1
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Wever BMM, Steenbergen RDM. Unlocking the potential of tumor-derived DNA in urine for cancer detection: methodological challenges and opportunities. Mol Oncol 2024. [PMID: 38462745 DOI: 10.1002/1878-0261.13628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/20/2023] [Accepted: 01/27/2024] [Indexed: 03/12/2024] Open
Abstract
High cancer mortality rates and the rising cancer burden worldwide drive the development of innovative methods in order to advance cancer diagnostics. Urine contains a viable source of tumor material and allows for self-collection from home. Biomarker testing in this liquid biopsy represents a novel approach that is convenient for patients and can be effective in detecting cancer at a curable stage. Here, we set out to provide a detailed overview of the rationale behind urine-based cancer detection, with a focus on non-urological cancers, and its potential for cancer diagnostics. Moreover, evolving methodological challenges and untapped opportunities for urine biomarker testing are discussed, particularly emphasizing DNA methylation of tumor-derived cell-free DNA. We also provide future recommendations for technical advancements in urine-based cancer detection and elaborate on potential mechanisms involved in the transrenal transport of cell-free DNA.
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Affiliation(s)
- Birgit M M Wever
- Department of Pathology, Amsterdam UMC, location Vrije Universiteit Amsterdam, The Netherlands
- Imaging and Biomarkers, Cancer Center Amsterdam, The Netherlands
| | - Renske D M Steenbergen
- Department of Pathology, Amsterdam UMC, location Vrije Universiteit Amsterdam, The Netherlands
- Imaging and Biomarkers, Cancer Center Amsterdam, The Netherlands
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2
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Liu J, Wu P, Lai S, Wang J, Wang J, Zhang Y. Identifying possible hub genes and biological mechanisms shared between bladder cancer and inflammatory bowel disease using machine learning and integrated bioinformatics. J Cancer Res Clin Oncol 2023; 149:16885-16904. [PMID: 37740761 DOI: 10.1007/s00432-023-05266-0] [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: 06/16/2023] [Accepted: 08/08/2023] [Indexed: 09/25/2023]
Abstract
BACKGROUND Recent studies have shown that inflammatory bowel disease (IBD) is associated with bladder cancer (BC) incidence. But there is still a lack of understanding regarding its pathogenesis. Thus, this study aimed to identify potential hub genes and their important pathways and pathological mechanisms of interactions between IBD and BC using bioinformatics methods. METHODS The data from Gene Expression Omnibus (GEO) and the cancer genome atlas (TCGA) were analyzed to screen common differentially expressed genes (DEGs) between IBD and BC. The "clusterProfiler" package was used to analyze GO term and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment in DEGs. After that, we conducted a weighted gene co-expression network analysis (WGCNA) on these DEGs to determine the vital modules and genes significantly related to BC. Protein-protein interaction (PPI) networks was used to identify hub genes. Further, the hub genes were used to develop a prognostic signature by Cox analysis. The validity of the ten hub DEGs was tested using three classification algorithms. Finally, we analyzed the microRNAs (miRNA)-mRNA, transcription factors (TFs)-mRNA regulatory network. RESULTS Positive regulation of organelle fission, chromosomal region, tubulin binding, and cell cycle signaling pathway were the major enriched pathways for the common DEGs. PPI networks identified three hub proteins (AURKB, CDK1, and CCNA2) with high connectivity. Three machine-learning classification algorithms based on ten hub genes performed well for IBD and BC (accuracy > 0.80). The robust predictive model based on the ten hub genes could accurately classify BC cases with various clinical outcomes. Based on the gene-TFs and gene-miRNAs network construction, 9 TFs and 6 miRNAs were identified as potential critical TFs and miRNAs. There are 13 drugs that interact with the hub gene based on gene-drug interaction analysis. CONCLUSIONS This study explored common gene signatures and the potential pathogenesis of IBD and BC. We revealed that an unbalanced immune response, cell cycle pathway, and neutrophil infiltration might be the common pathogenesis of IBD and BC. Molecular mechanisms for the treatment of IBD and CC still require further investigation.
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Affiliation(s)
- Jianyong Liu
- Department of Urology, Institute of the Geriatric Medicine, Beijing Hospital, National Center of Gerontology, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Beijing Hospital Continence Center, Beijing, People's Republic of China
| | - Pengjie Wu
- Department of Urology, Institute of the Geriatric Medicine, Beijing Hospital, National Center of Gerontology, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Beijing Hospital Continence Center, Beijing, People's Republic of China
| | - Shicong Lai
- Department of Urology, Peking University People's Hospital, Beijing, 100044, People's Republic of China
| | - Jianye Wang
- Department of Urology, Institute of the Geriatric Medicine, Beijing Hospital, National Center of Gerontology, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.
- Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, People's Republic of China.
- Beijing Hospital Continence Center, Beijing, People's Republic of China.
- , No. 1 DaHua Road, Dong Dan, Beijing, 100730, China.
| | - Jianlong Wang
- Department of Urology, Institute of the Geriatric Medicine, Beijing Hospital, National Center of Gerontology, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.
- Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, People's Republic of China.
- Beijing Hospital Continence Center, Beijing, People's Republic of China.
- , No. 1 DaHua Road, Dong Dan, Beijing, 100730, China.
| | - Yaoguang Zhang
- Department of Urology, Institute of the Geriatric Medicine, Beijing Hospital, National Center of Gerontology, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.
- Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, People's Republic of China.
- Beijing Hospital Continence Center, Beijing, People's Republic of China.
- , No. 1 DaHua Road, Dong Dan, Beijing, 100730, China.
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3
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Terrinoni A, Micheloni G, Moretti V, Caporali S, Bernardini S, Minieri M, Pieri M, Giaroni C, Acquati F, Costantino L, Ferrara F, Valli R, Porta G. OTX Genes in Adult Tissues. Int J Mol Sci 2023; 24:16962. [PMID: 38069286 PMCID: PMC10707059 DOI: 10.3390/ijms242316962] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/22/2023] [Accepted: 11/25/2023] [Indexed: 12/18/2023] Open
Abstract
OTX homeobox genes have been extensively studied for their role in development, especially in neuroectoderm formation. Recently, their expression has also been reported in adult physiological and pathological tissues, including retina, mammary and pituitary glands, sinonasal mucosa, in several types of cancer, and in response to inflammatory, ischemic, and hypoxic stimuli. Reactivation of OTX genes in adult tissues supports the notion of the evolutionary amplification of functions of genes by varying their temporal expression, with the selection of homeobox genes from the "toolbox" to drive or contribute to different processes at different stages of life. OTX involvement in pathologies points toward these genes as potential diagnostic and/or prognostic markers as well as possible therapeutic targets.
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Affiliation(s)
- Alessandro Terrinoni
- Department of Experimental Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
| | - Giovanni Micheloni
- Genomic Medicine Research Center, Department of Medicine and Surgery, University of Insubria, Via JH Dunant 5, 21100 Varese, Italy
| | - Vittoria Moretti
- Genomic Medicine Research Center, Department of Medicine and Surgery, University of Insubria, Via JH Dunant 5, 21100 Varese, Italy
| | - Sabrina Caporali
- Department of Industrial Engineering, University of Rome Tor Vergata, Via del Politecnico 1, 00133 Rome, Italy
| | - Sergio Bernardini
- Department of Experimental Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
| | - Marilena Minieri
- Department of Experimental Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
| | - Massimo Pieri
- Department of Experimental Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
| | - Cristina Giaroni
- Department of Medicina e Innovazione Tecnologica, University of Insubria, Via JH Dunant 5, 21100 Varese, Italy
| | - Francesco Acquati
- Genomic Medicine Research Center, Department of Medicine and Surgery, University of Insubria, Via JH Dunant 5, 21100 Varese, Italy
- Department of Biotechnology and Life Science, University of Insubria, Via JH Dunant 3, 21100 Varese, Italy
| | - Lucy Costantino
- Department of Molecular Genetics, Centro Diagnostico Italiano, Via Saint Bon 20, 20147 Milano, Italy
| | - Fulvio Ferrara
- Department of Molecular Genetics, Centro Diagnostico Italiano, Via Saint Bon 20, 20147 Milano, Italy
| | - Roberto Valli
- Genomic Medicine Research Center, Department of Medicine and Surgery, University of Insubria, Via JH Dunant 5, 21100 Varese, Italy
| | - Giovanni Porta
- Genomic Medicine Research Center, Department of Medicine and Surgery, University of Insubria, Via JH Dunant 5, 21100 Varese, Italy
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4
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Zheng J, Wang J, Qin X, Li K, Gao Q, Yang M, Liu H, Li S, Chang X, Sun Y. LncRNA HOTAIRM1 Involved in Nano NiO-Induced Pulmonary Fibrosis via Regulating PRKCB DNA Methylation-Mediated JNK/c-Jun Pathway. Toxicol Sci 2022; 190:64-78. [PMID: 36066426 DOI: 10.1093/toxsci/kfac092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Nickel oxide nanoparticles (Nano NiO) lead to pulmonary fibrosis, and the mechanisms are associated with epigenetics. This study aimed to clarify the regulatory relationship among long noncoding RNA HOXA transcript antisense RNA myeloid-specific 1 (HOTAIRM1), DNA methylation and expression of protein kinase C beta (PRKCB), and JNK/c-Jun pathway in Nano NiO-induced pulmonary fibrosis. Therefore, we constructed the rat pulmonary fibrosis model by intratracheal instillation of Nano NiO twice a week for 9 weeks and established the collagen deposition model by treating BEAS-2B cells with Nano NiO for 24 h. Here, the DNA methylation pattern was analyzed by whole-genome bisulfite sequencing in rat fibrotic lung tissues. Then, we integrated mRNA transcriptome data and found 93 DNA methylation genes with transcriptional significance. Meanwhile, the data showed that Nano NiO caused the down-regulation of lncRNA HOTAIRM1, the hypomethylation, and up-regulation of PRKCB2, JNK/c-Jun pathway activation, and collagen deposition (the up-regulated Col-I and α-SMA) both in vivo and in vitro. DNMTs inhibitor 5-AZDC attenuated Nano NiO-induced PRKCB2 expression, JNK/c-Jun pathway activation, and collagen deposition, but overexpression of PRKCB2 aggravated the changes mentioned indicators in Nano NiO-induced BEAS-2B cells. Furthermore, JNK/c-Jun pathway inhibitor (SP600125) alleviated Nano NiO-induced excessive collagen formation. Additionally, overexpression of HOTAIRM1 restrained the PRKCB hypomethylation, the activation of JNK/c-Jun pathway, and collagen formation induced by Nano NiO in BEAS-2B cells. In conclusion, these findings demonstrated that HOTAIRM1 could arrest Nano NiO-induced pulmonary fibrosis by suppressing the PRKCB DNA methylation-mediated JNK/c-Jun pathway.
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Affiliation(s)
- Jinfa Zheng
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Jinyu Wang
- Institute of Anthropotomy and Histoembryology, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Xin Qin
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Kun Li
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Qing Gao
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Mengmeng Yang
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Han Liu
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Sheng Li
- Department of Public Health, The First People's Hospital of Lanzhou City, Lanzhou 730050, China
| | - Xuhong Chang
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Yingbiao Sun
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou 730000, China
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5
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Teoh JYC, Kamat AM, Black PC, Grivas P, Shariat SF, Babjuk M. Recurrence mechanisms of non-muscle-invasive bladder cancer - a clinical perspective. Nat Rev Urol 2022; 19:280-294. [PMID: 35361927 DOI: 10.1038/s41585-022-00578-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2022] [Indexed: 12/24/2022]
Abstract
Non-muscle-invasive bladder cancer (NMIBC) is an early-stage cancer without invasion into the detrusor muscle layer. Transurethral resection of bladder tumour (TURBT) is a diagnostic and potentially curative procedure for NMIBC, but has some limitations, including difficulties in ascertaining complete tumour removal upon piecemeal resection and the possibility of tumour re-implantation after the procedure. The oncological control of NMIBC is far from satisfactory, with a 1-year recurrence rate of 15-61%, and a 5-year recurrence rate of 31-78%. Various recurrence mechanisms have been described for NMIBC, such as undetected tumours upon cystoscopy, incomplete resection during TURBT, tumour re-implantation after TURBT, drop metastasis from upper tract urothelial carcinoma and field change cancerization. Understanding the recurrence mechanisms from a clinical perspective has strong implications for the optimization of NMIBC oncological outcomes, as a cure for patients with NMIBC can only be achieved by tackling all possible recurrence mechanisms in a comprehensive manner.
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Affiliation(s)
- Jeremy Yuen-Chun Teoh
- S.H. Ho Urology Centre, Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China. .,European Association of Urology-Young Academic Urologists (EAU-YAU) Urothelial Cancer Working Group, Amsterdam, Netherlands.
| | - Ashish M Kamat
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Peter C Black
- Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Petros Grivas
- Division of Oncology, Department of Medicine, University of Washington, Washington, USA.,Fred Hutchinson Cancer Research Center, Seattle Cancer Care Alliance, Seattle, WA, USA
| | - Shahrokh F Shariat
- Department of Urology, Medical University of Vienna, Vienna, Austria.,Department of Urology, Weill Cornell Medical College, New York, NY, USA.,Department of Urology, University of Texas Southwestern, Dallas, TX, USA.,Institute for Urology and Reproductive Health, Sechenov University, Moscow, Russia.,Hourani Center for Applied Scientific Research, Al-Ahliyya Amman University, Amman, Jordan.,Department of Urology, 2nd Faculty of Medicine, Hospital Motol, Charles University, Prague, Czech Republic
| | - Marek Babjuk
- Department of Urology, Medical University of Vienna, Vienna, Austria.,Department of Urology, 2nd Faculty of Medicine, Hospital Motol, Charles University, Prague, Czech Republic
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6
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Alterations of Chromatin Regulators in the Pathogenesis of Urinary Bladder Urothelial Carcinoma. Cancers (Basel) 2021; 13:cancers13236040. [PMID: 34885146 PMCID: PMC8656749 DOI: 10.3390/cancers13236040] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/29/2021] [Accepted: 11/29/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Urinary bladder cancer is one of the ten major cancers worldwide, with higher incidences in males, in smokers, and in highly industrialized countries. New therapies beyond cytotoxic chemotherapy are urgently needed to improve treatment of these tumors. A better understanding of the mechanisms underlying their development may help in this regard. Recently, it was discovered that a group of proteins regulating the state of chromatin and thus gene expression is exceptionally and frequently affected by gene mutations in bladder cancers. Altered function of these mutated chromatin regulators must therefore be fundamental in their development, but how and why is poorly understood. Here we review the current knowledge on changes in chromatin regulators and discuss their possible consequences for bladder cancer development and options for new therapies. Abstract Urothelial carcinoma (UC) is the most frequent histological type of cancer in the urinary bladder. Genomic changes in UC activate MAPK and PI3K/AKT signal transduction pathways, which increase cell proliferation and survival, interfere with cell cycle and checkpoint control, and prevent senescence. A more recently discovered additional category of genetic changes in UC affects chromatin regulators, including histone-modifying enzymes (KMT2C, KMT2D, KDM6A, EZH2), transcription cofactors (CREBBP, EP300), and components of the chromatin remodeling complex SWI/SNF (ARID1A, SMARCA4). It is not yet well understood how these changes contribute to the development and progression of UC. Therefore, we review here the emerging knowledge on genomic and gene expression alterations of chromatin regulators and their consequences for cell differentiation, cellular plasticity, and clonal expansion during UC pathogenesis. Our analysis identifies additional relevant chromatin regulators and suggests a model for urothelial carcinogenesis as a basis for further mechanistic studies and targeted therapy development.
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7
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Han Z, Jia J, Lv Y, Wang R, Cao K. Transcriptional expression of ZICs as an independent indicator of survival in gliomas. Sci Rep 2021; 11:17532. [PMID: 34475426 PMCID: PMC8413274 DOI: 10.1038/s41598-021-93877-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 06/16/2021] [Indexed: 11/23/2022] Open
Abstract
The functional significance of the zinc-finger of the cerebellum (ZIC) gene family in gliomas remains to be elucidated. Clinical data from patients with gliomas, containing expression levels of ZIC genes, were extracted from CCLE, GEPIA2 and The Human Protein Atlas (HPA). Univariate survival analysis adjusted by Cox regression via OncoLnc was used to determine the prognostic significance of ZIC expression. We used cBioPortal to explore the correlation between gene mutations and overall survival (OS). ZIC expression was found to be related to immune cell infiltration in gliomas via TIMER analysis. GO term and KEGG pathway enrichment analyzes were performed with Metascape. PPI networks were constructed using STRING. The expression levels of ZIC1/3/4/5 in gliomas were significantly different from those in normal samples. High expression levels of ZIC1/5 were associated with poor OS in brain low-grade glioma (LGG) patients, while low ZIC3 expression combined was related to favorable OS in glioblastoma multiforme (GBM). ZIC alterations were associated with poor prognosis in LGG patients and related to favorable prognosis in GBM patients. We observed that the expression of ZICs was related to immune cell infiltration in glioma patients. ZICs were enriched in several pathways and biological processes involving Neuroactive ligand-receptor interaction (hsa04080). The PPI network revealed that some proteins coexpressed with ZICs played a role in the pathogenesis of gliomas. Differences in the expression levels of ZIC genes could provide a significant marker for predicting prognosis in gliomas.
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Affiliation(s)
- Zhaocheng Han
- Dongzhimen Hospital, Beijing University of Chinese Medicine, No.5 Haiyuncang Rd., Dongcheng District, Beijing, 100700, China
| | - Jingnan Jia
- Dongzhimen Hospital, Beijing University of Chinese Medicine, No.5 Haiyuncang Rd., Dongcheng District, Beijing, 100700, China
| | - Yangting Lv
- Dongzhimen Hospital, Beijing University of Chinese Medicine, No.5 Haiyuncang Rd., Dongcheng District, Beijing, 100700, China
| | - Rongyanqi Wang
- Dongzhimen Hospital, Beijing University of Chinese Medicine, No.5 Haiyuncang Rd., Dongcheng District, Beijing, 100700, China
| | - Kegang Cao
- Dongzhimen Hospital, Beijing University of Chinese Medicine, No.5 Haiyuncang Rd., Dongcheng District, Beijing, 100700, China.
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8
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Loras A, Segovia C, Ruiz-Cerdá JL. Epigenomic and Metabolomic Integration Reveals Dynamic Metabolic Regulation in Bladder Cancer. Cancers (Basel) 2021; 13:2719. [PMID: 34072826 PMCID: PMC8198168 DOI: 10.3390/cancers13112719] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/12/2021] [Accepted: 05/26/2021] [Indexed: 12/24/2022] Open
Abstract
Bladder cancer (BC) represents a clinical, social, and economic challenge due to tumor-intrinsic characteristics, limitations of diagnostic techniques and a lack of personalized treatments. In the last decade, the use of liquid biopsy has grown as a non-invasive approach to characterize tumors. Moreover, the emergence of omics has increased our knowledge of cancer biology and identified critical BC biomarkers. The rewiring between epigenetics and metabolism has been closely linked to tumor phenotype. Chromatin remodelers interact with each other to control gene silencing in BC, but also with stress-inducible factors or oncogenic signaling cascades to regulate metabolic reprogramming towards glycolysis, the pentose phosphate pathway, and lipogenesis. Concurrently, one-carbon metabolism supplies methyl groups to histone and DNA methyltransferases, leading to the hypermethylation and silencing of suppressor genes in BC. Conversely, α-KG and acetyl-CoA enhance the activity of histone demethylases and acetyl transferases, increasing gene expression, while succinate and fumarate have an inhibitory role. This review is the first to analyze the interplay between epigenome, metabolome and cell signaling pathways in BC, and shows how their regulation contributes to tumor development and progression. Moreover, it summarizes non-invasive biomarkers that could be applied in clinical practice to improve diagnosis, monitoring, prognosis and the therapeutic options in BC.
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Affiliation(s)
- Alba Loras
- Unidad Mixta de Investigación en TICs Aplicadas a la Reingeniería de Procesos Socio-Sanitarios (eRPSS), Universitat Politècnica de València-Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain
| | - Cristina Segovia
- Epithelial Carcinogenesis Group, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029 Madrid, Spain
| | - José Luis Ruiz-Cerdá
- Unidad Mixta de Investigación en Nanomedicina y Sensores, Universitat Politècnica de València-Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain;
- Servicio de Urología, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain
- Departamento de Cirugía, Facultad de Medicina y Odontología, Universitat de València, 46010 Valencia, Spain
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9
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CTLA-4 +49A/G Polymorphism Increases the Susceptibility to Bladder Cancer in Chinese Han Participants: A Case-Control Study. DISEASE MARKERS 2020; 2020:8143158. [PMID: 33335608 PMCID: PMC7723475 DOI: 10.1155/2020/8143158] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 02/01/2020] [Accepted: 03/05/2020] [Indexed: 01/12/2023]
Abstract
Cytotoxic T cell antigen-4 (CTLA-4) is reportedly involved in the development of bladder cancer (BC). This research was designed to address the potential link between the +49A/G polymorphism in CTLA-4 gene and BC susceptibility. In total, 355 BC cases and 435 match controls from Chinese Han individuals were included eventually. The PCR-RFLR method was utilized to screen for this polymorphism. The +49A/G polymorphism was shown to increase the risk of BC. Subgroup analyses showed that this polymorphism was linked to an increased susceptibility to BC among individuals aged < 60 years, smokers and drinkers. Additionally, this polymorphism significantly correlated with tumor node metastasis and tumor size (≥3 cm). To sum up, this study reveals that the CTLA-4 +49A/G polymorphism could increase the risk of BC in Chinese Han people. Further large cohort studies with enough sample sizes are urgently warranted to verify the findings of this present study.
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10
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Epigenetic silencing of ZIC4 contributes to cancer progression in hepatocellular carcinoma. Cell Death Dis 2020; 11:906. [PMID: 33097694 PMCID: PMC7584641 DOI: 10.1038/s41419-020-03109-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 10/06/2020] [Accepted: 10/08/2020] [Indexed: 12/28/2022]
Abstract
Inactivation of tumor suppressor gene played critical roles in the development and progression of human hepatocellular carcinoma (HCC). Zic family member 4 (ZIC4) is transcription factor and plays an important role in the developmental process. However, the expression and biological role of ZIC4 in HCC is poorly understood. Here, bioinformatics analysis based on The Cancer Genome Atlas (TCGA) database revealed an aberrant hypermethylation of ZIC4 in HCC. ZIC4 is frequently hypermethylated in promoter region and down expressed in HCC cells and tissues. Functionally, ZIC4 inhibition facilitated the proliferation, migration, invasion, and epithelial-mesenchymal transition (EMT) in vitro and in vivo. Conversely, ZIC4 overexpression reduced proliferation and invasiveness of HCC cells. In addition, ZIC4 inhibition rescued the antitumor effect induced by enhancer of zeste homolog 2 (EZH2) knockdown or EZH2 inhibitor. Mechanistically, EZH2 knockdown or EZH2 inhibitor reduced the enrichment of EZH2 and H3K27me3 in ZIC4 promoter region and leading to the upregulation of ZIC4. Altogether, these data indicate that epigenetic silencing of ZIC4 by EZH2 mediated H3K27me3 is an important mechanism in HCC and provide a new therapeutic target for the treatment of hepatocellular carcinoma disease.
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11
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Lozano F, Raventos CX, Carrion A, Trilla E, Morote J. Current status of genetic urinary biomarkers for surveillance of non-muscle invasive bladder cancer: a systematic review. BMC Urol 2020; 20:99. [PMID: 32664878 PMCID: PMC7362437 DOI: 10.1186/s12894-020-00670-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 07/08/2020] [Indexed: 01/22/2023] Open
Abstract
Background Genetic biomarkers are a promising and growing field in the management of bladder cancer in all stages. The aim of this paper is to understand the role of genetic urinary biomarkers in the follow up of patients with non muscle invasive bladder cancer where there is increasing evidence that they can play a role in avoiding invasive techniques. Methods Following PRISMA criteria, we have performed a systematic review. The search yielded 164 unique articles, of which 21 articles were included involving a total of 7261 patients. Sixteen of the articles were DNA based biomarkers, analyzing different methylations, microsatellite aberrations and gene mutations. Five articles studied the role of RNA based biomarkers, based on measuring levels of different combinations of mRNA. QUADAS2 critical evaluation of each paper has been reported. Results There are not randomized control trials comparing any biomarker with the gold standard follow-up, and the level of evidence is 2B in almost all the studies. Negative predictive value varies between 55 and 98.5%, being superior in RNA based biomarkers. Conclusions Although cystoscopy and cytology are the gold standard for non muscle invasive bladder cancer surveillance, genetic urinary biomarkers are a promising tool to avoid invasive explorations to the patients with a safe profile of similar sensitivity and negative predictive value. The accuracy that genetic biomarkers can offer should be taken into account to modify the paradigm of surveillance in non muscle invasive bladder cancer patients, especially in high-risk ones where many invasive explorations are recommended and biomarkers experiment better results.
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Affiliation(s)
- F Lozano
- Urology Department, Vall d'Hebron University Hospital, Pg. Vall d'Hebron 119-129, 08035, Barcelona, Spain. .,Universitat Autònoma de Barcelona, Barcelona, Spain.
| | - C X Raventos
- Urology Department, Vall d'Hebron University Hospital, Pg. Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | - A Carrion
- Urology Department, Vall d'Hebron University Hospital, Pg. Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | - E Trilla
- Urology Department, Vall d'Hebron University Hospital, Pg. Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | - J Morote
- Urology Department, Vall d'Hebron University Hospital, Pg. Vall d'Hebron 119-129, 08035, Barcelona, Spain.,Universitat Autònoma de Barcelona, Barcelona, Spain
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12
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Lu J, Xu Y, Wang YH, Huang XY, Wu Y, Xie JW, Wang JB, Lin JX, Li P, Zheng CH, Huang AM, Huang CM. TBX2 Expression predicts Tumor Recurrence and Adjuvant Chemotherapy Benefits in Gastric Cancer Patients following R0 Resection: a proposed approach for risk stratification. J Cancer 2020; 11:3172-3179. [PMID: 32231721 PMCID: PMC7097955 DOI: 10.7150/jca.34929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 09/22/2019] [Indexed: 11/29/2022] Open
Abstract
Aims: TBX2 is related to tumor progression and drug resistance. However, the roles of TBX2 in gastric cancer (GC) remain unclear. Our study aims at investigating the clinical roles of TBX2 in GC. Methods: The protein expression levels of TBX2 in fresh GC tissue (n=20) were investigated with Western blotting analyses. The correlation between TBX2 expression and its prognostic significance was evaluated by immunohistochemical analyses of 401 patients. The survival benefit of postoperative adjuvant chemotherapy (PAC) for patients was evaluated. Results: The expression of TBX2 was increased in GC tissue compared with adjacent paracancerous tissue (p=0.020). Immunohistochemistry demonstrated that TBX2 expression was significantly associated with lymphovascular invasion (p=0.024) and lymph node metastasis (p=0.044). A high level of TBX2 expression was an independent indicator of unfavorable recurrence-free and overall survival (p=0.002 and p=0.033, respectively). The prognostic model incorporating TBX2 expression exhibited greater predictive accuracy than the primary model. More importantly, the benefit of PAC noted in stage II/III GC patients with low TBX2 expression was superior to high TBX2 expression. Conclusion: TBX2 may be not only a useful prognostic marker for GC but also a predictive biomarker of response to PAC in stage II/III GC patients. The current findings warrant further verification.
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Affiliation(s)
- Jun Lu
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China.,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China.,Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - Yu Xu
- Department of Pathology, the School of Basic Medical Sciences, Fujian Medical University.,Institute of Oncology of Fujian Medical University, Fuzhou, China
| | - Yao-Hui Wang
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China.,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China.,Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - Xiao-Yan Huang
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China.,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China.,Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - Yuan Wu
- Department of Pathology, the School of Basic Medical Sciences, Fujian Medical University.,Institute of Oncology of Fujian Medical University, Fuzhou, China
| | - Jian-Wei Xie
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China.,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China.,Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - Jia-Bin Wang
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China.,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China.,Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - Jian-Xian Lin
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China.,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China.,Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - Ping Li
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China.,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China.,Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - Chao-Hui Zheng
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China.,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China.,Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - Ai-Min Huang
- Department of Pathology, the School of Basic Medical Sciences, Fujian Medical University.,Institute of Oncology of Fujian Medical University, Fuzhou, China
| | - Chang-Ming Huang
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China.,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China.,Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
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13
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Wang C, Liu Q, Huang M, Zhou Q, Zhang X, Zhang J, Xie R, Yu Y, Chen S, Fan J, Chen X. Loss of GATA6 expression promotes lymphatic metastasis in bladder cancer. FASEB J 2020; 34:5754-5766. [PMID: 32103545 DOI: 10.1096/fj.201903176r] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 02/06/2020] [Accepted: 02/18/2020] [Indexed: 12/19/2022]
Abstract
Lymph node metastasis is associated with tumor relapse and poor patient prognosis in bladder cancer. However, the mechanisms by which bladder carcinoma cells induce lymphangiogenesis and further promote metastasis in the lymphatic system remain unclear. Here, we show that the transcription factor GATA-binding factor 6 (GATA6) was substantially downregulated in bladder cancer via promoter hypermethylation. Low-level GATA6 expression significantly correlated with lymph node metastasis positivity and was able to predict earlier relapse and shorter survival of bladder cancer. Reconstitution of GATA6 inhibited lymphangiogenesis and lymph node metastasis in GATA6-low bladder cancer cells, while silencing of GATA6 rendered lymphatic metastasis in GATA6-high bladder cancer cells. Additionally, we demonstrated that GATA6 bound to the promoter of vascular endothelial growth factor (VEGF)-C, a lymphangiogenic factor, and acted as a transcriptional repressor. This GATA6/VEGF-C axis was essential for GATA6-mediated lymphatic metastasis. In bladder cancer patients, low GATA6 correlated with high VEGF-C and reduced overall survival. These findings indicate GATA6 as a pivotal regulator in the lymphatic dissemination of bladder cancer and suggest a new therapeutic target for the disease.
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Affiliation(s)
- Chanjuan Wang
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Qinghua Liu
- Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ming Huang
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Qianghua Zhou
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xiaoyu Zhang
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Jingtong Zhang
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ruihui Xie
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yanqi Yu
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Shang Chen
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Jianbing Fan
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Xu Chen
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
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14
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Zhu S, Yu W, Yang X, Wu C, Cheng F. Traditional Classification and Novel Subtyping Systems for Bladder Cancer. Front Oncol 2020; 10:102. [PMID: 32117752 PMCID: PMC7025453 DOI: 10.3389/fonc.2020.00102] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 01/20/2020] [Indexed: 12/31/2022] Open
Abstract
Bladder cancer is the most common tumor in the urinary system, with approximately 420,000 new cases and 160,000 deaths per year. The European Organization for Research and Treatment of Cancer (EOTRC) classifies non-muscular invasive bladder cancer (NMIBC) into low-risk, medium-risk and high-risk groups based on a comprehensive analysis of NMIBC pathological parameters and the risk of recurrence and progression to muscular invasive bladder cancer (MIBC). Traditional classification systems are based on pathologic grading, staging systems, and clinical prognosis. However, the pathological parameters of the tumor cannot fully reflect the “intrinsic characteristics” of bladder cancer, and tumors with a similar pathology exhibit different biological behaviors. Furthermore, although the traditional classification system cannot accurately predict the risk of recurrence or the progression of bladder cancer patients (BCs) individually, this method is widely used in clinical practice because of its convenient operation. With the development of sequencing and other technologies, the genetics-based molecular subtyping of bladder cancer has become increasingly studied. Compared with the traditional classification system, it provides more abundant tumor biological information and is expected to assist or even replace the traditional typing system in the future.
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Affiliation(s)
- Shaoming Zhu
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Weimin Yu
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Xiao Yang
- Department of Gynaecology and Obstetrics, Renmin Hospital of Peking University, Beijing, China
| | - Cheng Wu
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Fan Cheng
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
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15
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Khan SF, Damerell V, Omar R, Du Toit M, Khan M, Maranyane HM, Mlaza M, Bleloch J, Bellis C, Sahm BDB, Peres J, ArulJothi KN, Prince S. The roles and regulation of TBX3 in development and disease. Gene 2020; 726:144223. [PMID: 31669645 PMCID: PMC7108957 DOI: 10.1016/j.gene.2019.144223] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 10/18/2019] [Accepted: 10/22/2019] [Indexed: 12/18/2022]
Abstract
TBX3, a member of the ancient and evolutionary conserved T-box transcription factor family, is a critical developmental regulator of several structures including the heart, mammary glands, limbs and lungs. Indeed, mutations in the human TBX3 lead to ulnar mammary syndrome which is characterized by several clinical malformations including hypoplasia of the mammary and apocrine glands, defects of the upper limb, areola, dental structures, heart and genitalia. In contrast, TBX3 has no known function in adult tissues but is frequently overexpressed in a wide range of epithelial and mesenchymal derived cancers. This overexpression greatly impacts several hallmarks of cancer including bypass of senescence, apoptosis and anoikis, promotion of proliferation, tumour formation, angiogenesis, invasion and metastatic capabilities as well as cancer stem cell expansion. The debilitating consequences of having too little or too much TBX3 suggest that its expression levels need to be tightly regulated. While we have a reasonable understanding of the mutations that result in low levels of functional TBX3 during development, very little is known about the factors responsible for the overexpression of TBX3 in cancer. Furthermore, given the plethora of oncogenic processes that TBX3 impacts, it must be regulating several target genes but to date only a few have been identified and characterised. Interestingly, while there is compelling evidence to support oncogenic roles for TBX3, a few studies have indicated that it may also have tumour suppressor functions in certain contexts. Together, the diverse functional elasticity of TBX3 in development and cancer is thought to involve, in part, the protein partners that it interacts with and this area of research has recently received some attention. This review provides an insight into the significance of TBX3 in development and cancer and identifies research gaps that need to be explored to shed more light on this transcription factor.
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Affiliation(s)
- Saif F Khan
- Division of Cell Biology, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Observatory, 7925, Cape Town, South Africa
| | - Victoria Damerell
- Division of Cell Biology, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Observatory, 7925, Cape Town, South Africa
| | - Rehana Omar
- Division of Cell Biology, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Observatory, 7925, Cape Town, South Africa
| | - Michelle Du Toit
- Division of Cell Biology, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Observatory, 7925, Cape Town, South Africa
| | - Mohsin Khan
- Division of Cell Biology, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Observatory, 7925, Cape Town, South Africa
| | - Hapiloe Mabaruti Maranyane
- Division of Cell Biology, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Observatory, 7925, Cape Town, South Africa
| | - Mihlali Mlaza
- Division of Cell Biology, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Observatory, 7925, Cape Town, South Africa
| | - Jenna Bleloch
- Division of Cell Biology, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Observatory, 7925, Cape Town, South Africa
| | - Claire Bellis
- Division of Cell Biology, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Observatory, 7925, Cape Town, South Africa
| | - Bianca D B Sahm
- Division of Cell Biology, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Observatory, 7925, Cape Town, South Africa; Department of Pharmacology, Institute of Biomedical Science, University of São Paulo, São Paulo, SP 11030-400, Brazil
| | - Jade Peres
- Division of Cell Biology, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Observatory, 7925, Cape Town, South Africa
| | - K N ArulJothi
- Division of Cell Biology, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Observatory, 7925, Cape Town, South Africa
| | - Sharon Prince
- Division of Cell Biology, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Observatory, 7925, Cape Town, South Africa.
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16
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Perrard J, Morel A, Meznad K, Paget-Bailly P, Dalstein V, Guenat D, Mourareau C, Clavel C, Fauconnet S, Baguet A, Mougin C, Pretet JL. DNA demethylation agent 5azadC downregulates HPV16 E6 expression in cervical cancer cell lines independently of TBX2 expression. Oncol Lett 2019; 19:1074-1081. [PMID: 31897221 DOI: 10.3892/ol.2019.11158] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 09/09/2019] [Indexed: 12/18/2022] Open
Abstract
HPV16 is the most carcinogenic human papillomavirus and causes >50% of cervical cancers, the majority of anal cancers and 30% of oropharyngeal squamous cell carcinomas. HPV carcinogenesis relies on the continuous expression of the two main viral oncoproteins E6 and E7 that target >150 cellular proteins. Among them, epigenetic modifiers, including DNA Methyl Transferases (DNMT), are dysregulated, promoting an aberrant methylation pattern in HPV-positive cancer cells. It has been previously reported that the treatment of HPV-positive cervical cancer cells with DNMT inhibitor 5-aza-2'-deoxycytidine (5azadC) caused the downregulation of E6 expression due to mRNA destabilization that was mediated by miR-375. Recently, the T-box transcription factor 2 (TBX2) has been demonstrated to repress HPV LCR activity. In the current study, the role of TBX2 in E6 repression was investigated in HPV16 cervical cancer cell lines following 5azadC treatment. A decrease of E6 expression was accompanied by p53 and p21 restoration. While TBX2 mRNA was upregulated in 5azadC-treated SiHa and Ca Ski cells, TBX2 protein was not detectable. Furthermore, the overexpression of TBX2 protein in cervical cancer cells did not allow the repression of E6 expression. The TBX2 transcription factor is therefore unlikely to be associated with the repression of E6 following 5azadC treatment of SiHa and Ca Ski cells.
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Affiliation(s)
- Jerome Perrard
- Équipe d'Accueil 3181, University of Bourgogne Franche-Comté, Laboratoire d'Excellence Lipoprotéines et Santé, Prévention et Traitement des Maladies Inflammatoires et du Cancer, 25000 Besançon, France
| | - Adrien Morel
- Center For Research in Genetics and Genomics-CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá 112041, Colombia
| | - Koceila Meznad
- Équipe d'Accueil 3181, University of Bourgogne Franche-Comté, Laboratoire d'Excellence Lipoprotéines et Santé, Prévention et Traitement des Maladies Inflammatoires et du Cancer, 25000 Besançon, France
| | - Philippe Paget-Bailly
- Équipe d'Accueil 3181, University of Bourgogne Franche-Comté, Laboratoire d'Excellence Lipoprotéines et Santé, Prévention et Traitement des Maladies Inflammatoires et du Cancer, 25000 Besançon, France
| | - Veronique Dalstein
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche-S 1250 Pathologies Pulmonaires et Plasticité Cellulaire, Université de Reims Champagne-Ardenne, Faculté de Médecine, 51000 Reims, France.,Centre Hospitalier Universitaire Reims, Laboratoire Biopathologie, 51000 Reims, France
| | - David Guenat
- Équipe d'Accueil 3181, University of Bourgogne Franche-Comté, Laboratoire d'Excellence Lipoprotéines et Santé, Prévention et Traitement des Maladies Inflammatoires et du Cancer, 25000 Besançon, France.,Centre National de Référence Papillomavirus, CHU Besançon, Boulevard Alexandre Fleming, 25000 Besançon, France
| | - Celine Mourareau
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche-S 1250 Pathologies Pulmonaires et Plasticité Cellulaire, Université de Reims Champagne-Ardenne, Faculté de Médecine, 51000 Reims, France.,Centre Hospitalier Universitaire Reims, Laboratoire Biopathologie, 51000 Reims, France
| | - Christine Clavel
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche-S 1250 Pathologies Pulmonaires et Plasticité Cellulaire, Université de Reims Champagne-Ardenne, Faculté de Médecine, 51000 Reims, France.,Centre Hospitalier Universitaire Reims, Laboratoire Biopathologie, 51000 Reims, France
| | - Sylvie Fauconnet
- Équipe d'Accueil 3181, University of Bourgogne Franche-Comté, Laboratoire d'Excellence Lipoprotéines et Santé, Prévention et Traitement des Maladies Inflammatoires et du Cancer, 25000 Besançon, France
| | - Aurelie Baguet
- Équipe d'Accueil 3181, University of Bourgogne Franche-Comté, Laboratoire d'Excellence Lipoprotéines et Santé, Prévention et Traitement des Maladies Inflammatoires et du Cancer, 25000 Besançon, France
| | - Christiane Mougin
- Équipe d'Accueil 3181, University of Bourgogne Franche-Comté, Laboratoire d'Excellence Lipoprotéines et Santé, Prévention et Traitement des Maladies Inflammatoires et du Cancer, 25000 Besançon, France.,Centre National de Référence Papillomavirus, CHU Besançon, Boulevard Alexandre Fleming, 25000 Besançon, France
| | - Jean-Luc Pretet
- Équipe d'Accueil 3181, University of Bourgogne Franche-Comté, Laboratoire d'Excellence Lipoprotéines et Santé, Prévention et Traitement des Maladies Inflammatoires et du Cancer, 25000 Besançon, France.,Centre National de Référence Papillomavirus, CHU Besançon, Boulevard Alexandre Fleming, 25000 Besançon, France
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17
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Martinez VG, Munera-Maravilla E, Bernardini A, Rubio C, Suarez-Cabrera C, Segovia C, Lodewijk I, Dueñas M, Martínez-Fernández M, Paramio JM. Epigenetics of Bladder Cancer: Where Biomarkers and Therapeutic Targets Meet. Front Genet 2019; 10:1125. [PMID: 31850055 PMCID: PMC6902278 DOI: 10.3389/fgene.2019.01125] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 10/17/2019] [Indexed: 12/12/2022] Open
Abstract
Bladder cancer (BC) is the most common neoplasia of the urothelial tract. Due to its high incidence, prevalence, recurrence and mortality, it remains an unsolved clinical and social problem. The treatment of BC is challenging and, although immunotherapies have revealed potential benefit in a percentage of patients, it remains mostly an incurable disease at its advanced state. Epigenetic alterations, including aberrant DNA methylation, altered chromatin remodeling and deregulated expression of non-coding RNAs are common events in BC and can be driver events in BC pathogenesis. Accordingly, these epigenetic alterations are now being used as potential biomarkers for these disorders and are being envisioned as potential therapeutic targets for the future management of BC. In this review, we summarize the recent findings in these emerging and exciting new aspects paving the way for future clinical treatment of this disease.
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Affiliation(s)
- Victor G. Martinez
- Biomedical Research Institute I + 12, University Hospital 12 de Octubre, Madrid, Spain
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Madrid, Spain
| | - Ester Munera-Maravilla
- Biomedical Research Institute I + 12, University Hospital 12 de Octubre, Madrid, Spain
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Alejandra Bernardini
- Biomedical Research Institute I + 12, University Hospital 12 de Octubre, Madrid, Spain
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Carolina Rubio
- Biomedical Research Institute I + 12, University Hospital 12 de Octubre, Madrid, Spain
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Cristian Suarez-Cabrera
- Biomedical Research Institute I + 12, University Hospital 12 de Octubre, Madrid, Spain
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Madrid, Spain
| | - Cristina Segovia
- Biomedical Research Institute I + 12, University Hospital 12 de Octubre, Madrid, Spain
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Madrid, Spain
| | - Iris Lodewijk
- Biomedical Research Institute I + 12, University Hospital 12 de Octubre, Madrid, Spain
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Madrid, Spain
| | - Marta Dueñas
- Biomedical Research Institute I + 12, University Hospital 12 de Octubre, Madrid, Spain
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Mónica Martínez-Fernández
- Genomes & Disease Lab, CiMUS (Center for Research in Molecular Medicine and Chronic Diseases), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Jesus Maria Paramio
- Biomedical Research Institute I + 12, University Hospital 12 de Octubre, Madrid, Spain
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
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18
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Zhang N, Chen S, Wu L, Wu Y, Jiang G, Shao J, Chen L, Sun J, Na R, Wang X, Xu J. Identification of Cancer-Specific Methylation of Gene Combination for the Diagnosis of Bladder Cancer. J Cancer 2019; 10:6761-6766. [PMID: 31777606 PMCID: PMC6856882 DOI: 10.7150/jca.28192] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 05/27/2019] [Indexed: 01/30/2023] Open
Abstract
Here we conducted an evidence-based study in developing and validating a urinary biomarker combination of gene methylation assays in patients with hematuria. A number of 99 urine samples were obtained and detected from Chinese patients with hematuria. The Cancer Genome Atlas cohort with methylation (HM450) beta-values and clinical data of 412 bladder cancer and 21 matching normal tissue was included as a validation series. A risk score formula was then developed and calculated by the targeted genes, weighted by their estimated regression coefficients from the multivariable binary logistic regression analyses, and evaluated by receiver operating characteristic (ROC) curves analysis. The combination assay of HOXA9, ONECUT2, PCDH17, PENK, TWIST1, VIM and ZNF154 was singled out according to the results of multivariate logistic regression analysis. The higher probability of DNA methylation of all the selected 7 genes was found in bladder cancer group than the control group. Remarkable higher DNA methylation beta-values of all the selected 7 genes were also displayed in bladder cancer tissues compared with their matching normal bladder tissues. And the AUC value of our risk score model were 0.894 and 0.851 in respective cohort, revealing highlighted predictive value of our risk score model on bladder cancer diagnosis. In conclusions, a urinary combined methylation assay of HOXA9, ONECUT2, PCDH17, PENK, TWIST1, VIM and ZNF154 displayed accurate prediction of bladder cancer in hematuria patients, which provided the guidance for the patients at early stage tumor and during the follow-up after operation. Of course, prospective study based on a hematuria cohort with a large sample size should be conducted to validate these findings in the future.
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Affiliation(s)
- Ning Zhang
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Siteng Chen
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lingfeng Wu
- Department of Urology, Songjiang District Central Hospital, Shanghai, China
| | - Yishuo Wu
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Guangliang Jiang
- Department of Urology, Shengzhen Second People's Hospital, Guangdong, China
| | - Jialiang Shao
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lixin Chen
- Department of Urology, Songjiang District Central Hospital, Shanghai, China
| | - Jishan Sun
- Program for Personalized Cancer Care, Northshore University HealthSystem, Chicago, IL 60201
| | - Rong Na
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiang Wang
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianfeng Xu
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China.,Program for Personalized Cancer Care, Northshore University HealthSystem, Chicago, IL 60201
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19
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Classification of early and late stage liver hepatocellular carcinoma patients from their genomics and epigenomics profiles. PLoS One 2019; 14:e0221476. [PMID: 31490960 PMCID: PMC6730898 DOI: 10.1371/journal.pone.0221476] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 08/07/2019] [Indexed: 02/07/2023] Open
Abstract
Background Liver Hepatocellular Carcinoma (LIHC) is one of the major cancers worldwide, responsible for millions of premature deaths every year. Prediction of clinical staging is vital to implement optimal therapeutic strategy and prognostic prediction in cancer patients. However, to date, no method has been developed for predicting the stage of LIHC from the genomic profile of samples. Methods The Cancer Genome Atlas (TCGA) dataset of 173 early stage (stage-I), 177 late stage (stage-II, Stage-III and stage-IV) and 50 adjacent normal tissue samples for 60,483 RNA transcripts and 485,577 methylation CpG sites, was extensively analyzed to identify the key transcriptomic expression and methylation-based features using different feature selection techniques. Further, different classification models were developed based on selected key features to categorize different classes of samples implementing different machine learning algorithms. Results In the current study, in silico models have been developed for classifying LIHC patients in the early vs. late stage and cancerous vs. normal samples using RNA expression and DNA methylation data. TCGA datasets were extensively analyzed to identify differentially expressed RNA transcripts and methylated CpG sites that can discriminate early vs. late stages and cancer vs. normal samples of LIHC with high precision. Naive Bayes model developed using 51 features that combine 21 CpG methylation sites and 30 RNA transcripts achieved maximum MCC (Matthew’s correlation coefficient) 0.58 with an accuracy of 78.87% on the validation dataset in discrimination of early and late stage. Additionally, the prediction models developed based on 5 RNA transcripts and 5 CpG sites classify LIHC and normal samples with an accuracy of 96–98% and AUC (Area Under the Receiver Operating Characteristic curve) 0.99. Besides, multiclass models also developed for classifying samples in the normal, early and late stage of cancer and achieved an accuracy of 76.54% and AUC of 0.86. Conclusion Our study reveals stage prediction of LIHC samples with high accuracy based on the genomics and epigenomics profiling is a challenging task in comparison to the classification of cancerous and normal samples. Comprehensive analysis, differentially expressed RNA transcripts, methylated CpG sites in LIHC samples and prediction models are available from CancerLSP (http://webs.iiitd.edu.in/raghava/cancerlsp/).
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20
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Biology of nonmuscle-invasive bladder cancer: pathology, genomic implications, and immunology. Curr Opin Urol 2019; 28:598-603. [PMID: 30138123 DOI: 10.1097/mou.0000000000000543] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
PURPOSE OF REVIEW Despite that nearly 75% of bladder cancer patients are diagnosed with nonmuscle-invasive disease, our understanding of the biological landscape in bladder cancer is primarily within the context of muscle-invasive bladder cancer. More recent studies addressing the genomic changes and immunology of nonmuscle-invasive bladder cancer (NMIBC) have helped to extend our understanding of this prevalent disease. RECENT FINDINGS Genomic studies reveal that NMIBC possesses complexity that can be defined by specific gene expression signatures and has helped to define subsets within this disease. These subsets possess different risk profiles that may impact treatment decisions. In addition, the baseline or posttreatment immunological response to the growing tumor may help to inform whether a specific NMIBC subset is likely to progress. SUMMARY Findings from studies addressing the molecular landscape of NMIBC may help to establish parameters for stratifying patient risk within this disease as well as establish novel or targeted treatment strategies. Inclusion of information about the immune response within tumors will likely contribute to defining the relative risk and treatment strategy for these patients.
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21
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The Role and Importance of Timely Radical Cystectomy for High-Risk Non-muscle-Invasive Bladder Cancer. Cancer Treat Res 2019; 175:193-214. [PMID: 30168123 DOI: 10.1007/978-3-319-93339-9_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Non-muscle-invasive bladder cancer accounts for the majority of incident bladder cancers but is a heterogeneous disease with variation in clinical presentation, course, and outcomes. Risk stratification techniques have attempted to identify those at highest risk of cancer recurrence and progression to help personalize and individualize treatment options. Radical cystectomy during the optimal window of curability could improve cancer outcomes; however, identifying the disease and patient characteristics as well as the correct timing to intervene remains difficult. We review the natural history of non-muscle-invasive bladder cancer, discuss different risk-stratification techniques and how they can help identify those most likely to benefit from radical treatment, and examine the evidence supporting the benefit of timely cystectomy.
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22
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Köhler CU, Bonberg N, Ahrens M, Behrens T, Hovanec J, Eisenacher M, Noldus J, Deix T, Braun K, Gohlke H, Walter M, Tannapfel A, Tam Y, Sommerer F, Marcus K, Jöckel KH, Erbel R, Cantor CR, Käfferlein HU, Brüning T. Noninvasive diagnosis of urothelial cancer in urine using DNA hypermethylation signatures-Gender matters. Int J Cancer 2019; 145:2861-2872. [PMID: 31008534 DOI: 10.1002/ijc.32356] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 04/01/2019] [Indexed: 01/28/2023]
Abstract
Urothelial cancer (UCa) is the most predominant cancer of the urinary tract and noninvasive diagnosis using hypermethylation signatures in urinary cells is promising. Here, we assess gender differences in a newly identified set of methylation biomarkers. UCa-associated hypermethylated sites were identified in urine of a male screening cohort (n = 24) applying Infinium-450K-methylation arrays and verified in two separate mixed-gender study groups (n = 617 in total) using mass spectrometry as an independent technique. Additionally, tissue samples (n = 56) of mixed-gender UCa and urological controls (UCt) were analyzed. The hypermethylation signature of UCa in urine was specific and sensitive across all stages and grades of UCa and independent on hematuria. Individual CpG sensitivities reached up to 81.3% at 95% specificity. Albeit similar methylation differences in tissue of both genders, differences were less pronounced in urine from women, most likely due to the frequent presence of squamous epithelial cells and leukocytes. Increased repression of methylation levels was observed at leukocyte counts ≥500/μl urine which was apparent in 30% of female and 7% of male UCa cases, further confirming the significance of the relative amounts of cancerous and noncancerous cells in urine. Our study shows that gender difference is a most relevant issue when evaluating the performance of urinary biomarkers in cancer diagnostics. In case of UCa, the clinical benefits of methylation signatures to male patients may outweigh those in females due to the general composition of women's urine. Accordingly, these markers offer a diagnostic option specifically in males to decrease the number of invasive cystoscopies.
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Affiliation(s)
- Christina U Köhler
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr-University Bochum (IPA), Bochum, Germany
| | - Nadine Bonberg
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr-University Bochum (IPA), Bochum, Germany
| | - Maike Ahrens
- Medical Proteome Center, Ruhr University Bochum, Bochum, Germany
| | - Thomas Behrens
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr-University Bochum (IPA), Bochum, Germany
| | - Jan Hovanec
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr-University Bochum (IPA), Bochum, Germany
| | | | - Joachim Noldus
- Department of Urology, Marien Hospital Herne, Ruhr-University Bochum, Herne, Germany
| | - Thomas Deix
- Department of Urology, Marien Hospital Herne, Ruhr-University Bochum, Herne, Germany
| | - Katharina Braun
- Department of Urology, Marien Hospital Herne, Ruhr-University Bochum, Herne, Germany
| | | | - Michael Walter
- c.ATG Core Facility for NGS and Microarrays, University of Tübingen, Tübingen, Germany
| | - Andrea Tannapfel
- Institute of Pathology, Georgius Agricola Foundation, Ruhr-University Bochum, Bochum, Germany
| | - Yu Tam
- Institute of Pathology, Georgius Agricola Foundation, Ruhr-University Bochum, Bochum, Germany
| | - Florian Sommerer
- Institute of Pathology, Georgius Agricola Foundation, Ruhr-University Bochum, Bochum, Germany
| | - Katrin Marcus
- Medical Proteome Center, Ruhr University Bochum, Bochum, Germany
| | - Karl-Heinz Jöckel
- Institute for Medical Informatics, Biometry and Epidemiology (IMIBE), University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Raimund Erbel
- Institute for Medical Informatics, Biometry and Epidemiology (IMIBE), University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Charles R Cantor
- Department of Biomedical Engineering, School of Medicine, Boston University, Boston, MA
| | - Heiko U Käfferlein
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr-University Bochum (IPA), Bochum, Germany
| | - Thomas Brüning
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr-University Bochum (IPA), Bochum, Germany
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Yang Z, Liu A, Xiong Q, Xue Y, Liu F, Zeng S, Zhang Z, Li Y, Sun Y, Xu C. Prognostic value of differentially methylated gene profiles in bladder cancer. J Cell Physiol 2019; 234:18763-18772. [PMID: 30953370 DOI: 10.1002/jcp.28515] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 02/18/2019] [Accepted: 02/20/2019] [Indexed: 01/03/2023]
Abstract
DNA methylation can regulate gene expression and is pivotal in the occurrence and development of bladder cancer. In this study, we analyzed whole-genome DNA methylation on the basis of data from The Cancer Genome Atlas to select epigenetic biomarkers predictive of survival and further understand the molecular mechanisms underlying methylation patterns in bladder cancer. We identified 540 differentially methylated genes between tumor and normal tissues, including a number of independent prognostic factors based on univariate analysis. Genes (MIR6732, SOWAHC, SERPINI1, OR10W1, OR7G3, AIM1, and ZFAND5) were integrated to establish a risk model for prognostic assessment based on multivariate Cox analysis. The methylation of SOWAHC was negatively correlated with its messenger RNA expression, and together these were significantly correlated with prognosis. This study took advantage of high-throughput data mining to provide new bioinformatics evidence and ideas for further study into the pathogenesis and prognosis of bladder cancer.
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Affiliation(s)
- Zeyu Yang
- Department of Urology, Changhai Hospital Affiliated with Second Military Medical University, Shanghai, China
| | - Anwei Liu
- Department of Urology, Changhai Hospital Affiliated with Second Military Medical University, Shanghai, China
| | - Qiao Xiong
- Department of Urology, Changhai Hospital Affiliated with Second Military Medical University, Shanghai, China
| | - Yongping Xue
- Department of Urology, Changhai Hospital Affiliated with Second Military Medical University, Shanghai, China
| | - Fei Liu
- Department of Urology, Changhai Hospital Affiliated with Second Military Medical University, Shanghai, China
| | - Shuxiong Zeng
- Department of Urology, Changhai Hospital Affiliated with Second Military Medical University, Shanghai, China
| | - Zhensheng Zhang
- Department of Urology, Changhai Hospital Affiliated with Second Military Medical University, Shanghai, China
| | - Yunfei Li
- Department of Urology, The Thrid Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Yinghao Sun
- Department of Urology, Changhai Hospital Affiliated with Second Military Medical University, Shanghai, China
| | - Chuanliang Xu
- Department of Urology, Changhai Hospital Affiliated with Second Military Medical University, Shanghai, China
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Epigenetic Suppression of the T-box Subfamily 2 ( TBX2) in Human Non-Small Cell Lung Cancer. Int J Mol Sci 2019; 20:ijms20051159. [PMID: 30866410 PMCID: PMC6429281 DOI: 10.3390/ijms20051159] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/15/2019] [Accepted: 02/18/2019] [Indexed: 12/25/2022] Open
Abstract
(1) The TBX2 subfamily of transcription factors (TBXs 2, 3, 4 and 5) are markedly down-regulated in human non-small cell lung cancer (NSCLC) and exert tumor suppressor effects in lung malignancy. Yet, mechanisms underlying suppressed expression of the TBX2 subfamily in NSCLC are elusive. Here, we interrogated probable epigenetic mechanisms in suppressed expression of the TBX2 subfamily in human NSCLC. (2) TBX2 subfamily gene expression and methylation levels in NSCLC and normal lung tissues were surveyed using publicly available RNA-sequence and genome-wide methylation datasets. Methylation β-values of the four genes were statistically compared between NSCLCs and normal lung tissues, correlated with gene expression levels, and interrogated with clinicopathological variables. Expression and methylation levels of TBXs were quantified in NSCLC cells using real-time PCR and methylation-specific PCR assays, respectively. Effects of the DNA methyltransferase inhibitor 5-azacytidine (Aza) on TBX2 subfamily expression were assessed in NSCLC cells. Impact of TBX2 subfamily expression on Aza-treated cells was evaluated by RNA interference. (3) All four TBXs were significantly hypermethylated in NSCLCs relative to normal lung tissues (p < 0.05). Methylation β-values of the genes, with exception of TBX2, were significantly inversely correlated with corresponding mRNA expression levels (p < 0.05). We found no statistically significant differences in hypermethylation levels of the TBX2 subfamily by clinicopathological features including stage and tobacco history. Expression levels of the TBX genes were overall suppressed in NSCLC cells relative to normal alveolar cells. Members of the subfamily were significantly hypermethylated in all tested NSCLC cell lines relative to normal alveolar cells. Treatment with Aza induced the expression of the TBX2 subfamily concomitant with NSCLC cell growth inhibition. Further, simultaneous knockdown of the four TBX genes markedly reduced anti-growth effects of Aza in NSCLC cells. (4) Our study sheds light on new epigenetic profiles in the molecular pathogenesis of human NSCLC.
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Ding W, Chen G, Shi T. Integrative analysis identifies potential DNA methylation biomarkers for pan-cancer diagnosis and prognosis. Epigenetics 2019; 14:67-80. [PMID: 30696380 DOI: 10.1080/15592294.2019.1568178] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
DNA methylation status is closely associated with diverse diseases, and is generally more stable than gene expression, thus abnormal DNA methylation could be important biomarkers for tumor diagnosis, treatment and prognosis. However, the signatures regarding DNA methylation changes for pan-cancer diagnosis and prognosis are less explored. Here we systematically analyzed the genome-wide DNA methylation patterns in diverse TCGA cancers with machine learning. We identified seven CpG sites that could effectively discriminate tumor samples from adjacent normal tissue samples for 12 main cancers of TCGA (1216 samples, AUC > 0.99). Those seven potential diagnostic biomarkers were further validated in the other 9 different TCGA cancers and 4 independent datasets (AUC > 0.92). Three out of the seven CpG sites were correlated with cell division, DNA replication and cell cycle. We also identified 12 CpG sites that can effectively distinguish 26 different cancers (7605 samples), and the result was repeatable in independent datasets as well as two disparate tumors with metastases (micro-average AUC > 0.89). Furthermore, a series of potential signatures that could significantly predict the prognosis of tumor patients for 7 different cancer were identified via survival analysis (p-value < 1e-4). Collectively, DNA methylation patterns vary greatly between tumor and adjacent normal tissues, as well as among different types of cancers. Our identified signatures may aid the decision of clinical diagnosis and prognosis for pan-cancer and the potential cancer-specific biomarkers could be used to predict the primary site of metastatic breast and prostate cancers.
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Affiliation(s)
- Wubin Ding
- a Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences , East China Normal University , Shanghai , China
| | - Geng Chen
- a Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences , East China Normal University , Shanghai , China
| | - Tieliu Shi
- a Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences , East China Normal University , Shanghai , China.,b National Center for International Research of Biological Targeting Diagnosis and Therapy, Guangxi Key Laboratory of Biological Targeting Diagnosis and Therapy Research, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy , Guangxi Medical University , Nanning , China
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26
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Li Z, Wang Y, Duan S, Shi Y, Li S, Zhang X, Ren J. Expression of TBX3 in Hepatocellular Carcinoma and Its Clinical Implication. Med Sci Monit 2018; 24:9324-9333. [PMID: 30578408 PMCID: PMC6320639 DOI: 10.12659/msm.909378] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) is the fifth most common malignancy in China, and China’s annual number of new cases accounts for about 45% of the world total. This research was aimed to study the expression of TBX3 protein in HCC and exploring its clinical significance. Material/Methods We collected tumor tissues and adjacent non-tumoral tissues of 174 patients with HCC undergoing surgical resection. The expression of TBX3 protein in different tissues and cell lines in vitro (LO2, HHL-5, MHC97-L, MHC97-H) was detected by immunohistochemistry or Western blotting, and the relationship between TBX3 expression and clinical data of patients with HCC was analyzed. Results The expression of TBX3 protein in HCC was significantly correlated with histological grade, tumor size, cancer cell metastasis, hepatitis B surface antigen, and the expression of Ki-67 in tumor tissues (P<0.05), and it was positively correlated with serum AFP level (r=0.766, P<0.05). The expression of TBX3 increased with increased histological grade in HCC (P<0.05). Cox regression analysis showed that the expression of TBX3 protein in HCC was an independent risk factor for prognosis (OR=0.524, 95% CI=0.283–0.964). The 5-year survival rate of patients with HCC that highly expressed TBX3 protein was 20.83%, which was significantly lower than the 40.20% rate in patients with low expression (P<0.05). Conclusions The expression of TBX3 in HCC patients undergoing surgical resection is high, and its expression increases with the degree of tumor differentiation. It is related to the metastasis of tumor cells and is positively correlated with the serum level of AFP and may affect the survival time of HCC patients undergoing surgical resection.
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Affiliation(s)
- Zhian Li
- Department of Ultrasound Medicine, The Affiliated Hospital of Inner Mongolia Medical University, Huhhot, Huhhot, China (mainland)
| | - Yaxi Wang
- Department of Ultrasound Medicine, The Affiliated Hospital of Inner Mongolia Medical University, Huhhot, Huhhot, China (mainland)
| | - Shasha Duan
- Department of Ultrasound Medicine, The Affiliated Hospital of Inner Mongolia Medical University, Huhhot, Huhhot, China (mainland)
| | - Yilu Shi
- Department of Ultrasound Medicine, The Affiliated Hospital of Inner Mongolia Medical University, Huhhot, Huhhot, China (mainland)
| | - Shuling Li
- Department of Ultrasound Medicine, The Affiliated Hospital of Inner Mongolia Medical University, Huhhot, Huhhot, China (mainland)
| | - Xiaoshan Zhang
- Department of Ultrasound, The Affiliated Hospital of Inner Mongolia Medical University, Huhhot, Huhhot, China (mainland)
| | - Jianjun Ren
- Department of Hepatobiliary, Pancreatic, and Splenic Surgery, The Affiliated Hospital of Inner Mongolia Medical University, Huhhot, Huhhot, China (mainland)
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27
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Abstract
PURPOSE OF REVIEW Epigenetics refers to processes that alter gene expression without altering primary DNA. Over that past decade, there is a growing focus on epigenetic mechanisms in cancer research and its importance in cancer biology. This review summarizes epigenetic dysregulation in bladder cancer. RECENT FINDINGS Epigenetic alterations are overall shared across various grades and stages of bladder cancer. High grade invasive tumors demonstrate a greater degree and intensity of methylation and may have a unique methylation pattern. Environmental exposures may influence epigenetic alterations directly independent of genomic change. Non-coding RNAs play an important role in cancer phenotype, especially in the context of integrative genomic analyses. DNA hypermethylation and non-coding RNAs have potential as robust bladder cancer biomarkers; however, they require further study and validation. Changes in chromatin and histone modification are attractive targets for therapy and are currently in clinical trials. Epigenetic dysregulation may be an important key in improving the understanding of bladder cancer pathogenesis, especially through integrative genomic analyses. Deeper understanding of these pathways can help identify clinically relevant biomarkers and therapeutic targets to validate for diagnosis, monitoring, prognosis, and treatment for bladder cancer.
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Affiliation(s)
- Sima P Porten
- Department of Urology, University of California San Francisco (UCSF), Mailbox Code 1695, 550 16th Street, 6th Floor, San Francisco, CA, 94143, USA.
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28
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Wu Y, Jiang G, Zhang N, Liu S, Lin X, Perschon C, Zheng SL, Ding Q, Wang X, Na R, Sun J, Xu J. HOXA9, PCDH17, POU4F2, and ONECUT2 as a Urinary Biomarker Combination for the Detection of Bladder Cancer in Chinese Patients with Hematuria. Eur Urol Focus 2018; 6:284-291. [PMID: 30309818 DOI: 10.1016/j.euf.2018.09.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 09/12/2018] [Accepted: 09/28/2018] [Indexed: 11/29/2022]
Abstract
BACKGROUND DNA methylation biomarkers for bladder cancer (BCa) have not been evaluated extensively in the Chinese population. OBJECTIVE To develop and validate a urinary biomarker combination of methylation assays in a group of Chinese patients with hematuria. DESIGN, SETTING, AND PARTICIPANTS A total of 192 urine samples were collected and evaluated from patients with microscopic or gross hematuria, including 97 BCa patients and 95 controls with benign diseases. A two-stage study was conducted: the first stage being assay construction and the second stage being assay validation. Eighty-one urine samples were analyzed for the hypermethylation of eight selected genes in stage 1 and then a four-gene panel was constructed. An additional 111 urine samples were analyzed using the four-gene panel (including HOXA9, PCDH17, POU4F2, and ONECUT2) for independent validation. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS The positive predictive value (PPV) and negative predictive value (NPV) were calculated for the combination methylation assay. Uni- and multivariate binary logistic regression analyses (backward elimination, conditional) were performed to calculate the association between BCa and each predictor variable. RESULTS AND LIMITATIONS The combination assay of HOXA9, PCDH17, POU4F2, and ONECUT2 was selected based on the results of multivariate logistic regression analysis in stage 1. Using a strategy of three-level risk stratification, the assay yielded a consistent PPV of 100%. With an estimated BCa prevalence of 10% in a general hematuria population, the assay would result in an overall NPV of 98%. This combined methylation biomarker would yield an overall area under the receiver operating characteristic curve of 0.871 (with a sensitivity of 90.5% and a specificity of 73.2%) if using the prediction model from multivariate regression analysis. In addition, over half of BCa cases would be predicted accurately and ∼60% of unnecessary cystoscopies could be spared. This study had several limitations. First, the sample size was relatively small. Second, it was performed in a case-control population rather than in a natural hematuria cohort. CONCLUSIONS A combination methylation assay of HOXA9, PCDH17, POU4F2, and ONECUT2 resulted in high PPV and NPV in Chinese patients with hematuria. With accurate risk prediction, the urinary biomarker combination could spare a sizeable proportion of low-risk patients from extensive and invasive examination. PATIENT SUMMARY In the present study, we looked at the predictive performance of a urinary biomarker combination of HOXA9, PCDH17, POU4F2, and ONECUT2. We found that this urinary biomarker combination may help discriminate bladder cancer from other benign diseases in patients with hematuria, resulting in a reduction of unnecessary invasive examination in patients at low risk.
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Affiliation(s)
- Yishuo Wu
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, PR China; Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, PR China; Program for Personalized Cancer Care, NorthShore University Health System, Evanston, Illinois, USA
| | - Guangliang Jiang
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, PR China; Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, PR China; Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong, PR China
| | - Ning Zhang
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Shenghua Liu
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, PR China; Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, PR China
| | - Xiaoling Lin
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, PR China
| | - Chelsea Perschon
- Program for Personalized Cancer Care, NorthShore University Health System, Evanston, Illinois, USA
| | - S Lilly Zheng
- Program for Personalized Cancer Care, NorthShore University Health System, Evanston, Illinois, USA
| | - Qiang Ding
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, PR China; Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, PR China
| | - Xiang Wang
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Rong Na
- Department of Urology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, PR China.
| | - Jishan Sun
- Program for Personalized Cancer Care, NorthShore University Health System, Evanston, Illinois, USA.
| | - Jianfeng Xu
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, PR China; Program for Personalized Cancer Care, NorthShore University Health System, Evanston, Illinois, USA.
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29
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Peng D, Ge G, Xu Z, Ma Q, Shi Y, Zhou Y, Gong Y, Xiong G, Zhang C, He S, He Z, Li X, Ci W, Zhou L. Diagnostic and prognostic biomarkers of common urological cancers based on aberrant DNA methylation. Epigenomics 2018; 10:1189-1199. [PMID: 30182734 DOI: 10.2217/epi-2018-0017] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
AIM We intended to construct DNA methylation-based models for the diagnosis and prognosis of three common urological cancers including prostate adenocarcinoma, renal clear cell carcinoma and bladder urothelial carcinoma. MATERIALS & METHODS Total 450K methylation array data from the cancer genome atlas and gene expression omnibus datasets were downloaded. Moderated t-statistics and least absolute shrinkage and selection operator method were used to build diagnosis and prognosis models. RESULTS Our diagnostic panels including 128 CpG sites had high sensitivity and accuracy in distinguishing samples and could identify lymphatic metastases in prostate adenocarcinoma patients. The prognostic models with 19 CpG sites for renal clear cell carcinoma and 21 CpG sites for bladder urothelial carcinoma were able to distinguish high- and low-risk patients and improve the predictive ability of the tumor node metastasis staging system. CONCLUSION DNA methylation may afford reliable biomarkers in the diagnosis and prognosis of common urological cancers.
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Affiliation(s)
- Ding Peng
- Department of Urology, Peking University First Hospital, Beijing, PR China.,Key Laboratory of Genomics & Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, PR China.,Institute of Urology, Peking University, Beijing, PR China.,National Urological Cancer Center, Beijing, PR China.,Urogenital Diseases (Male) Molecular Diagnosis & Treatment Centre, Peking University, Beijing, PR China
| | - Guangzhe Ge
- Key Laboratory of Genomics & Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, PR China.,University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Zhengzheng Xu
- Key Laboratory of Genomics & Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, PR China.,University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Qin Ma
- Key Laboratory of Genomics & Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yue Shi
- Key Laboratory of Genomics & Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yuanyuan Zhou
- Key Laboratory of Genomics & Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yanqing Gong
- Department of Urology, Peking University First Hospital, Beijing, PR China.,Institute of Urology, Peking University, Beijing, PR China.,National Urological Cancer Center, Beijing, PR China.,Urogenital Diseases (Male) Molecular Diagnosis & Treatment Centre, Peking University, Beijing, PR China
| | - Gengyan Xiong
- Department of Urology, Peking University First Hospital, Beijing, PR China.,Institute of Urology, Peking University, Beijing, PR China.,National Urological Cancer Center, Beijing, PR China.,Urogenital Diseases (Male) Molecular Diagnosis & Treatment Centre, Peking University, Beijing, PR China
| | - Cuijian Zhang
- Department of Urology, Peking University First Hospital, Beijing, PR China.,Institute of Urology, Peking University, Beijing, PR China.,National Urological Cancer Center, Beijing, PR China.,Urogenital Diseases (Male) Molecular Diagnosis & Treatment Centre, Peking University, Beijing, PR China
| | - Shiming He
- Department of Urology, Peking University First Hospital, Beijing, PR China.,Institute of Urology, Peking University, Beijing, PR China.,National Urological Cancer Center, Beijing, PR China.,Urogenital Diseases (Male) Molecular Diagnosis & Treatment Centre, Peking University, Beijing, PR China
| | - Zhisong He
- Department of Urology, Peking University First Hospital, Beijing, PR China.,Institute of Urology, Peking University, Beijing, PR China.,National Urological Cancer Center, Beijing, PR China.,Urogenital Diseases (Male) Molecular Diagnosis & Treatment Centre, Peking University, Beijing, PR China
| | - Xuesong Li
- Department of Urology, Peking University First Hospital, Beijing, PR China.,Institute of Urology, Peking University, Beijing, PR China.,National Urological Cancer Center, Beijing, PR China.,Urogenital Diseases (Male) Molecular Diagnosis & Treatment Centre, Peking University, Beijing, PR China
| | - Weimin Ci
- Key Laboratory of Genomics & Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, PR China.,University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Liqun Zhou
- Department of Urology, Peking University First Hospital, Beijing, PR China.,Institute of Urology, Peking University, Beijing, PR China.,National Urological Cancer Center, Beijing, PR China.,Urogenital Diseases (Male) Molecular Diagnosis & Treatment Centre, Peking University, Beijing, PR China
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30
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Pan CC. The value of molecular markers in classification and prediction of progression in non-muscle-invasive bladder cancer. Transl Androl Urol 2018; 7:736-739. [PMID: 30211064 PMCID: PMC6127537 DOI: 10.21037/tau.2018.07.11] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Chin-Chen Pan
- Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
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31
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Sun X, Wang M, Zhang F, Kong X. An integrated analysis of genome-wide DNA methylation and gene expression data in hepatocellular carcinoma. FEBS Open Bio 2018; 8:1093-1103. [PMID: 29988590 PMCID: PMC6026698 DOI: 10.1002/2211-5463.12433] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 01/11/2018] [Accepted: 04/10/2018] [Indexed: 12/13/2022] Open
Abstract
Despite progress in the treatment of hepatocellular carcinoma (HCC), 5-year survival rates remain low. Thus, a more comprehensive approach to explore the mechanism of HCC is needed to provide new leads for targeted therapy. We performed an integrated analysis to discover the relationship between DNA methylation and gene expression in hepatocellular carcinoma (HCC). DNA methylation and gene expression data for HCC were downloaded from The Cancer Genome Atlas (TCGA) database, and differential analysis was performed. Correlation analysis between DNA methylation and gene expression data was then performed in R language. Finally, we selected several crucial genes and evaluated their potential use as diagnostic biomarkers for HCC. In total, 1135 differentially DNA-methylated CpG sites (DMCs), 377 differentially methylated regions (DMRs), and 1194 differentially expressed genes (DEGs) were identified in HCC. Among the DEGs, 14 genes (ALX3, B4GALNT1,CTHRC1,DLX5,EMX1,IRX3,OTX1,SIX2,TLX1,VASH2,ZIC2,ZIC4,ZIC5, and ZNF695) exhibited changes in DNA methylation in terms of CpG sites or CpG island (CGI) level, of which TLX1 and ZIC4 had the most DMCs (12 and 13, respectively). Further analysis of CTHRC1,ZIC4,SIX2,VASH2,IL17D,TLX1,OTX1, and LART, examining alterations in both DNA methylation and gene expression level in HCC, showed their potential diagnostic value for HCC was better at the gene expression level than that the DNA methylation level. The DNA methylation status of CTHRC1,VASH2, and IL7D was significantly associated with HCC overall survival (P-value <0.05). This systemic analysis identified a group of novel gene signatures (CTHRC1,ZIC4, and OTX1) that may be regulated by DNA hypermethylation, which may be closely associated with HCC.
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32
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Han W, Zhang C, Gao XJ, Wang HB, Chen F, Cao F, Hu YW, Ma J, Gu X, Ding HZ. Clinicopathologic and Prognostic Significance of the Zinc Finger of the Cerebellum Family in Invasive Breast Cancer. J Breast Cancer 2018; 21:51-61. [PMID: 29628984 PMCID: PMC5880966 DOI: 10.4048/jbc.2018.21.1.51] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 03/07/2018] [Indexed: 01/24/2023] Open
Abstract
Purpose Five members of the zinc finger of the cerebellum (ZIC) family-ZIC1, ZIC2, ZIC3, ZIC4, and ZIC5-have been shown to be involved in various carcinomas. Here, we aimed to explore the clinicopathologic and prognostic roles of ZIC family members in invasive breast cancer patients using immunohistochemical analysis, western blotting analysis, and real-time quantitative polymerase chain reaction (RT-qPCR). Methods A total of 241 female invasive breast cancer patients who underwent radical mastectomy between 2009 and 2011 were enrolled. ZIC proteins in 241 pairs of breast tumors and corresponding normal tissues were investigated using immunohistochemistry and the clinicopathologic roles of proteins were analyzed using Pearson's chi-square test. Kaplan-Meier curves and Cox regression analysis were also used to analyze the prognostic value of the ZIC proteins. In addition, 12 pairs of fresh-frozen breast tumors and matched normal tissues were used in the western blotting analysis and RT-qPCR. Results Only ZIC1 expression in normal tissues was obviously higher than that in tumors (p<0.001). On multivariate analysis, ZIC1 expression (in overall survival analysis: hazard ratio [HR], 0.405, 95% confidence interval [CI], 0.233-0.702, p=0.001; in disease-free survival analysis: HR, 0.395, 95% CI, 0.234-0.669, p=0.001) was identified as a prognostic indicator of invasive breast cancer. Conclusion ZIC1, but not the other proteins, was obviously decreased in breast tumors and associated with clinicopathologic factors. Thus, ZIC1 might be a novel indicator to predict the overall and disease-free survival of invasive breast cancer patients.
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Affiliation(s)
- Wei Han
- Department of General Surgery, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, China
| | - Cong Zhang
- Department of Pharmacy, Kunshan Hospital of Traditional Chinese Medicine, Kunshan, China
| | - Xiao-Jiao Gao
- Department of Pathology, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, China
| | - Hua-Bing Wang
- Department of General Surgery, Luan First People's Hospital, Luan, China
| | - Fang Chen
- Department of Pathology, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, China
| | - Fang Cao
- Department of General Surgery, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, China
| | - Yong-Wei Hu
- Department of General Surgery, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, China
| | - Jun Ma
- Department of Urinary Surgery, Kunshan Hospital of Traditional Chinese Medicine, Kunshan, China
| | - Xing Gu
- Department of Gynecology, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, China
| | - Hou-Zhong Ding
- Department of General Surgery, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, China
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Sanford T, Meng MV, Railkar R, Agarwal PK, Porten SP. Integrative analysis of the epigenetic basis of muscle-invasive urothelial carcinoma. Clin Epigenetics 2018; 10:19. [PMID: 29456764 PMCID: PMC5809922 DOI: 10.1186/s13148-018-0451-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 01/30/2018] [Indexed: 12/20/2022] Open
Abstract
Background Elucidation of epigenetic alterations in bladder cancer will lead to further understanding of the biology of the disease and hopefully improved therapies. Our aim was to perform an integrative epigenetic analysis of invasive urothelial carcinoma of the bladder to identify the epigenetic abnormalities involved in the development and progression of this cancer. Methods Pre-processed methylation data and RNA-seq data were downloaded from The Cancer Genome Atlas (TCGA) and processed using the R package TCGA-Assembler. An R package MethylMix was used to perform an analysis incorporating both methylation and gene expression data on all samples, as well as a subset analysis comparing patients surviving less than 2 years and patients surviving more than 2 years. Genes associated with poor prognosis were individually queried. Pathway analysis was performed on statistically significant genes identified by MethylMix criteria using ConsensusPathDB. Validation was performed using flow cytometry on bladder cancer cell lines. Results A total of 408 patients met all inclusion criteria. There were a total of 240 genes differentially methylated by MethylMix criteria. Review of individual genes specific to poor-prognosis patients revealed the majority to be candidate tumor suppressors in other cancer types. Pathway analysis showed increase in methylation of genes involved in antioxidant pathways including glutathione and NRF2. Genes involved in estrogen metabolism were also hypermethylated while genes involved in the EGFR pathway were found to be hypomethylated. EGFR expression was confirmed to be elevated in six bladder cancer cell lines. Conclusions In patients with invasive urothelial carcinoma, we found differential methylation in patients with better and worse prognosis after cystectomy. Differentially methylated genes are involved in many relevant oncologic pathways, including EGFR and antioxidant pathways, that may be a target for therapy or chemoprevention.
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Affiliation(s)
- Thomas Sanford
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, Building 10—Hatfield CRC, Room 2-5952, Bethesda, MD 20892-1210 USA
| | - Maxwell V. Meng
- Department of Urology, University of California, Mail code 1695, 550 16th Street, 6th Floor, San Francisco, CA 94143 USA
| | - Reema Railkar
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, Building 10—Hatfield CRC, Room 2-5952, Bethesda, MD 20892-1210 USA
| | - Piyush K. Agarwal
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, Building 10—Hatfield CRC, Room 2-5952, Bethesda, MD 20892-1210 USA
| | - Sima P. Porten
- Department of Urology, University of California, Mail code 1695, 550 16th Street, 6th Floor, San Francisco, CA 94143 USA
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van Kessel KE, van der Keur KA, Dyrskjøt L, Algaba F, Welvaart NY, Beukers W, Segersten U, Keck B, Maurer T, Simic T, Horstmann M, Grimm MO, Hermann GG, Mogensen K, Hartmann A, Harving N, Petersen AC, Jensen JB, Junker K, Boormans JL, Real FX, Malats N, Malmström PU, Ørntoft TF, Zwarthoff EC. Molecular Markers Increase Precision of the European Association of Urology Non–Muscle-Invasive Bladder Cancer Progression Risk Groups. Clin Cancer Res 2018; 24:1586-1593. [DOI: 10.1158/1078-0432.ccr-17-2719] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 11/14/2017] [Accepted: 01/08/2018] [Indexed: 11/16/2022]
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35
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Hoogland AM, Böttcher R, Verhoef E, Jenster G, van Leenders GJLH. Gene-expression analysis of gleason grade 3 tumor glands embedded in low- and high-risk prostate cancer. Oncotarget 2018; 7:37846-37856. [PMID: 27191985 PMCID: PMC5122354 DOI: 10.18632/oncotarget.9344] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 04/25/2016] [Indexed: 12/02/2022] Open
Abstract
The Gleason score (GS) of prostate cancer on diagnostic biopsies is an important parameter for therapeutic decision-making. Biopsy GS under-estimates the actual GS at radical prostatectomy in a significant number of patients due to sampling artifact. The aim of this study was to identify markers that are differentially expressed in Gleason grade 3 (GG3) tumor glands embedded in GS 4 + 3 = 7 and GS 3 + 3 = 6 prostate cancer using laser capture microdissection and RNA sequencing. GG3 tumor glands embedded in nine GS 3 + 3 = 6 and nine GS 4 + 3 = 7 prostate cancers were isolated by laser capture microdissection of frozen radical prostatectomy specimens. After RNA amplification and RNA sequencing, differentially expressed genes in both GG3 components were identified by a 2log fold change > 1.0 and p-value < 0.05. We applied immunohistochemistry on a tissue micro-array representing 481 radical prostatectomy samples for further validation on protein level. A total of 501 genes were up-regulated and 421 down-regulated in GG3 glands embedded in GS 4 + 3 = 7 as compared to GS 3 + 3 = 6 prostate cancer. We selected HELLS, ZIC2 and ZIC5 genes for further validation. ZIC5 mRNA was up-regulated 17 fold (p = 8.4E–07), ZIC2 8 fold (p = 1.3E–05) and HELLS 2 fold (p = 0.006) in GG3 glands derived from GS 4 + 3 = 7. HELLS expression of ≥ 1% occurred in 10% GS < 7, 17% GS 7 and 43% GS >7 prostate cancer (p < 0.001). Using a cut-off of ≥ 1%, protein expression of ZIC5 was present in 28% GS < 7, 43% GS 7 and 57% GS > 7 cancer (p < 0.001). ZIC2 was neither associated with GS nor outcome in our validation set. HELLS was independently predictive for biochemical-recurrence after radical prostatectomy (HR 2.3; CI 1.5–3.6; p < 0.01). In conclusion, HELLS and ZIC5 might be promising candidate markers for selection of biopsy GS 6 prostate cancer being at risk for up-grading at prostatectomy.
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Affiliation(s)
- A Marije Hoogland
- Departments of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - René Böttcher
- Departments of Urology, Erasmus Medical Center, Rotterdam, The Netherlands.,Department of Bioinformatics, University of Applied Sciences Wildau, Wildau, Germany
| | - Esther Verhoef
- Departments of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Guido Jenster
- Departments of Urology, Erasmus Medical Center, Rotterdam, The Netherlands
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Houtmeyers R, Souopgui J, Tejpar S. Deregulation of ZIC Family Members in Oncogenesis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1046:329-338. [DOI: 10.1007/978-981-10-7311-3_16] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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37
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Li J, Zhou C, Ni S, Wang S, Ni C, Yang P, Ye M. Methylated claudin-11 associated with metastasis and poor survival of colorectal cancer. Oncotarget 2017; 8:96249-96262. [PMID: 29221203 PMCID: PMC5707097 DOI: 10.18632/oncotarget.21997] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 08/17/2017] [Indexed: 12/22/2022] Open
Abstract
As one of crucial epigenetic modification, DNA methylation plays an important role during the carcinogenesis of colorectal cancer (CRC). In the current study, we used a human genome methylation array to detect the aberrant methylation genes in CRC. We further identified the hypermethylation of claudin-11 (CLDN11) and proved inverse correlation between CLDN11 methylation and its expression in CRC. In vitro experiments showed debased migration ability of colonic cancer cells in accompany with the converted methylation of CLDN11 after colonic cancer cells treated with demethylation agent, 5-aza-2'-deoxycytidine. Besides, our results also represented that hypermethylation of CLDN11 was associated with increased metastatic potential of CRC and with low progression free survival (PFS) of CRC. In conclusion, our findings supported that the hypermethylated CLDN11 is associated with metastasis of CRC and prognosis of poor survival of CRC.
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Affiliation(s)
- Jinyun Li
- Department of Oncology and Hematology, Affiliated Hospital, Medical School of Ningbo University, Ningbo, Zhejiang 315000, China
| | - Chongchang Zhou
- Department of Otorhinolaryngology Head and Neck Surgery, Lihuili Hospital of Ningbo University, Ningbo 315040, Zhejiang, China
| | - Shumin Ni
- Department of Oncology and Hematology, Affiliated Hospital, Medical School of Ningbo University, Ningbo, Zhejiang 315000, China
| | - Shaomin Wang
- Department of Oncology and Hematology, Affiliated Hospital, Medical School of Ningbo University, Ningbo, Zhejiang 315000, China
| | - Chao Ni
- Medical School, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Ping Yang
- Medical School, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Meng Ye
- Department of Oncology and Hematology, Affiliated Hospital, Medical School of Ningbo University, Ningbo, Zhejiang 315000, China
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38
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Casadevall D, Kilian AY, Bellmunt J. The prognostic role of epigenetic dysregulation in bladder cancer: A systematic review. Cancer Treat Rev 2017; 61:82-93. [PMID: 29121502 DOI: 10.1016/j.ctrv.2017.10.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 10/14/2017] [Accepted: 10/16/2017] [Indexed: 02/07/2023]
Abstract
BACKGROUND Despite adequate treatment and follow-up, around one fifth of patients with localized bladder cancer will present with disease progression. Adequate prognostic biomarkers are lacking to define patients who are at risk. Mutations in chromatin remodeling genes are more frequently found in bladder cancer than in any other solid tumor. However, the prognostic relevance of epigenetic dysregulation has not been established and may offer an opportunity for biomarker discovery. METHODS Looking for prognostic epigenetic factors, we performed a comprehensive PubMed search using keywords such as "bladder cancer", "chromatin remodeling", "gene methylation" and "epigenetics". We only included studies reporting on the association of epigenetic markers with prognostic outcomes such as recurrence, progression or survival. RESULTS Of 1113 results, 87 studies met the inclusion criteria, which represented a total of 85 epigenetic markers with potential prognostic relevance. No prospective studies were identified. Seventy-three percent (64/87) of the studies involved mixed cohorts of muscle invasive and non-muscle invasive bladder cancer. Promoter methylation of genes with putative prognostic value affected cellular processes such as cell cycle, apoptosis, cell-adhesion or migration, as well as critical pathways such as MAP-kinase or Wnt. Alteration of chromatin regulatory elements suggest a prognostic relevance alterations leading to a predominantly silenced chromatin state. CONCLUSIONS The prognostic impact of epigenetic alterations in bladder cancer is still unclear. Prospective evaluation of methylation marks and chromatin remodeling gene alterations using consistent methods and criteria is warranted.
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Affiliation(s)
- David Casadevall
- Cancer Research Program, PSMAR-IMIM (Hospital del Mar Medical Research Institute), Carrer Dr. Aiguader 88, 08003 Barcelona, Spain.
| | | | - Joaquim Bellmunt
- Cancer Research Program, PSMAR-IMIM (Hospital del Mar Medical Research Institute), Carrer Dr. Aiguader 88, 08003 Barcelona, Spain; Dana-Farber Cancer Institute, 450 Brookline Ave, DANA 1230, Boston, MA 02215, USA.
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Angulo JC, López JI, Ropero S. DNA Methylation and Urological Cancer, a Step Towards Personalized Medicine: Current and Future Prospects. Mol Diagn Ther 2017; 20:531-549. [PMID: 27501813 DOI: 10.1007/s40291-016-0231-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Urologic malignancies are some of the commonest tumors often curable when diagnosed at early stage. However, accurate diagnostic markers and faithful predictors of prognosis are needed to avoid over-diagnosis leading to overtreatment. Many promising exploratory studies have identified epigenetic markers in urinary malignancies based on DNA methylation, histone modification and non-coding ribonucleic acid (ncRNA) expression that epigenetically regulate gene expression. We review and discuss the current state of development and the future potential of epigenetic biomarkers for more accurate and less invasive detection of urological cancer, tumor recurrence and progression of disease serving to establish diagnosis and monitor treatment efficacies. The specific clinical implications of such methylation tests on therapeutic decisions and patient outcome and current limitations are also discussed.
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Affiliation(s)
- Javier C Angulo
- Servicio de Urología, Hospital Universitario de Getafe, Departamento Clínico, Facultad de Ciencias Biomédicas, Universidad Europea de Madrid, Laureate Universities, Hospital Universitario de Getafe, Carretera de Toledo Km 12.5, Getafe, 28905, Madrid, Spain.
| | - Jose I López
- Servicio de Anatomía Patológica, Hospital Universitario de Cruces, Instituto BioCruces,Universidad del País Vasco (UPV-EHU), Bilbao, Spain
| | - Santiago Ropero
- Departamento de Biología de Sistemas, Unidad Docente de Bioquímica y Biología Molecular, Universidad de Alcalá, Alcalá de Henares, Madrid, Spain
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40
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Rani L, Mathur N, Gupta R, Gogia A, Kaur G, Dhanjal JK, Sundar D, Kumar L, Sharma A. Genome-wide DNA methylation profiling integrated with gene expression profiling identifies PAX9 as a novel prognostic marker in chronic lymphocytic leukemia. Clin Epigenetics 2017; 9:57. [PMID: 28572861 PMCID: PMC5450117 DOI: 10.1186/s13148-017-0356-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 05/18/2017] [Indexed: 12/22/2022] Open
Abstract
Background In chronic lymphocytic leukemia (CLL), epigenomic and genomic studies have expanded the existing knowledge about the disease biology and led to the identification of potential biomarkers relevant for implementation of personalized medicine. In this study, an attempt has been made to examine and integrate the global DNA methylation changes with gene expression profile and their impact on clinical outcome in early stage CLL patients. Results The integration of DNA methylation profile (n = 14) with the gene expression profile (n = 21) revealed 142 genes as hypermethylated-downregulated and; 62 genes as hypomethylated-upregulated in early stage CLL patients compared to CD19+ B-cells from healthy individuals. The mRNA expression levels of 17 genes identified to be differentially methylated and/or differentially expressed was further examined in early stage CLL patients (n = 93) by quantitative real time PCR (RQ-PCR). Significant differences were observed in the mRNA expression of MEIS1, PMEPA1, SOX7, SPRY1, CDK6, TBX2, and SPRY2 genes in CLL cells as compared to B-cells from healthy individuals. The analysis in the IGHV mutation based categories (Unmutated = 39, Mutated = 54) revealed significantly higher mRNA expression of CRY1 and PAX9 genes in the IGHV unmutated subgroup (p < 0.001). The relative risk of treatment initiation was significantly higher among patients with high expression of CRY1 (RR = 1.91, p = 0.005) or PAX9 (RR = 1.87, p = 0.001). High expression of CRY1 (HR: 3.53, p < 0.001) or PAX9 (HR: 3.14, p < 0.001) gene was significantly associated with shorter time to first treatment. The high expression of PAX9 gene (HR: 3.29, 95% CI 1.172–9.272, p = 0.016) was also predictive of shorter overall survival in CLL. Conclusions The DNA methylation changes associated with mRNA expression of CRY1 and PAX9 genes allow risk stratification of early stage CLL patients. This comprehensive analysis supports the concept that the epigenetic changes along with the altered expression of genes have the potential to predict clinical outcome in early stage CLL patients. Electronic supplementary material The online version of this article (doi:10.1186/s13148-017-0356-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lata Rani
- Laboratory Oncology Unit, Dr. B.R.A.IRCH, All India Institute of Medical Sciences (AIIMS), Ansari Nagar, New Delhi, 110029 India
| | - Nitin Mathur
- Laboratory Oncology Unit, Dr. B.R.A.IRCH, All India Institute of Medical Sciences (AIIMS), Ansari Nagar, New Delhi, 110029 India
| | - Ritu Gupta
- Laboratory Oncology Unit, Dr. B.R.A.IRCH, All India Institute of Medical Sciences (AIIMS), Ansari Nagar, New Delhi, 110029 India
| | - Ajay Gogia
- Department of Medical Oncology, Dr. B.R.A.IRCH, All India Institute of Medical Sciences (AIIMS), Ansari Nagar, New Delhi, 110029 India
| | - Gurvinder Kaur
- Laboratory Oncology Unit, Dr. B.R.A.IRCH, All India Institute of Medical Sciences (AIIMS), Ansari Nagar, New Delhi, 110029 India
| | - Jaspreet Kaur Dhanjal
- Department of Biochemical Engineering and Biotechnology, DBT-AIST International Laboratory of Advanced Biomedicine (DAILAB), Indian Institute of Technology (IIT) Delhi, Hauz Khas, New Delhi, 110016 India
| | - Durai Sundar
- Department of Biochemical Engineering and Biotechnology, DBT-AIST International Laboratory of Advanced Biomedicine (DAILAB), Indian Institute of Technology (IIT) Delhi, Hauz Khas, New Delhi, 110016 India
| | - Lalit Kumar
- Department of Medical Oncology, Dr. B.R.A.IRCH, All India Institute of Medical Sciences (AIIMS), Ansari Nagar, New Delhi, 110029 India
| | - Atul Sharma
- Department of Medical Oncology, Dr. B.R.A.IRCH, All India Institute of Medical Sciences (AIIMS), Ansari Nagar, New Delhi, 110029 India
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41
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Pietrusiński M, Kȩpczyński Ƚ, Jȩdrzejczyk A, Borkowska E, Traczyk-Borszyńska M, Constantinou M, Kaƚużewski B, Borowiec M. Detection of bladder cancer in urine sediments by a hypermethylation panel of selected tumor suppressor genes. Cancer Biomark 2017; 18:47-59. [PMID: 27814275 DOI: 10.3233/cbm-160673] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
BACKGROUND Promoter hypermethylation can be a useful biomarker for early detection and prognosis of bladder cancer, monitoring response to treatment and complement classical diagnostic procedures. OBJECTIVE The molecular test was performed on DNA from bladder cancer cells in voided urine samples, tumor tissue DNA and normal control DNAs. We aimed to assess the diagnostic potential of epigenetic changes in urine DNA from bladder cancer cases at various clinico-pathological stages of the disease. METHODS The methylation status of 5 genes (p14ARF, p16INK4A, RASSF1A, DAPK, APC) in 113 tumor samples paired with voided urine specimens was analyzed by MSP. We compared the results of methylation analysis with UroVysion test. RESULTS The methylation profile in tumor/urine DNA was significantly correlated (p ≤ 0,05) with tumor grade in p14ARF, RASSF1a, APC/p14ARF, APC genes, respectively and with stage in p14ARF, RASSF1a/p14ARF genes, respectively. The results of UroVysion test were in correlation with hypermethylation both in tumor and urine DNA in p14ARF, RASSF1a and APC genes (p = 0,008; 0,02 and 0,04, respectively). CONCLUSIONS Promoter hypermethylation of tumor suppressor genes is a frequent mechanism in bladder cancer. We found promoter hypermethylation in all grades and stages of all cases examined. Methylation profile of selected suppressor genes may be a potential useful biomarker and enhance early detection of bladder cancer using a noninvasive urine test.
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Affiliation(s)
| | - Ƚukasz Kȩpczyński
- Department of Clinical Genetics, Medical University of Łódź, Łódź, Poland
| | - Adam Jȩdrzejczyk
- Department of Urology, John Paul II Regional Hospital Beƚchatów, Beƚchatów, Poland
| | - Edyta Borkowska
- Department of Clinical Genetics, Medical University of Łódź, Łódź, Poland
| | | | - Maria Constantinou
- Department of Clinical Genetics, Medical University of Łódź, Łódź, Poland
| | - Bogdan Kaƚużewski
- Department of Clinical Genetics, Medical University of Łódź, Łódź, Poland
| | - Maciej Borowiec
- Department of Clinical Genetics, Medical University of Łódź, Łódź, Poland
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Willmer T, Cooper A, Peres J, Omar R, Prince S. The T-Box transcription factor 3 in development and cancer. Biosci Trends 2017; 11:254-266. [DOI: 10.5582/bst.2017.01043] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Tarryn Willmer
- Department of Human Biology, Faculty of Health Sciences, Anzio Road, University of Cape Town
| | - Aretha Cooper
- Department of Human Biology, Faculty of Health Sciences, Anzio Road, University of Cape Town
| | - Jade Peres
- Department of Human Biology, Faculty of Health Sciences, Anzio Road, University of Cape Town
| | - Rehana Omar
- Department of Human Biology, Faculty of Health Sciences, Anzio Road, University of Cape Town
| | - Sharon Prince
- Department of Human Biology, Faculty of Health Sciences, Anzio Road, University of Cape Town
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43
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Abstract
Genomic and transcriptional studies have identified discrete molecular subtypes of bladder cancer. These observations could be the starting point to identify new treatments. Several members of the forkhead box (FOX) superfamily of transcription factors have been found to be differentially expressed in the different bladder cancer subtypes. In addition, the FOXA protein family are key regulators of embryonic bladder development and patterning. Both experimental and clinical data support a role for FOXA1 and FOXA2 in urothelial carcinoma. FOXA1 is expressed in embryonic and adult urothelium and its expression is altered in urothelial carcinomas and across disparate molecular bladder cancer subtypes. FOXA2 is normally absent from the adult urothelium, but developmental studies identified FOXA2 as a marker of a transient urothelial progenitor cell population during bladder development. Studies also implicate FOXA2 in bladder cancer and several other FOX proteins might be involved in development and/or progression of this disease; for example, FOXA1 and FOXO3A have been associated with clinical patient outcomes. Future studies should investigate to what extent and by which mechanisms FOX proteins might be directly involved in bladder cancer pathogenesis and treatment responses.
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44
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Farkas SA, Sorbe BG, Nilsson TK. Epigenetic changes as prognostic predictors in endometrial carcinomas. Epigenetics 2016; 12:19-26. [PMID: 27874289 DOI: 10.1080/15592294.2016.1252891] [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] [Indexed: 11/12/2022] Open
Abstract
Endometrial carcinoma is one of the most frequent gynecological malignancies of the female. The diagnostic and prognostic markers for the high-risk subgroups with unfavorable prognosis are under intense debate worldwide, and, therefore, the aim of this study was to identify new potential DNA methylation markers for the high-risk groups. We used the Illumina Infinium HumanMethylation450 BeadChip to analyze the DNA methylation pattern and investigated its association with clinicopathological features important for defining the high-risk (FIGO-grade 3) and low-risk (FIGO-grade 1) groups of patients with endometrial cancer (n = 31 and n = 39, respectively). We identified specific DNA methylation signature in high-risk endometrial tumors, and potential molecular biomarker genes (TBX2, CHST11, and NID2) associated with unfavorable clinical predictive and prognostic factors.
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Affiliation(s)
- Sanja A Farkas
- a Department of Laboratory Medicine , Örebro University , Örebro , Sweden
| | - Bengt G Sorbe
- b Department of Oncology , University Hospital and Örebro University , Örebro , Sweden
| | - Torbjörn K Nilsson
- c Department of Medical Biosciences/Clinical Chemistry , Umeå University , Umeå , Sweden
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45
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Genetic and Epigenetic Alterations in Bladder Cancer. Int Neurourol J 2016; 20:S84-94. [PMID: 27915480 PMCID: PMC5169086 DOI: 10.5213/inj.1632752.376] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 10/27/2016] [Indexed: 12/11/2022] Open
Abstract
Bladder cancer is one of the most common cancers worldwide, with a high rate of recurrence and poor outcomes as a result of relapse. Bladder cancer patients require lifelong invasive monitoring and treatment, making bladder cancer one of the most expensive malignancies. Lines of evidence increasingly point to distinct genetic and epigenetic alteration patterns in bladder cancer, even between the different stages and grades of disease. In addition, genetic and epigenetic alterations have been demonstrated to play important roles during bladder tumorigenesis. This review will focus on bladder cancer-associated genomic and epigenomic alterations, which are common in bladder cancer and provide potential diagnostic markers and therapeutic targets for bladder cancer treatment.
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46
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van Kessel KEM, Beukers W, Lurkin I, Ziel-van der Made A, van der Keur KA, Boormans JL, Dyrskjøt L, Márquez M, Ørntoft TF, Real FX, Segersten U, Malats N, Malmström PU, Van Criekinge W, Zwarthoff EC. Validation of a DNA Methylation-Mutation Urine Assay to Select Patients with Hematuria for Cystoscopy. J Urol 2016; 197:590-595. [PMID: 27746284 DOI: 10.1016/j.juro.2016.09.118] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2016] [Indexed: 10/20/2022]
Abstract
PURPOSE Only 3% to 28% of patients referred to the urology clinic for hematuria are diagnosed with bladder cancer. Cystoscopy leads to high diagnostic costs and a high patient burden. Therefore, to improve the selection of patients for cystoscopy and reduce costs and over testing we aimed to validate a recently developed diagnostic urine assay. MATERIALS AND METHODS Included in study were 200 patients from a total of 3 European countries who underwent cystoscopy for hematuria, including 97 with bladder cancer and 103 with nonmalignant findings. Voided urine samples were collected prior to cystoscopy. DNA was extracted and analyzed for mutations in FGFR3, TERT and HRAS, and methylation of OTX1, ONECUT2 and TWIST1. Logistic regression was used to analyze the association between predictor variables and bladder cancer. RESULTS Combining the methylation and mutation markers with age led to an AUC of 0.96 (95% CI 0.92-0.99) with 93% sensitivity and 86% specificity, and an optimism corrected AUC of 0.95. The AUC was higher for T1 or greater tumors compared to Ta tumors (0.99 vs 0.93). The AUC was also higher for high grade tumors compared to low grade tumors (1.00 vs 0.93). Overall negative predictive value was 99% based on the 5% to 10% prevalence of bladder cancer in patients with hematuria. This would lead to a 77% reduction in diagnostic cystoscopy. CONCLUSIONS Analyzing hematuria patients for the risk of bladder cancer using novel molecular markers may lead to a reduction in diagnostic cystoscopy. Combining methylation analysis (OTX1, ONECUT2 and TWIST1) with mutation analysis (FGFR3, TERT and HRAS) and patient age resulted in a validated accurate prediction model.
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Affiliation(s)
- Kim E M van Kessel
- Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Willemien Beukers
- Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Irene Lurkin
- Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | | | - Joost L Boormans
- Department of Urology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Mirari Márquez
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre, Madrid
| | - Torben F Ørntoft
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Francisco X Real
- Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre, Madrid; Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Ulrika Segersten
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Núria Malats
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre, Madrid
| | - Per-Uno Malmström
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Wim Van Criekinge
- MDxHealth, Inc., Irvine, California; Laboratory of Bioinformatics and Computational Genomics, Ghent University, Belgium
| | - Ellen C Zwarthoff
- Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands.
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47
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Abstract
DNA methylation alterations are common in urothelial carcinoma, a prevalent cancer worldwide caused predominantly by chemical carcinogens. Recent studies have proposed sets of hypermethylated genes as promising diagnostic and prognostic biomarkers from urine or tissue samples, which require validation. Other studies have revealed intriguing links between specific carcinogens and DNA methylation alterations in cancer tissues or blood that might clarify carcinogenesis mechanisms and aid prevention. Like DNA methylation alterations, mutations in chromatin regulators are frequent, underlining the importance of epigenetic changes. However, the relations between the two changes and their functions in urothelial carcinogenesis remain unclear. Transcription factor genes with altered methylation deserve particular interest. Elucidating the functional impact of methylation changes is a prerequisite for their therapeutic targeting.
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Affiliation(s)
- Wolfgang A Schulz
- Department of Urology, Medical Faculty, Heinrich Heine University Duesseldorf, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - Wolfgang Goering
- Department of Pathology, Medical Faculty, Heinrich Heine University Duesseldorf, Germany
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48
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Paluszczak J, Wiśniewska D, Kostrzewska-Poczekaj M, Kiwerska K, Grénman R, Mielcarek-Kuchta D, Jarmuż-Szymczak M. Prognostic significance of the methylation of Wnt pathway antagonists-CXXC4, DACT2, and the inhibitors of sonic hedgehog signaling-ZIC1, ZIC4, and HHIP in head and neck squamous cell carcinomas. Clin Oral Investig 2016; 21:1777-1788. [PMID: 27553089 PMCID: PMC5442212 DOI: 10.1007/s00784-016-1946-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 08/16/2016] [Indexed: 12/18/2022]
Abstract
Objectives Aberrations in Wnt and Shh signaling pathways are related to the pathogenesis of head and neck carcinomas, and their activation frequently results from epigenetic alterations. This study aimed to assess the frequency of methylation of negative regulators of Wnt signaling: CXXC4, DACT2, HDPR1, and FBXW11 and Shh signaling: HHIP, PTCH1, SUFU, ZIC1, and ZIC4 and correlate it with clinicopathological features in this group of patients. Materials and methods Methylation-specific PCR was used to detect gene promoter methylation, and real-time PCR was used to assess gene expression level. Results The analysis of the occurrence of gene promoter methylation in head and neck carcinoma cell lines indicated that CXXC4, DACT2, HHIP, ZIC1, and ZIC4 are methylated in these tumors. These genes were further analyzed in tumor sections from oral and laryngeal cancer patients. Gene methylation rate was higher in laryngeal tumors. The methylation index in tumor samples correlated with the overall survival in a subgroup of oral cancer patients who died of the disease. Moreover, ZIC4 methylation correlated with lymph node involvement in oral cancer patients. Conclusions Our findings corroborate that the activation of Wnt signaling in head and neck squamous cell carcinoma (HNSCC) is related to epigenetic silencing of its negative regulators. Moreover, the results indicate that the same mechanism of activation may operate in the case of Shh signaling. Clinical relevance The methylation of ZIC4 may be considered a new prognostic marker in oral cavity and oropharyngeal tumors. Further investigations should determine the diagnostic significance of methylation of ZIC4, HHIP, and DACT2 in head and neck carcinomas.
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Affiliation(s)
- Jarosław Paluszczak
- Department of Pharmaceutical Biochemistry, Poznan University of Medical Sciences, ul. Święcickiego 4, 60-781, Poznań, Poland.
| | - Dorota Wiśniewska
- Department of Pharmaceutical Biochemistry, Poznan University of Medical Sciences, ul. Święcickiego 4, 60-781, Poznań, Poland
| | | | - Katarzyna Kiwerska
- Department of Cancer Genetics, Institute of Human Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Reidar Grénman
- Department of Otorhinolaryngology, Head and Neck Surgery and Department of Medical Biochemistry, Turku University Central Hospital and Turku University, Turku, Finland
| | - Daniela Mielcarek-Kuchta
- Department of Otolaryngology and Laryngological Oncology, Poznan University of Medical Sciences, Poznań, Poland
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49
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Yeh CM, Chen PC, Hsieh HY, Jou YC, Lin CT, Tsai MH, Huang WY, Wang YT, Lin RI, Chen SS, Tung CL, Wu SF, Chang DC, Shen CH, Hsu CD, Chan MWY. Methylomics analysis identifies ZNF671 as an epigenetically repressed novel tumor suppressor and a potential non-invasive biomarker for the detection of urothelial carcinoma. Oncotarget 2016; 6:29555-72. [PMID: 26320192 PMCID: PMC4745746 DOI: 10.18632/oncotarget.4986] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 07/16/2015] [Indexed: 11/25/2022] Open
Abstract
The molecular mechanism underlying the lethal phenomenon of urothelial carcinoma (UC) tumor recurrence remains unresolved. Here, by methylation microarray, we identified promoter methylation of the zinc-finger protein gene, ZNF671 in bladder UC tumor tissue samples, a finding that was independently validated by bisulphite pyrosequencing in cell lines and tissue samples. Subsequent assays including treatment with epigenetic depressive agents and in vitro methylation showed ZNF671 methylation to result in its transcriptional repression. ZNF671 re-expression in UC cell lines, via ectopic expression, inhibited tumor growth and invasion, in possible conjunction with downregulation of cancer stem cell markers (c-KIT, NANOG, OCT4). Clinically, high ZNF671 methylation in UC tumor tissues (n=96; 63 bladder, 33 upper urinary tract) associated with tumor grade and poor locoregional disease-free survival. Quantitative MSP analysis in a training (n=97) and test (n=61) sets of voided urine samples from bladder UC patients revealed a sensitivity and specificity of 42%-48% and 89%-92.8%, respectively, for UC cancer detection. Moreover, combining DNA methylation of ZNF671 and 2 other genes (IRF8 and sFRP1) further increased the sensitivity to 96.2%, suggesting a possible three-gene UC biomarker. In summary, ZNF671, an epigenetically silenced novel tumor suppressor, represents a potential predictor for UC relapse and non-invasive biomarker that could assist in UC clinical decision-making.
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Affiliation(s)
- Chia-Ming Yeh
- Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan.,Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan
| | - Pi-Che Chen
- Department of Urology, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi, Taiwan
| | - Hsiao-Yen Hsieh
- Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan.,Department of Medical Research, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi, Taiwan
| | - Yeong-Chin Jou
- Department of Urology, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi, Taiwan
| | - Chang-Te Lin
- Department of Urology, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi, Taiwan
| | - Ming-Hsuan Tsai
- Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan
| | - Wen-Yu Huang
- Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan.,Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan
| | - Yi-Ting Wang
- Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan.,Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan
| | - Ru-Inn Lin
- Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan.,Departments of Radiation Oncology, Buddhist Dalin Tzu Chi General Hospital, Chia Yi, Taiwan
| | - Szu-Shan Chen
- Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan.,Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan
| | - Chun-Liang Tung
- Department of Pathology, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi, Taiwan
| | - Shu-Fen Wu
- Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan.,Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan
| | - D Ching Chang
- Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan.,Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan
| | - Cheng-Huang Shen
- Department of Urology, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi, Taiwan
| | - Cheng-Da Hsu
- Department of Medical Research, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi, Taiwan
| | - Michael W Y Chan
- Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan.,Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan
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50
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Abstract
T-box (Tbx) genes encode an ancient group of transcription factors that play important roles in patterning, specification, proliferation, and differentiation programs in vertebrate organogenesis. This is testified by severe organ malformation syndromes in mice homozygous for engineered null alleles of specific T-box genes and by the large number of human inherited organ-specific diseases that have been linked to mutations in these genes. One of the organ systems that has not been associated with loss of specific T-box gene function in human disease for long is the excretory system. However, this has changed with the finding that mutations in TBX18, a member of a vertebrate-specific subgroup within the Tbx1-subfamily of T-box transcription factor genes, cause congenital anomalies of the kidney and urinary tract, predominantly hydroureter and ureteropelvic junction obstruction. Gene expression analyses, loss-of-function studies, and lineage tracing in the mouse suggest a primary role for this transcription factor in specifying the ureteric mesenchyme in the common anlage of the kidney, the ureter, and the bladder. We review the function of Tbx18 in ureterogenesis and discuss the body of evidence that Tbx18 and other members of the T-box gene family, namely, Tbx1, Tbx2, Tbx3, and Tbx20, play additional roles in development and homeostasis of other components of the excretory system in vertebrates.
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