HRS cells important in HL pathogenesis.
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Affiliation(s)
- Paul G Murray
- Cancer Research UK Institute for Cancer Studies, University of Birmingham, Birmingham, UK
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Jin W, Liu Y, Chen L, Zhu H, Di GH, Ling H, Wu J, Shao ZM. Involvement of MyoD and c-myb in regulation of basal and estrogen-induced transcription activity of the BRCA1 gene. Breast Cancer Res Treat 2010; 125:699-713. [PMID: 20364308 DOI: 10.1007/s10549-010-0876-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2010] [Accepted: 03/25/2010] [Indexed: 01/12/2023]
Abstract
BRCA1 is closely related to the pathogenesis of breast cancer, BRCA1 mRNA is reduced in sporadic breast cancer cells despite the lack of mutations. In the present report, we find that MyoD expression and BRCA1 expression is correlated in sporadic breast tumors, overexpression of MyoD and c-myb stimulates BRCA1 expression, knockdown of MyoD and c-myb attenuates BRCA1 expression and attenuates the ability of BRCA1 to protect cells against hydrogen peroxide. MyoD and c-myb interact with p300 and PCAF, forming activating transcriptional complexes which bind to E-box and c-myb sites on the BRCA1 promoter and activate its transcription by inducing histone acetylation. Regulation of BRCA1 expression by MyoD and c-myb complexes may be part of an integral signaling pathway that determines and explains breast cancer susceptibility. Detection expression status of the various proteins in these complexes may predispose to the onset of sporadic breast cancer.
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Affiliation(s)
- Wei Jin
- Department of Breast Surgery, Breast Cancer Institute, Cancer Hospital/Cancer Institute, Department of Oncology, Shanghai Medical College, Fudan University, 270 Dong An Road Road, Shanghai, 200032, People's Republic of China
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Hepatocellular carcinoma displays distinct DNA methylation signatures with potential as clinical predictors. PLoS One 2010; 5:e9749. [PMID: 20305825 PMCID: PMC2840036 DOI: 10.1371/journal.pone.0009749] [Citation(s) in RCA: 149] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2009] [Accepted: 03/01/2010] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is characterized by late detection and fast progression, and it is believed that epigenetic disruption may be the cause of its molecular and clinicopathological heterogeneity. A better understanding of the global deregulation of methylation states and how they correlate with disease progression will aid in the design of strategies for earlier detection and better therapeutic decisions. METHODS AND FINDINGS We characterized the changes in promoter methylation in a series of 30 HCC tumors and their respective surrounding tissue and identified methylation signatures associated with major risk factors and clinical correlates. A wide panel of cancer-related gene promoters was analyzed using Illumina bead array technology, and CpG sites were then selected according to their ability to classify clinicopathological parameters. An independent series of HCC tumors and matched surrounding tissue was used for validation of the signatures. We were able to develop and validate a signature of methylation in HCC. This signature distinguished HCC from surrounding tissue and from other tumor types, and was independent of risk factors. However, aberrant methylation of an independent subset of promoters was associated with tumor progression and etiological risk factors (HBV or HCV infection and alcohol consumption). Interestingly, distinct methylation of an independent panel of gene promoters was strongly correlated with survival after cancer therapy. CONCLUSION Our study shows that HCC tumors exhibit specific DNA methylation signatures associated with major risk factors and tumor progression stage, with potential clinical applications in diagnosis and prognosis.
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High-throughput assessment of CpG site methylation for distinguishing between HCV-cirrhosis and HCV-associated hepatocellular carcinoma. Mol Genet Genomics 2010; 283:341-9. [PMID: 20165882 DOI: 10.1007/s00438-010-0522-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2009] [Accepted: 01/27/2010] [Indexed: 02/07/2023]
Abstract
Methylation of promoter CpG islands has been associated with gene silencing and demonstrated to lead to chromosomal instability. Therefore, some postulate that aberrantly methylated CpG regions may be important biomarkers indicative of cancer development. In this study we used the Illumina GoldenGate Methylation BeadArray Cancer Panel I for simultaneously profiling methylation of 1,505 CpG sites in order to identify methylation differences in 76 liver tissues ranging from normal to pre-neoplastic and neoplastic states. CpG sites for ESR1, GSTM2, and MME were significantly differentially methylated when comparing the pre-neoplastic tissues from patients with concomitant hepatocellular carcinoma (HCC) to the pre-neoplastic tissues from patients without HCC. When comparing paired HCC tissues to their corresponding pre-neoplastic non-tumorous tissues, eight CpG sites, including one CpG site that was hypermethylated (APC) and seven (NOTCH4, EMR3, HDAC9, DCL1, HLA-DOA, HLA-DPA1, and ERN1) that were hypomethylated in HCC, were identified. Our study demonstrates that high-throughput methylation technologies may be used to identify differentially methylated CpG sites that may prove to be important molecular events involved in carcinogenesis.
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Lu CY, Hsieh SY, Lu YJ, Wu CS, Chen LC, Lo SJ, Wu CT, Chou MY, Huang THM, Chang YS. Aberrant DNA methylation profile and frequent methylation of KLK10 and OXGR1 genes in hepatocellular carcinoma. Genes Chromosomes Cancer 2009; 48:1057-68. [PMID: 19760608 DOI: 10.1002/gcc.20708] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Investigating aberrant DNA methylation in the cancer genome may identify genes that play an important role in tumor progression. In this study, we combined differential methylation hybridization and a CpG microarray platform to characterize methylation profiles and identify novel candidate genes associated with hepatocellular carcinoma (HCC). The genomic DNA of 21 paired adjacent normal and HCC samples was used, and results were analyzed by hierarchical clustering. Twenty-seven hypermethylated candidates and 38 hypomethylated candidates were obtained. Six candidate genes from the hypermethylated group were validated by combined bisulfite restriction analysis; two genes, human kallikrein 10 gene (KLK10) and oxoglutarate (alpha-ketoglutarate) receptor 1 gene (OXGR1), were further analyzed by bisulfite sequencing. The DNA hypermethylation status of KLK10 and OXGR1 were subsequently examined in HCC cell lines and clinical samples using methylation-specific PCR. In 49 HCC samples, 46 (94%) showed that at least one of these two genes was highly methylated. Moreover, KLK10 and OXGR1 mRNA levels were inversely correlated (r = -0.435 and -0.497, P < 0.05) with DNA methylation as examined in paired adjacent normal and tumor samples. Statistical analyses further indicated that KLK10 hypermethylation was significantly associated with cirrhosis (P = 0.042) and HCV infection (P = 0.017) as well as inversely associated with HBV infection (P = 0.023). Furthermore, restoration of KLK10 and OXGR1 expression reduced the ability of anchorage-independent growth, and sensitized HCC cells to doxorubicin- or 5-fluorouracil-induced cytotoxicity. Our results suggest that the hypermethylated KLK10 and OXGR1 are frequent in HCC and may be useful as markers for clinical application.
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Affiliation(s)
- Chang-Yi Lu
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
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45
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Calvisi DF, Ladu S, Pinna F, Frau M, Tomasi ML, Sini M, Simile MM, Bonelli P, Muroni MR, Seddaiu MA, Lim DS, Feo F, Pascale RM. SKP2 and CKS1 promote degradation of cell cycle regulators and are associated with hepatocellular carcinoma prognosis. Gastroenterology 2009; 137:1816-26.e1-10. [PMID: 19686743 DOI: 10.1053/j.gastro.2009.08.005] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2009] [Revised: 07/08/2009] [Accepted: 08/06/2009] [Indexed: 12/02/2022]
Abstract
BACKGROUND & AIMS The cell cycle regulators P21(WAF1), P27(KIP1), P57(KIP2), P130, RASSF1A, and FOXO1 are down-regulated during hepatocellular carcinoma (HCC) pathogenesis. We investigated the role of the ubiquitin ligase subunits CKS1 and SKP2, which regulate proteasome degradation of cell cycle regulators, in HCC progression. METHODS Human HCC tissues from patients with better (HCCB, >3 years survival) and poorer prognosis (HCCP, <3 years survival) and HCC cell lines were analyzed. RESULTS The promoters of P21(WAF1), P27(KIP1), and P57(KIP2) were more frequently hypermethylated in HCCP than HCCB. Messenger RNA levels of these genes were up-regulated in samples in which these genes were not methylated; protein levels increased only in HCCB because of CKS1- and SKP2-dependent ubiquitination of these proteins in HCCP. The level of SKP2 expression correlated with rate of HCC cell proliferation and level of microvascularization of samples and was inversely correlated with apoptosis and survival. In HCCB, SKP2 activity was balanced by degradation by the ubiquitin ligase anaphase-promoting complex/cyclosome (APC/C)-CDH1 and up-regulation of SKP2 suppressor histidine triad nucleotide binding protein 1 (HINT1). In HCCP, however, SKP2 was not degraded because of down-regulation of the phosphatase CDC14B, CDK2-dependent serine phosphorylation (which inhibits interaction between CDH1 and SKP2), and HINT1 inactivation. In HCC cells, small interfering RNA knockdown of SKP2 reduced proliferation and ubiquitination of the cell cycle regulators, whereas SKP2 increased proliferation and reduced expression of cell cycle regulators. CONCLUSIONS Ubiquitination and proteasome degradation of P21WAF1, P27KIP1, P57KIP2, P130, RASSF1A, and FOXO1 and mechanisms that prevent degradation of SKP2 by APC/C-CDH1 contribute to HCC progression. CKS1-SKP2 ligase might be developed as a therapeutic target or diagnostic marker.
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Affiliation(s)
- Diego F Calvisi
- Department of Biomedical Sciences, Division of Experimental Pathology and Oncology, University of Sassari, Sassari, Italy
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Cheng Y, Zhang C, Zhao J, Wang C, Xu Y, Han Z, Jiang G, Guo X, Li R, Bu X, Wu M, Wei L. Correlation of CpG island methylator phenotype with poor prognosis in hepatocellular carcinoma. Exp Mol Pathol 2009; 88:112-7. [PMID: 19879258 DOI: 10.1016/j.yexmp.2009.10.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2009] [Revised: 10/16/2009] [Accepted: 10/20/2009] [Indexed: 02/06/2023]
Abstract
CpG island methylator phenotype (CIMP), in which multiple genes are concurrently methylated, is an important mechanism in hepatocellular carcinoma development. We determined a hypermethylation profile in hepatocellular carcinoma (HCC). We examined the promoter methylation status of 10 genes in 60 cases of hepatocellular carcinoma (HCC), 60 cases of paired non-tumor tissues, and 6 cases of normal tissues by methylation-specific PCR. The average methylated gene numbers were significantly different between HCC and nontumor tissues (p<0.001). We found metastasis, gamma-glutamyl transpeptidase (GGT) and tumor node metastasis (TNM) stage were significantly different among patients with different CIMP status. Patients with high frequency CIMP tumors had significantly worse survival than patients with intermediate frequency or no CIMP tumors (p<0.01 and p<0.05, respectively). Our results suggested that CIMP could serve as a molecular marker of late stage and poorly prognostic HCC development.
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Affiliation(s)
- Yue Cheng
- Tumor Immunology and Gene Therapy Center, Eastern Hepatobiliary Hospital, Second Military Medical University, 225 Changhai Road, Shanghai 200438, China
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Moribe T, Iizuka N, Miura T, Kimura N, Tamatsukuri S, Ishitsuka H, Hamamoto Y, Sakamoto K, Tamesa T, Oka M. Methylation of multiple genes as molecular markers for diagnosis of a small, well-differentiated hepatocellular carcinoma. Int J Cancer 2009; 125:388-97. [PMID: 19384946 DOI: 10.1002/ijc.24394] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The current study was conducted to identify robust methylation markers and their combinations that may prove useful for the diagnosis of early hepatocellular carcinoma (HCC). To achieve this, we performed in silico CpG mapping, direct sequencing and pyrosequencing after bisulfite treatment, and quantitative methylation-specific PCR (MSP) in HCC and non-HCC liver tissues. In the filtering group (25 HCCs), our direct sequencing analysis showed that, among the 12 methylation genes listed by in silico CpG mapping, 7 genes (RASSF1A, CCND2, SPINT2, RUNX3, GSTP1, APC and CFTR) were aberrantly methylated in stages I and II HCCs. In the validation group (20 pairs of HCCs and the corresponding non-tumor liver tissues), pyrosequencing analysis confirmed that the 7 genes were aberrantly and strongly methylated in early HCCs, but not in any of the corresponding non- tumor liver tissues (p < 0.00001). The results obtained using our novel quantitative MSP assay correlated well with those observed using the pyrosequencing analysis. Notably, in MSP assay, RASSF1A showed the most robust performance for the discrimination of HCC and non-HCC liver tissues. Furthermore, a combination of RASSF1A, CCND2 and SPINT2 showed 89-95% sensitivity, 91-100% specificity and 89-97% accuracy in discriminating between HCC and non-HCC tissues, and correctly diagnosed all early HCCs. These results indicate that the combination of these 3 genes may aid in the accurate diagnosis of early HCC.
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Affiliation(s)
- Toyoki Moribe
- Research Group, Molecular Diagnostics R&D Department, Roche Diagnostics K.K., Minato-ku, Tokyo, Japan
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Jee CD, Kim MA, Jung EJ, Kim J, Kim WH. Identification of genes epigenetically silenced by CpG methylation in human gastric carcinoma. Eur J Cancer 2009; 45:1282-1293. [DOI: 10.1016/j.ejca.2008.12.027] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2008] [Revised: 12/17/2008] [Accepted: 12/19/2008] [Indexed: 12/13/2022]
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Huang J, Lin Y, Li L, Qing D, Teng XM, Zhang YL, Hu X, Hu Y, Yang P, Han ZG. ARHI, as a novel suppressor of cell growth and downregulated in human hepatocellular carcinoma, could contribute to hepatocarcinogenesis. Mol Carcinog 2009; 48:130-40. [PMID: 18612997 DOI: 10.1002/mc.20461] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The identification of cancer genes differentially expressed in hepatocellular carcinoma (HCC) plays an important role in understanding the molecular mechanisms of hepatocarcinogenesis. Here, ARHI gene expression was analyzed by real-time RT-PCR and it was significantly downregulated in 33 of the 42 (78.6%, more than two folds) HCC specimens compared with adjacent noncancerous livers (P < 0.01). In addition, ARHI expression was reduced in some HCC samples at protein level confirmed by immunohistochemistry. Furthermore, our data suggested that the overexpression of ARHI can significantly inhibit cell growth and colony formation of Hep3B cells (P < 0.01), whilst silencing endogenous ARHI gene by RNAi could promote cell growth of Huh-7 and Focus. LOH of microsatellite markers D1S2806 and D1S2803 was only found in 2.4% (1 of 42 HCCs) of HCC cases. The expression of ARHI was obviously re-expressed in some HCC cells, Bel-7402, Bel-7405, QGY-7703 and Hep3B, by a demethylation agent, 5-aza-2'-deoxycytidine (DAC). DNA hypermethylation within ARHI promoter was identified in 47.1% of HCC specimens without ARHI expression. Our current observations provide evidences that ARHI downregulated in HCCs could play a role in liver cancer via acting as a tumor suppressor gene, which mainly was triggered by the epigenetic events in HCC specimens.
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Affiliation(s)
- Jian Huang
- Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Chinese National Human Genome Center at Shanghai, Shanghai, China
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Zhu J, Yao X. Use of DNA methylation for cancer detection: Promises and challenges. Int J Biochem Cell Biol 2009; 41:147-54. [DOI: 10.1016/j.biocel.2008.09.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Revised: 09/08/2008] [Accepted: 09/10/2008] [Indexed: 01/12/2023]
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