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Köhler CU, Schork K, Turewicz M, Eisenacher M, Roghmann F, Noldus J, Marcus K, Brüning T, Käfferlein HU. Use of Multiple Machine Learning Approaches for Selecting Urothelial Cancer-Specific DNA Methylation Biomarkers in Urine. Int J Mol Sci 2024; 25:738. [PMID: 38255812 PMCID: PMC10815677 DOI: 10.3390/ijms25020738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 01/03/2024] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
Diagnosing urothelial cancer (UCa) via invasive cystoscopy is painful, specifically in men, and can cause infection and bleeding. Because the UCa risk is higher for male patients, urinary non-invasive UCa biomarkers are highly desired to stratify men for invasive cystoscopy. We previously identified multiple DNA methylation sites in urine samples that detect UCa with a high sensitivity and specificity in men. Here, we identified the most relevant markers by employing multiple statistical approaches and machine learning (random forest, boosted trees, LASSO) using a dataset of 251 male UCa patients and 111 controls. Three CpG sites located in ALOX5, TRPS1 and an intergenic region on chromosome 16 have been concordantly selected by all approaches, and their combination in a single decision matrix for clinical use was tested based on their respective thresholds of the individual CpGs. The combination of ALOX5 and TRPS1 yielded the best overall sensitivity (61%) at a pre-set specificity of 95%. This combination exceeded both the diagnostic performance of the most sensitive bioinformatic approach and that of the best single CpG. In summary, we showed that overlap analysis of multiple statistical approaches identifies the most reliable biomarkers for UCa in a male collective. The results may assist in stratifying men for cystoscopy.
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Affiliation(s)
- Christina U. Köhler
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Ruhr University Bochum (IPA), Bürkle-de-la-Camp Platz 1, 44789 Bochum, Germany; (C.U.K.)
| | - Karin Schork
- Medizinisches Proteom-Center, Medical Faculty, Ruhr-University Bochum and Medical Proteome Analysis, Center for Protein Diagnostics (PRODI), Gesundheitscampus 4, 44081 Bochum, Germany
| | - Michael Turewicz
- Medizinisches Proteom-Center, Medical Faculty, Ruhr-University Bochum and Medical Proteome Analysis, Center for Protein Diagnostics (PRODI), Gesundheitscampus 4, 44081 Bochum, Germany
| | - Martin Eisenacher
- Medizinisches Proteom-Center, Medical Faculty, Ruhr-University Bochum and Medical Proteome Analysis, Center for Protein Diagnostics (PRODI), Gesundheitscampus 4, 44081 Bochum, Germany
| | - Florian Roghmann
- Department of Urology, Marien Hospital Herne, University Hospital of the Ruhr University Bochum, Hölkeskampring 40, 44625 Herne, Germany
| | - Joachim Noldus
- Department of Urology, Marien Hospital Herne, University Hospital of the Ruhr University Bochum, Hölkeskampring 40, 44625 Herne, Germany
| | - Katrin Marcus
- Medizinisches Proteom-Center, Medical Faculty, Ruhr-University Bochum and Medical Proteome Analysis, Center for Protein Diagnostics (PRODI), Gesundheitscampus 4, 44081 Bochum, Germany
| | - Thomas Brüning
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Ruhr University Bochum (IPA), Bürkle-de-la-Camp Platz 1, 44789 Bochum, Germany; (C.U.K.)
| | - Heiko U. Käfferlein
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Ruhr University Bochum (IPA), Bürkle-de-la-Camp Platz 1, 44789 Bochum, Germany; (C.U.K.)
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Mat Lazim N, Yousaf A, Abusalah MAH, Sulong S, Mohd Ismail ZI, Mohamud R, Abu-Harirah HA, AlRamadneh TN, Hassan R, Abdullah B. The Epigenesis of Salivary Glands Carcinoma: From Field Cancerization to Carcinogenesis. Cancers (Basel) 2023; 15:cancers15072111. [PMID: 37046772 PMCID: PMC10093474 DOI: 10.3390/cancers15072111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 03/17/2023] [Accepted: 03/24/2023] [Indexed: 04/05/2023] Open
Abstract
Salivary gland carcinomas (SGCs) are a diverse collection of malignant tumors with marked differences in biological activity, clinical presentation and microscopic appearance. Although the etiology is varied, secondary radiation, oncogenic viruses as well as chromosomal rearrangements have all been linked to the formation of SGCs. Epigenetic modifications may also contribute to the genesis and progression of SGCs. Epigenetic modifications are any heritable changes in gene expression that are not caused by changes in DNA sequence. It is now widely accepted that epigenetics plays an important role in SGCs development. A basic epigenetic process that has been linked to a variety of pathological as well as physiological conditions including cancer formation, is DNA methylation. Transcriptional repression is caused by CpG islands hypermethylation at gene promoters, whereas hypomethylation causes overexpression of a gene. Epigenetic changes in SGCs have been identified, and they have been linked to the genesis, progression as well as prognosis of these neoplasms. Thus, we conduct a thorough evaluation of the currently known evidence on the involvement of epigenetic processes in SGCs.
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Affiliation(s)
- Norhafiza Mat Lazim
- Department of Otorhinolaryngology-Head and Neck Surgery, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia
- Hospital USM, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Anam Yousaf
- Department of Molecular Pathology Laboratory, Pakistan Kidney and Liver Institute and Research Centre, Lahore 54000, Pakistan
| | - Mai Abdel Haleem Abusalah
- Department of Medical Laboratory Sciences, Faculty of Allied Medical Sciences, Zarqa University, Al-Zarqa 13132, Jordan
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kota Bharu 16150, Kelantan, Malaysia
| | - Sarina Sulong
- Hospital USM, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
- Department of Immunology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
- Human Genome Centre, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Zul Izhar Mohd Ismail
- Hospital USM, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
- Department of Anatomy, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Rohimah Mohamud
- Hospital USM, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
- Department of Immunology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Hashem A. Abu-Harirah
- Department of Medical Laboratory Sciences, Faculty of Allied Medical Sciences, Zarqa University, Al-Zarqa 13132, Jordan
| | - Tareq Nayef AlRamadneh
- Department of Medical Laboratory Sciences, Faculty of Allied Medical Sciences, Zarqa University, Al-Zarqa 13132, Jordan
| | - Rosline Hassan
- Hospital USM, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
- Department of Haematology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Baharudin Abdullah
- Department of Otorhinolaryngology-Head and Neck Surgery, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia
- Hospital USM, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
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Matsumiya-Matsumoto Y, Morita Y, Uzawa N. Pleomorphic Adenoma of the Salivary Glands and Epithelial–Mesenchymal Transition. J Clin Med 2022; 11:jcm11144210. [PMID: 35887973 PMCID: PMC9324325 DOI: 10.3390/jcm11144210] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 07/18/2022] [Accepted: 07/18/2022] [Indexed: 01/06/2023] Open
Abstract
Pleomorphic adenoma (PA) is a localized tumor that presents pleomorphic or mixed characteristics of epithelial origin and is interwoven with mucoid tissue, myxoid tissue, and chondroid masses. The literature reported that PA most often occurs in adults aged 30–60 years and is a female predilection; the exact etiology remains unclear. Epithelial–mesenchymal transition (EMT) is the transdifferentiation of stationary epithelial cells primarily activated by a core set of transcription factors (EMT-TFs) involved in DNA repair and offers advantages under various stress conditions. Data have suggested that EMTs represent the basic principle of tissue heterogeneity in PAs, demonstrating the potential of adult epithelial cells to transdifferentiate into mesenchymal cells. It has also been reported that multiple TFs, such as TWIST and SLUG, are involved in EMT in PA and that SLUG could play an essential role in the transition from myoepithelial to mesenchymal cells. Given this background, this review aims to summarize and clarify the involvement of EMT in the development of PA, chondrocyte differentiation, and malignant transformation to contribute to the fundamental elucidation of the mechanisms underlying EMT.
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Salas LA, Peres LC, Thayer ZM, Smith RWA, Guo Y, Chung W, Si J, Liang L. A transdisciplinary approach to understand the epigenetic basis of race/ethnicity health disparities. Epigenomics 2021; 13:1761-1770. [PMID: 33719520 PMCID: PMC8579937 DOI: 10.2217/epi-2020-0080] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/07/2020] [Indexed: 11/21/2022] Open
Abstract
Health disparities correspond to differences in disease burden and mortality among socially defined population groups. Such disparities may emerge according to race/ethnicity, socioeconomic status and a variety of other social contexts, and are documented for a wide range of diseases. Here, we provide a transdisciplinary perspective on the contribution of epigenetics to the understanding of health disparities, with a special emphasis on disparities across socially defined racial/ethnic groups. Scientists in the fields of biological anthropology, bioinformatics and molecular epidemiology provide a summary of theoretical, statistical and practical considerations for conducting epigenetic health disparities research, and provide examples of successful applications from cancer research using this approach.
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Affiliation(s)
- Lucas A Salas
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, NH 03756, USA
| | - Lauren C Peres
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Zaneta M Thayer
- Department of Anthropology, Dartmouth College, Hanover, NH 03755, USA
| | - Rick WA Smith
- Department of Anthropology, Dartmouth College, Hanover, NH 03755, USA
- The William H. Neukom Institute for Computational Science, Dartmouth College, Hanover, NH 03755, USA
| | | | - Wonil Chung
- Department of Statistics & Actuarial Science, Soongsil University, Seoul, 06478, Korea
- Program in Genetic Epidemiology & Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Jiahui Si
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Department of Biostatistics & Epidemiology, Peking University School of Public Health, Beijing, 100191, China
| | - Liming Liang
- Program in Genetic Epidemiology & Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
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Mohammadinejad R, Biagioni A, Arunkumar G, Shapiro R, Chang KC, Sedeeq M, Taiyab A, Hashemabadi M, Pardakhty A, Mandegary A, Thiery JP, Aref AR, Azimi I. EMT signaling: potential contribution of CRISPR/Cas gene editing. Cell Mol Life Sci 2020; 77:2701-2722. [PMID: 32008085 PMCID: PMC11104910 DOI: 10.1007/s00018-020-03449-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 12/24/2019] [Accepted: 01/02/2020] [Indexed: 02/06/2023]
Abstract
Epithelial to mesenchymal transition (EMT) is a complex plastic and reversible cellular process that has critical roles in diverse physiological and pathological phenomena. EMT is involved in embryonic development, organogenesis and tissue repair, as well as in fibrosis, cancer metastasis and drug resistance. In recent years, the ability to edit the genome using the clustered regularly interspaced palindromic repeats (CRISPR) and associated protein (Cas) system has greatly contributed to identify or validate critical genes in pathway signaling. This review delineates the complex EMT networks and discusses recent studies that have used CRISPR/Cas technology to further advance our understanding of the EMT process.
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Affiliation(s)
- Reza Mohammadinejad
- Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
| | - Alessio Biagioni
- Section of Experimental Pathology and Oncology, Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Ganesan Arunkumar
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Rebecca Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Kun-Che Chang
- Department of Ophthalmology, School of Medicine, Byers Eye Institute, Stanford University, Palo Alto, CA, 94303, USA
| | - Mohammed Sedeeq
- Division of Pharmacy, College of Health and Medicine, University of Tasmania, Hobart, TAS, Australia
| | - Aftab Taiyab
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, L8S 4L8, Canada
| | - Mohammad Hashemabadi
- Department of Biology, Faculty of Sciences, Shahid Bahonar University, Kerman, Iran
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Abbas Pardakhty
- Neuroscience Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
| | - Ali Mandegary
- Physiology Research Center, Institute of Neuropharmacology and Department of Toxicology & Pharmacology, Kerman University of Medical Sciences, Kerman, Iran
| | - Jean-Paul Thiery
- Guangzhou Regenerative Medicine and Health, Guangdong Laboratory, Guangzhou, China
| | - Amir Reza Aref
- Department of Medical Oncology, Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA.
| | - Iman Azimi
- Division of Pharmacy, College of Health and Medicine, University of Tasmania, Hobart, TAS, Australia.
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Yang T, Fan J, Liang H, He D, Zeng X, Fan J, Wu K. Reduced E-cadherin expression as a prognostic factor in non-muscle-invasive bladder cancer: A systematic review and meta-analysis. Prog Urol 2020; 30:66-74. [PMID: 32061496 DOI: 10.1016/j.purol.2019.12.004] [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: 09/27/2019] [Revised: 12/04/2019] [Accepted: 12/14/2019] [Indexed: 11/18/2022]
Abstract
INTRODUCTION AND OBJECTIVES The exact role of E-cadherin in non-muscle-invasive bladder cancer (NMIBC) is still unknown, and the aims of this study were to prove whether reduced E-cadherin expression can be a prognostic factor in patients with NMIBC. MATERIALS AND METHODS A meta-analysis was conducted to assess the prognostic value of reduced E-cadherin expression in NMIBC. The PubMed, Embase and Web of Science databases were included in the study search. RESULTS Fifteen studies with a total of 1538 NMIBC patients were included. The results showed that reduced E-cadherin expression was significantly associated with poor recurrence-free survival (RFS) (pooled HR 2.16, 95% CI 1.22-3.85) and progression-free survival (PFS) (pooled HR 1.91, 95% CI 1.52-2.40) in NMIBC patients. CONCLUSION E-cadherin can be a prognostic factor for patients with NMIBC.
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Affiliation(s)
- T Yang
- Department of Urology, First Affiliated Hospital of Xi'an Jiaotong University, 710061 Xi'an, PR China
| | - J Fan
- Department of Urology, First Affiliated Hospital of Xi'an Jiaotong University, 710061 Xi'an, PR China
| | - H Liang
- Department of Pathology, First Affiliated Hospital of Xi'an Jiaotong University, 710061 Xi'an, PR China
| | - D He
- Department of Urology, First Affiliated Hospital of Xi'an Jiaotong University, 710061 Xi'an, PR China
| | - X Zeng
- Center for Evidence-Based and Translational Medicine, Zhongnan Hospital, Wuhan University, 430071 Wuhan, PR China
| | - J Fan
- Department of Urology, First Affiliated Hospital of Xi'an Jiaotong University, 710061 Xi'an, PR China
| | - K Wu
- Department of Urology, First Affiliated Hospital of Xi'an Jiaotong University, 710061 Xi'an, PR China.
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Xia L, Hu Y, Gu T, Wang L, Tian Z. Promoter hypermethylation may contribute to E‑cadherin repression in the human salivary carcinoma ex pleomorphic adenoma. Int J Oncol 2017; 52:496-504. [PMID: 29207084 DOI: 10.3892/ijo.2017.4210] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 10/13/2017] [Indexed: 11/06/2022] Open
Abstract
The role of promoter methylation in the inactivation of E‑cadherin (CDH1) in salivary carcinoma ex pleomorphic adenoma (CXPA) is unknown. The objective of this study was to determine the role and potential clinical implications of CDH1 promoter methylation in salivary CXPA. The CDH1 promoter methylation status was determined by bisulfite sequencing PCR in 37 primary CXPA tissues and 2 CXPA cell lines. E‑cadherin expression levels were determined by immunohistochemical analysis of each tumor. E‑cadherin protein levels and CDH1 mRNA levels were examined by immunoblotting and quantitative real-time PCR, respectively, in 2 CXPA cell lines. Cells were treated with 5‑Aza-dC or TGF‑β1 to test the influence of promoter methylation on CDH1 mRNA and protein expression. Associations between CDH1 molecular alterations and patients' clinicopathologic characteristics and prognosis were statistically evaluated. CDH1 promoter hypermethylation was detected in 21 of 37 tumors (56.76%). Of these 37 tumors, 13 tumors (35.14%) showed low E‑cadherin expression. Tumors that had CDH1 promoter methylation had a histological tendency toward luminal differentiation (P=0.004), high tumor grade (P=0.005), high T stage (P=0.024) and high TNM stage (P=0.038) compared with tumors that did not. The two CXPA cell lines exhibited an inverse relationship between CDH1 promoter methylation status and CDH1 mRNA and protein expression. Treatment of the hypermethylated cell line with 5‑Aza-dC restored CDH1 mRNA and E‑cadherin protein expression. The induction of hypermethylation by TGF‑β1 resulted in the repression of CDH1 mRNA and protein expression. CDH1 is commonly silenced in CXPA through promoter methylation. CDH1 methylation is closely related to tumor cell differentiation, histological grade, lymph node metastasis and advanced TNM stage, indicating that CDH1 methylation may play a role in the initiation and progression of CXPA.
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Affiliation(s)
- Liang Xia
- Department of Oral Pathology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, P.R. China
| | - Yuhua Hu
- Department of Oral Pathology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, P.R. China
| | - Ting Gu
- Department of Oral Pathology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, P.R. China
| | - Lizhen Wang
- Department of Oral Pathology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, P.R. China
| | - Zhen Tian
- Department of Oral Pathology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, P.R. China
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Wong SHM, Fang CM, Chuah LH, Leong CO, Ngai SC. E-cadherin: Its dysregulation in carcinogenesis and clinical implications. Crit Rev Oncol Hematol 2017; 121:11-22. [PMID: 29279096 DOI: 10.1016/j.critrevonc.2017.11.010] [Citation(s) in RCA: 241] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 10/15/2017] [Accepted: 11/16/2017] [Indexed: 02/06/2023] Open
Abstract
E-cadherin is a transmembrane glycoprotein which connects epithelial cells together at adherens junctions. In normal cells, E-cadherin exerts its tumour suppressing role mainly by sequestering β-catenin from its binding to LEF (Lymphoid enhancer factor)/TCF (T cell factor) which serves the function of transcribing genes of the proliferative Wnt signaling pathway. Despite the ongoing debate on whether the loss of E-cadherin is the cause or effect of epithelial-mesenchymal transition (EMT), E-cadherin functional loss has frequently been associated with poor prognosis and survival in patients of various cancers. The dysregulation of E-cadherin expression that leads to carcinogenesis happens mostly at the epigenetic level but there are cases of genetic alterations as well. E-cadherin expression has been linked to the cellular functions of invasiveness reduction, growth inhibition, apoptosis, cell cycle arrest and differentiation. Studies on various cancers have shown that these different cellular functions are also interdependent. Recent studies have reported a rapid expansion of E-cadherin clinical relevance in various cancers. This review article summarises the multifaceted effect E-cadherin expression has on cellular functions in the context of carcinogenesis as well as its clinical implications in diagnosis, prognosis and therapeutics.
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Affiliation(s)
- Sonia How Ming Wong
- School of Biosciences, Faculty of Science, University of Nottingham Malaysia Campus, 43500, Semenyih, Selangor, Malaysia.
| | - Chee Mun Fang
- School of Pharmacy, Faculty of Science, University of Nottingham Malaysia Campus, 43500, Semenyih, Selangor, Malaysia.
| | - Lay-Hong Chuah
- School of Pharmacy, Monash University Malaysia, Bandar Sunway, 47500, Subang Jaya, Selangor, Malaysia.
| | - Chee Onn Leong
- School of Pharmacy, International Medical University, Bukit Jalil, 57000, Kuala Lumpur, Malaysia; Centre for Cancer and Stem Cell Research, International Medical University, Bukit Jalil, 57000, Kuala Lumpur, Malaysia.
| | - Siew Ching Ngai
- School of Biosciences, Faculty of Science, University of Nottingham Malaysia Campus, 43500, Semenyih, Selangor, Malaysia.
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Ishiguro H, Wakasugi T, Terashita Y, Sakamoto N, Tanaka T, Mizoguchi K, Sagawa H, Okubo T, Takeyama H. Decreased expression of CDH1 or CTNNB1 affects poor prognosis of patients with esophageal cancer. World J Surg Oncol 2016; 14:240. [PMID: 27600761 PMCID: PMC5012100 DOI: 10.1186/s12957-016-0956-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 07/20/2016] [Indexed: 12/13/2022] Open
Abstract
Background E-cadherin/CDH1 is one of the proteins involved in cell adhesion, and it is known that decreased expression of E-cadherin induces lymph node metastasis in esophageal cancer. Beta catenin/CTNNB1, which is an important component of the Wnt signaling pathway, binds to E-cadherin at the cell membrane, where the complex of these two proteins functions in the stabilization of cell adhesion. However, its role in the pathogenesis of esophageal cancer is still unknown. Methods This study included 86 patients with esophageal cancer who underwent surgery between 1998 and 2007. The expression of the E-cadherin/CDH1 gene product (E-cadherin/CDH1) and that of the beta catenin/CTNNB1 protein in the cell membrane were analyzed by immunohistochemistry. We examined the correlations among CDH1 or CTNNB1 expression, clinicopathological factors, and the prognosis of patients with ESCC. Results CDH1 and CTNNB1 were expressed in 52.3 % (45/86) and 36.0 % (31/86) of tumor samples, respectively. Both CDH1 and CTNNB1 were co-expressed in 22.1 % (19/86) of esophageal cancer tissues. CDH1 expression correlated with the p-stage (stages I–II vs stages III–IV, p = 0.032), T factor (T1–2 vs T3–4, p = 0.0088), and lymphatic invasion (p = 0.019). However, CDH1 expression did not correlate with the N factor or the blood vessel invasion. CTNNB1 expression correlated with the T factor (T1–2 vs T3–4, p = 0.0015), p-stage (stages I–II vs stages III–IV, p = 0.030), and lymphatic invasion (p = 0.007). The CDH1(+)/CTNNB1(+) phenotype was inversely correlated with the T factor, N factor, p-stage, lymphatic invasion, and blood vessel invasion. Furthermore, patients whose tumors were double-positive for CDH1 and CTNNB1 had a significantly higher survival rate than those whose tumors were negative for CDH1 or CTNNB1 (log-rank test, p = 0.0192). The T factor and N factor had a strong negative correlation with double-positive tumors. These were both independent prognostic factors, as was the double-positive phenotype. A univariate analysis indicated that the T factor, the N factor, and CDH1 and CTNNB1 co-expression were significant variables that predicted survival (hazard ratio, 2.387; 95 % confidence interval, 1.115–5.102; p = 0.025). Conclusions Decreased expression of CDH1 or CTNNB1 in the cell membranes of cancer cells is associated with poor survival of patients with esophageal cancer.
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Affiliation(s)
- Hideyuki Ishiguro
- Gastroenterological Surgery, Nagoya City University Graduate School of Medical Science, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya, 467-8601, Japan.
| | - Takehiro Wakasugi
- Gastroenterological Surgery, Nagoya City University Graduate School of Medical Science, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya, 467-8601, Japan
| | - Yukio Terashita
- Gastroenterological Surgery, Nagoya City University Graduate School of Medical Science, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya, 467-8601, Japan
| | - Nobuhiro Sakamoto
- Gastroenterological Surgery, Nagoya City University Graduate School of Medical Science, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya, 467-8601, Japan
| | - Tatsuya Tanaka
- Gastroenterological Surgery, Nagoya City University Graduate School of Medical Science, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya, 467-8601, Japan
| | - Koji Mizoguchi
- Gastroenterological Surgery, Nagoya City University Graduate School of Medical Science, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya, 467-8601, Japan
| | - Hiroyuki Sagawa
- Gastroenterological Surgery, Nagoya City University Graduate School of Medical Science, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya, 467-8601, Japan
| | - Tomotaka Okubo
- Gastroenterological Surgery, Nagoya City University Graduate School of Medical Science, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya, 467-8601, Japan
| | - Hiromitsu Takeyama
- Gastroenterological Surgery, Nagoya City University Graduate School of Medical Science, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya, 467-8601, Japan
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10
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Genome-wide measures of DNA methylation in peripheral blood and the risk of urothelial cell carcinoma: a prospective nested case-control study. Br J Cancer 2016; 115:664-73. [PMID: 27490804 PMCID: PMC5023776 DOI: 10.1038/bjc.2016.237] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 05/13/2016] [Accepted: 07/08/2016] [Indexed: 12/23/2022] Open
Abstract
Background: Global DNA methylation has been reported to be associated with urothelial cell carcinoma (UCC) by studies using blood samples collected at diagnosis. Using the Illumina HumanMethylation450 assay, we derived genome-wide measures of blood DNA methylation and assessed them for their prospective association with UCC risk. Methods: We used 439 case–control pairs from the Melbourne Collaborative Cohort Study matched on age, sex, country of birth, DNA sample type, and collection period. Conditional logistic regression was used to compute odds ratios (OR) of UCC risk per s.d. of each genome-wide measure of DNA methylation and 95% confidence intervals (CIs), adjusted for potential confounders. We also investigated associations by disease subtype, sex, smoking, and time since blood collection. Results: The risk of superficial UCC was decreased for individuals with higher levels of our genome-wide DNA methylation measure (OR=0.71, 95% CI: 0.54–0.94; P=0.02). This association was particularly strong for current smokers at sample collection (OR=0.47, 95% CI: 0.27–0.83). Intermediate levels of our genome-wide measure were associated with decreased risk of invasive UCC. Some variation was observed between UCC subtypes and the location and regulatory function of the CpGs included in the genome-wide measures of methylation. Conclusions: Higher levels of our genome-wide DNA methylation measure were associated with decreased risk of superficial UCC and intermediate levels were associated with reduced risk of invasive disease. These findings require replication by other prospective studies.
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Tsui KH, Lin YH, Chung LC, Chuang ST, Feng TH, Chiang KC, Chang PL, Yeh CJ, Juang HH. Prostate-derived ets factor represses tumorigenesis and modulates epithelial-to-mesenchymal transition in bladder carcinoma cells. Cancer Lett 2016; 375:142-151. [PMID: 26965996 DOI: 10.1016/j.canlet.2016.02.056] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 02/27/2016] [Accepted: 02/29/2016] [Indexed: 12/27/2022]
Abstract
Prostate-derived Ets (E-twenty six) factor (PDEF), an epithelium-specific member of the Ets family of transcription factors, has been shown to play a role in suppressing the development of many epithelium-derived cancers such as prostate and breast cancer. It is not clear, however, whether PDEF is involved in the development or progression of bladder cancer. In a comparison between normal urothelium and bladder tumor tissue, we identified significant decreases of PDEF in the tumor tissue. Further, the immunohistochemistry assays indicated a significantly higher immunostaining of PDEF in low-grade bladder tumors. Additionally, the highly differentiated transitional-cell bladder carcinoma RT-4 cells expressed significantly more PDEF levels than the bladder carcinoma HT1376 and the T24 cells. Ectopic overexpression of PDEF attenuated proliferation, invasion, and tumorigenesis of bladder carcinoma cells in vitro and in vivo. PDEF enhanced the expression levels of mammary serine protease inhibitor (MASPIN), N-myc downstream regulated gene 1 (NDRG1), KAI1, and B-cell translocation gene 2 (BTG2). PDEF modulated epithelial-mesenchymal-transition (EMT) by upregulating E-cadherin expression and downregulating the expression of N-cadherin, SNAIL, SLUG, and vimentin, leading to lower migration and invasion abilities of bladder carcinoma cells. Filamentous actin (F-actin) polarization and remodeling were observed in PDEF-knockdown RT-4 cells. Our results suggest that PDEF gene expression is associated with the extent of bladder neoplasia and PDEF modulated the expressions of EMT-related genes. The induction of BTG2, NDRG1, MASPIN, and KAI1 gene expressions by PDEF may explain the inhibitory functions of PDEF on the proliferation, invasion, and tumorigenesis in bladder carcinoma cells.
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Affiliation(s)
- Ke-Hung Tsui
- Department of Urology, Chang Gung Memorial Hospital, Kwei-Shan, Tao-Yuan, Taiwan; Department of Traditional Chinese Medicine, College of Medicine, Chang Gung University, Kwei-Shan, Tao-Yuan, Taiwan
| | - Yu-Hsiang Lin
- Department of Urology, Chang Gung Memorial Hospital, Kwei-Shan, Tao-Yuan, Taiwan; Graduate Institute of Clinical Medical Science, College of Medicine, Chang Gung University, Kwei-Shan, Tao-Yuan, Taiwan
| | - Li-Chuan Chung
- Department of Anatomy, College of Medicine, Chang Gung University, Kwei-Shan, Tao-Yuan, Taiwan
| | - Sung-Ting Chuang
- Department of Anatomy, College of Medicine, Chang Gung University, Kwei-Shan, Tao-Yuan, Taiwan
| | - Tsui-Hsia Feng
- School of Nursing, College of Medicine, Chang Gung University, Kwei-Shan, Tao-Yuan, Taiwan
| | - Kun-Chun Chiang
- Zebafish Center, General Surgery Department, Chang Gung Memorial Hospital, Keelung, Taiwan
| | - Phei-Lang Chang
- Department of Urology, Chang Gung Memorial Hospital, Kwei-Shan, Tao-Yuan, Taiwan; Department of Traditional Chinese Medicine, College of Medicine, Chang Gung University, Kwei-Shan, Tao-Yuan, Taiwan
| | - Chi-Ju Yeh
- Department of Pathology, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Kwei-Shan, Tao-Yuan, Taiwan
| | - Horng-Heng Juang
- Department of Urology, Chang Gung Memorial Hospital, Kwei-Shan, Tao-Yuan, Taiwan; Department of Anatomy, College of Medicine, Chang Gung University, Kwei-Shan, Tao-Yuan, Taiwan.
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12
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Insight into the molecular basis of Schistosoma haematobium-induced bladder cancer through urine proteomics. Tumour Biol 2016; 37:11279-87. [PMID: 26951512 DOI: 10.1007/s13277-016-4997-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 02/25/2016] [Indexed: 12/21/2022] Open
Abstract
Infection due to Schistosoma haematobium is carcinogenic. However, the cellular and molecular mechanisms underlying urogenital schistosomiasis (UGS)-induced carcinogenesis have not been well defined. Conceptually, early molecular detection of this phenomenon, through non-invasive procedures, seems feasible and is desirable. Previous analysis of urine collected during UGS suggests that estrogen metabolites, including depurinating adducts, may be useful for this purpose. Here, a new direction was pursued: the identification of molecular pathways and potential biomarkers in S. haematobium-induced bladder cancer by analyzing the proteome profiling of urine samples from UGS patients. GeLC-MS/MS followed by protein-protein interaction analysis indicated oxidative stress and immune defense systems responsible for microbicide activity are the most representative clusters in UGS patients. Proteins involved in immunity, negative regulation of endopeptidase activity, and inflammation were more prevalent in UGS patients with bladder cancer, whereas proteins with roles in renal system process, sensory perception, and gas and oxygen transport were more abundant in subjects with urothelial carcinoma not associated with UGS. These findings highlighted a Th2-type immune response induced by S. haematobium, which seems to be further modulated by tumorigenesis, resulting in high-grade bladder cancer characterized by an inflammatory response and complement activation alternative pathway. These findings established a starting point for the development of multimarker strategies for the early detection of UGS-induced bladder cancer.
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Wang X, Chen E, Yang X, Wang Y, Quan Z, Wu X, Luo C. 5-azacytidine inhibits the proliferation of bladder cancer cells via reversal of the aberrant hypermethylation of the hepaCAM gene. Oncol Rep 2015; 35:1375-84. [PMID: 26677113 DOI: 10.3892/or.2015.4492] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 07/24/2015] [Indexed: 11/06/2022] Open
Abstract
Hepatocyte cell adhesion molecule (hepaCAM), a tumor-suppressor gene, is rarely expressed in bladder carcinoma. However, little is known concerning the mechanisms of low hepaCAM expression in bladder cancer. Abnormal hypermethylation in the promoter plays a crucial role in cancer by silencing tumor-suppressor genes, which is catalyzed by DNA methyltransferases (DNMTs). In the present study, a total of 31 bladder cancer and 22 adjacent tissues were assessed by immunohistochemistry to detect DNMT3A/3B and hepaCAM expression. Methylation of hepaCAM was determined by methylation‑specific polymerase chain reaction (MSP). The mRNA and protein levels of DNMT3A/3B and hepaCAM were determined by RT-PCR and western blot analysis after treatment with 5-azacytidine (AZAC). Following AZAC treatment, the proliferation of bladder cancer cells was detected by CCK-8 and colony formation assays. Cell cycle distribution was examined by flow cytometry. To further evaluate the tumor‑suppressive roles of AZAC and the involved mechanisms, the anti-tumorigenicity of AZAC was tested in vivo. The expression of DNMT3A/3B protein was markedly increased in the bladder carcinoma tissues (P<0.05), and had a negative linear correlation with hepaCAM expression in the same patients according to Pearson's analysis (r=-0.7176/-0.7127, P<0.05). The MSP results indicated that the hepaCAM gene was hypermethylated in three bladder cancer cell lines. Furthermore, we found that downregulation of DNMT3A/3B expression, after treatment with AZAC, reversed the hypermethylation and expression of hepaCAM in bladder cancer cells. In addition, AZAC inhibited the proliferation of bladder cancer cells and arrested cells at the G0/G1 phase. The in vivo results showed that expression of DNMT3A/3B and hepaCAM as well as tumor growth of nude mice were markedly altered which corresponded with the in vitro results. Due to the ability to reactivate expression of hepaCAM and inhibit growth of bladder cancer cells, AZAC may represent an effective treatment for bladder cancer.
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Affiliation(s)
- Xiaorong Wang
- Key Laboratory of Diagnostic Medicine designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, P.R. China
| | - E Chen
- Key Laboratory of Diagnostic Medicine designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, P.R. China
| | - Xue Yang
- Key Laboratory of Diagnostic Medicine designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, P.R. China
| | - Yin Wang
- Key Laboratory of Diagnostic Medicine designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, P.R. China
| | - Zhen Quan
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, P.R. China
| | - Xiaohou Wu
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, P.R. China
| | - Chunli Luo
- Key Laboratory of Diagnostic Medicine designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, P.R. China
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Zhang RL, Peng LX, Yang JP, Zheng LS, Xie P, Wang MY, Huang BJ, Zhao HR, Bao YX, Qian CN. IL-8 suppresses E-cadherin expression in nasopharyngeal carcinoma cells by enhancing E-cadherin promoter DNA methylation. Int J Oncol 2015; 48:207-14. [PMID: 26530812 DOI: 10.3892/ijo.2015.3226] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 10/13/2015] [Indexed: 11/06/2022] Open
Abstract
Nasopharyngeal carcinoma (NPC) has the highest metastasis potential among head and neck cancers. Distant metastasis is the major cause of treatment failure. Recent studies from our laboratory have revealed that IL-8 promotes NPC metastasis via activation of AKT signaling and induction of epithelial-mesenchymal transition (EMT) in the cells. In the present study, we found that IL-8 treatment for NPC cells resulted in an accumulation of DNMT1 protein through activating AKT1 pathway and consequent DNMT1 protein stabilization. Then DNMT1 suppressed E-cadherin expression by increasing the methylation of its promoter region. LY-294002 blocked IL-8-induced p-AKT1 activation resulting in reduction of DNMT1 and increase of E-cadherin expression, whereas forced demethylation using 5-aza-2'-deoxycytidine restored E-cadherin expression. In conclusion, our study, for the first time, shows that the IL-8/AKT1 signaling pathway stabilizes DNMT1 protein, consequently enhancing hypermethylation of E-cadherin promoter regions and downregulating E-cadherin protein level in NPC cells. Upon blockage of the IL-8/AKT pathway and inhibition of DNMT1, E-cadherin expression can be reversed. These data suggest that targeting the IL-8/AKT1 signaling pathway and DNMT1 may provide a potential therapeutic approach for blocking NPC metastasis.
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Affiliation(s)
- Rui-Li Zhang
- Cancer Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi 830054, P.R. China
| | - Li-Xia Peng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, P.R. China
| | - Jun-Ping Yang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, P.R. China
| | - Li-Sheng Zheng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, P.R. China
| | - Ping Xie
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, P.R. China
| | - Meng-Yao Wang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, P.R. China
| | - Bi-Jun Huang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, P.R. China
| | - Hua-Rong Zhao
- Cancer Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi 830054, P.R. China
| | - Yong-Xing Bao
- Cancer Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi 830054, P.R. China
| | - Chao-Nan Qian
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, P.R. China
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Tsui KH, Hsu SY, Chung LC, Lin YH, Feng TH, Lee TY, Chang PL, Juang HH. Growth differentiation factor-15: a p53- and demethylation-upregulating gene represses cell proliferation, invasion, and tumorigenesis in bladder carcinoma cells. Sci Rep 2015; 5:12870. [PMID: 26249737 PMCID: PMC4528199 DOI: 10.1038/srep12870] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 06/29/2015] [Indexed: 12/22/2022] Open
Abstract
Growth differentiation factor-15 (GDF15), a member of the TGF-β superfamily, affects tumor biology of certain cancers, but remains poorly understood in bladder cancer cells. This study determined the expression, regulation, function, and potential downstream target genes of GDF15 in bladder carcinoma cells. The transitional papilloma carcionoma cells (RT4) expressed higher levels of GDF15 as compared with the bladder carcinoma cells (HT1376 and T24). Treatments of recombinant human GDF15 (rhGDF15) reduced the proliferations of HT1376 and T24 cells. Expression of GDF15 was upregulated via DNA demethylation and p53. The cell proliferation, invasion, and tumorigenesis were reduced in ectopic overexpression of GDF15, while enhanced in GDF15 knockdown. The expressions of mammary serine protease inhibitor (MASPIN) and N-myc downstream-regulated family genes (NDRG1, NDRG2, and NDRG3) were upregulated by GDF15 overexpressions and rhGDF15 treatments in bladder carcinoma cells. GDF15 knockdown induced epithelial-mesenchymal transition (EMT) and F-actin polarization in HT1376 cells. Our results suggest that enhanced expressions of MASPIN and N-myc downstream-regulated family genes and the modulation of EMT may account for the inhibitory functions of GDF15 in the cell proliferation, invasion, and tumorigenesis of bladder carcinoma cells. The GDF15 should be considered as a tumor suppressor in human bladder carcinoma cells.
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Affiliation(s)
- Ke-Hung Tsui
- 1] Department of Urology, Chang Gung Memorial Hospital, Kwei-Shan, Tao-Yuan, Taiwan, ROC [2] Department of Traditional Chinese Medicine, College of Medicine, Chang Gung University, Kwei-Shan, Tao-Yuan, Taiwan, ROC
| | - Shu-Yuan Hsu
- Department of Anatomy, College of Medicine, Chang Gung University, Kwei-Shan, Tao-Yuan, Taiwan, ROC
| | - Li-Chuan Chung
- Department of Anatomy, College of Medicine, Chang Gung University, Kwei-Shan, Tao-Yuan, Taiwan, ROC
| | - Yu-Hsiang Lin
- Department of Urology, Chang Gung Memorial Hospital, Kwei-Shan, Tao-Yuan, Taiwan, ROC
| | - Tsui-Hsia Feng
- School of Nursing, College of Medicine, Chang Gung University, Kwei-Shan, Tao-Yuan, Taiwan, ROC
| | - Tzu-Yi Lee
- Department of Anatomy, College of Medicine, Chang Gung University, Kwei-Shan, Tao-Yuan, Taiwan, ROC
| | - Phei-Lang Chang
- 1] Department of Urology, Chang Gung Memorial Hospital, Kwei-Shan, Tao-Yuan, Taiwan, ROC [2] Department of Traditional Chinese Medicine, College of Medicine, Chang Gung University, Kwei-Shan, Tao-Yuan, Taiwan, ROC
| | - Horng-Heng Juang
- Department of Anatomy, College of Medicine, Chang Gung University, Kwei-Shan, Tao-Yuan, Taiwan, ROC
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16
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Zhang C, Zhao H, Li J, Liu H, Wang F, Wei Y, Su J, Zhang D, Liu T, Zhang Y. The identification of specific methylation patterns across different cancers. PLoS One 2015; 10:e0120361. [PMID: 25774687 PMCID: PMC4361543 DOI: 10.1371/journal.pone.0120361] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 01/20/2015] [Indexed: 12/16/2022] Open
Abstract
Abnormal DNA methylation is known as playing an important role in the tumorgenesis. It is helpful for distinguishing the specificity of diagnosis and therapeutic targets for cancers based on characteristics of DNA methylation patterns across cancers. High throughput DNA methylation analysis provides the possibility to comprehensively filter the epigenetics diversity across various cancers. We integrated whole-genome methylation data detected in 798 samples from seven cancers. The hierarchical clustering revealed the existence of cancer-specific methylation pattern. Then we identified 331 differentially methylated genes across these cancers, most of which (266) were specifically differential methylation in unique cancer. A DNA methylation correlation network (DMCN) was built based on the methylation correlation between these genes. It was shown the hubs in the DMCN were inclined to cancer-specific genes in seven cancers. Further survival analysis using the part of genes in the DMCN revealed high-risk group and low-risk group were distinguished by seven biomarkers (PCDHB15, WBSCR17, IGF1, GYPC, CYGB, ACTG2, and PRRT1) in breast cancer and eight biomarkers (ZBTB32, OR51B4, CCL8, TMEFF2, SALL3, GPSM1, MAGEA8, and SALL1) in colon cancer, respectively. At last, a protein-protein interaction network was introduced to verify the biological function of differentially methylated genes. It was shown that MAP3K14, PTN, ACVR1 and HCK sharing different DNA methylation and gene expression across cancers were relatively high degree distribution in PPI network. The study suggested that not only the identified cancer-specific genes provided reference for individual treatment but also the relationship across cancers could be explained by differential DNA methylation.
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Affiliation(s)
- Chunlong Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Hongyan Zhao
- Department of Gastroenterology, The fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jie Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Hongbo Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Fang Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yanjun Wei
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jianzhong Su
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Dongwei Zhang
- Department of General Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Tiefu Liu
- Department of Gastroenterology, The fourth Affiliated Hospital of Harbin Medical University, Harbin, China
- * E-mail: (YZ); (TL)
| | - Yan Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
- * E-mail: (YZ); (TL)
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Transcription regulation of E-cadherin by zinc finger E-box binding homeobox proteins in solid tumors. BIOMED RESEARCH INTERNATIONAL 2014; 2014:921564. [PMID: 25197668 PMCID: PMC4147210 DOI: 10.1155/2014/921564] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 07/13/2014] [Accepted: 07/28/2014] [Indexed: 12/19/2022]
Abstract
Downregulation of E-cadherin in solid tumors with regional migration and systematic metastasis is well recognized. In view of its significance in tumorigenesis and solid cancer progression, studies on the regulatory mechanisms are important for the development of target treatment and prediction of clinical behavior for cancer patients. The vertebrate zinc finger E-box binding homeobox (ZEB) protein family comprises 2 major members: ZEB1 and ZEB2. Both contain the motif for specific binding to multiple enhancer boxes (E-boxes) located within the short-range transcription regulatory regions of the E-cadherin gene. Binding of ZEB1 and ZEB2 to the spaced E-cadherin E-boxes has been implicated in the regulation of E-cadherin expression in multiple human cancers. The widespread functions of ZEB proteins in human malignancies indicate their significance. Given the significance of E-cadherin in the solid tumors, a deeper understanding of the functional role of ZEB proteins in solid tumors could provide insights in the design of target therapy against the migratory nature of solid cancers.
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