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Luo J, Xu J, Ou L, Zhou Y, Yun H, Yang Y, Wu X, Wang Y. Role of hypermethylated-lncRNAs in the prognosis of bladder cancer patients. J Int Med Res 2021; 49:3000605211049946. [PMID: 34617815 PMCID: PMC8504649 DOI: 10.1177/03000605211049946] [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] [Indexed: 12/18/2022] Open
Abstract
OBJECTIVE To explore the hypermethylated long non-coding (lnc)RNAs involved in bladder carcinogenesis and prognosis. METHODS Reduced representation bisulfite sequencing and RNA sequencing were performed on five paired tumor and adjacent normal tissue samples from bladder cancer patients. The differentially methylated regions around transcription start sites and differentially expressed genes, including lncRNAs, were analyzed. Correlations between DNA methylation modifications and the expression of lncRNAs were examined. Survival analysis was surveyed on the GEPIA web server. RESULTS We identified 19,560 hypomethylated and 68,781 hypermethylated differentially methylated regions around transcription start sites in bladder cancer tissues. In total, 2321 differentially expressed genes were found in bladder tumors, among which, 367 were upregulated and 1954 were downregulated. There were 141 downregulated genes involving eight lncRNAs that were consistently hypermethylated, while 24 upregulated genes were consistently hypomethylated. Survival analysis demonstrated that hypermethylation of lncRNAs LINC00683 and MSC-AS1 were associated with poor overall survival in bladder cancer patients. CONCLUSION Some lncRNAs are controlled by DNA methylation in bladder cancer and they might be important factors in bladder carcinogenesis. Hypermethylated lncRNAs including LINC00683 and MSC-AS1 have the potential to be prognostic biomarkers for bladder cancer.
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Affiliation(s)
- Junhua Luo
- Department of Urology, 74573Peking University Shenzhen Hospital, Peking University Shenzhen Hospital, Shenzhen, P.R. China
| | - Jinming Xu
- Department of Urology, 74573Peking University Shenzhen Hospital, Peking University Shenzhen Hospital, Shenzhen, P.R. China
| | - Longhua Ou
- Department of Urology, 74573Peking University Shenzhen Hospital, Peking University Shenzhen Hospital, Shenzhen, P.R. China
| | - Yingchen Zhou
- Department of Urology, 74573Peking University Shenzhen Hospital, Peking University Shenzhen Hospital, Shenzhen, P.R. China
| | - Haichao Yun
- Department of Urology, 74573Peking University Shenzhen Hospital, Peking University Shenzhen Hospital, Shenzhen, P.R. China
| | - Yu Yang
- Department of Urology, 74573Peking University Shenzhen Hospital, Peking University Shenzhen Hospital, Shenzhen, P.R. China
| | - Xionghui Wu
- Department of Urology, 74573Peking University Shenzhen Hospital, Peking University Shenzhen Hospital, Shenzhen, P.R. China
| | - Yan Wang
- Department of Urology, 74573Peking University Shenzhen Hospital, Peking University Shenzhen Hospital, Shenzhen, P.R. China
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Current status of development of methylation biomarkers for in vitro diagnostic IVD applications. Clin Epigenetics 2020; 12:100. [PMID: 32631437 PMCID: PMC7336678 DOI: 10.1186/s13148-020-00886-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 06/17/2020] [Indexed: 02/06/2023] Open
Abstract
A significant volume of research clearly shows that disease-related methylation changes can be used as biomarkers at all stages of clinical disease management, including risk assessment and predisposition screening through early diagnostics to personalization of patient care and monitoring of the relapse and chronic disease. Thus disease-related methylation changes are an attractive source of the biomarkers that can have significant impact on precision medicine. However, the translation of the research findings in methylation biomarkers field to clinical practice is at the very least not satisfactory. That is mainly because the evidence generated in research studies indicating the utility of the disease-related methylation change to predict clinical outcome is in majority of the cases not sufficient to postulate the diagnostic use of the biomarker. The research studies need to be followed by well-designed and systematic investigations of clinical utility of the biomarker that produce data of sufficient quality to meet regulatory approval for the test to be used to make clinically valid decision. In this review, we describe methylation-based IVD tests currently approved for IVD use or at the advanced stages of the development for the diagnostic use. For each of those tests, we analyze the technologies that the test utilizes for methylation detection as well as describe the types of the clinical studies that were performed to show clinical validity of the test and warrant regulatory approval. The examples reviewed here should help with planning of clinical investigations and delivery of the clinical evidence required for the regulatory approval of potential methylation biomarker based IVD tests.
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Zhang S, Feng XL, Shi L, Gong CJ, He ZJ, Wu HJ, Ling TY. Genome-wide analysis of DNA methylation in tongue squamous cell carcinoma. Oncol Rep 2013; 29:1819-26. [PMID: 23446731 DOI: 10.3892/or.2013.2309] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2012] [Accepted: 01/23/2013] [Indexed: 11/06/2022] Open
Abstract
Tongue squamous cell carcinoma (TSCC) is one of the most common types of oral cancer; however, its molecular mechanisms remain unclear. In this study, methylated DNA immunoprecipitation (MeDIP) coupled with methylation microarray analysis was performed to screen for aberrantly methylated genes in adjacent normal control and TSCC tissues from 9 patients. Roche NimbleGen Human DNA Methylation 385K Promoter Plus CpG Island Arrays were used to detect 28,226 CpG sites. A total of 1,269 hypermethylated CpG sites covering 330 genes and 1,385 hypomethylated CpG sites covering 321 genes were found in TSCC tissue, compared to the adjacent normal tissue. Furthermore, we chose three candidate genes (FBLN1, ITIH5 and RUNX3) and validated the DNA methylation status by methylation-specific PCR (MS-PCR) and the mRNA expression levels by reverse transcription PCR (RT-PCR). In TSCC tissue, FBLN1 and ITIH5 were shown to be hypermethylated and their expression was found to be decreased, and RUNX3 was shown to be hypomethylated, however, its mRNA expression was found to be increased. In addition, another three genes (BCL2L14, CDCP1 and DIRAS3) were tested by RT-PCR. In TSCC tissue, BCL2L14 and CDCP1 expressions were markedly upregulated, and DIRAS3 expression was significantly downregulated. Our data demonstrated that aberrant DNA methylation is observed in TSCC tissue and plays an important role in the tumorigenesis, development and progression of TSCC.
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Affiliation(s)
- Sheng Zhang
- Department of Oral and Maxillofacial Surgery, the Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, PR China.
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Paz N, Levanon EY, Amariglio N, Heimberger AB, Ram Z, Constantini S, Barbash ZS, Adamsky K, Safran M, Hirschberg A, Krupsky M, Ben-Dov I, Cazacu S, Mikkelsen T, Brodie C, Eisenberg E, Rechavi G. Altered adenosine-to-inosine RNA editing in human cancer. Genome Res 2007; 17:1586-95. [PMID: 17908822 PMCID: PMC2045141 DOI: 10.1101/gr.6493107] [Citation(s) in RCA: 261] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Adenosine-to-inosine (A-to-I) RNA editing was recently shown to be abundant in the human transcriptome, affecting thousands of genes. Employing a bioinformatic approach, we identified significant global hypoediting of Alu repetitive elements in brain, prostate, lung, kidney, and testis tumors. Experimental validation confirmed this finding, showing significantly reduced editing in Alu sequences within MED13 transcripts in brain tissues. Looking at editing of specific recoding and noncoding sites, including in cancer-related genes, a more complex picture emerged, with a gene-specific editing pattern in tumors vs. normal tissues. Additionally, we found reduced RNA levels of all three editing mediating enzymes, ADAR, ADARB1, and ADARB2, in brain tumors. The reduction of ADARB2 correlated with the grade of malignancy of glioblastoma multiforme, the most aggressive of brain tumors, displaying a 99% decrease in ADARB2 RNA levels. Consistently, overexpression of ADAR and ADARB1 in the U87 glioblastoma multiforme cell line resulted in decreased proliferation rate, suggesting that reduced A-to-I editing in brain tumors is involved in the pathogenesis of cancer. Altered epigenetic control was recently shown to play a central role in oncogenesis. We suggest that A-to-I RNA editing may serve as an additional epigenetic mechanism relevant to cancer development and progression.
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Affiliation(s)
- Nurit Paz
- Cancer Research Center, Chaim Sheba Medical Center, Tel Hashomer 52621, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | | | - Ninette Amariglio
- Cancer Research Center, Chaim Sheba Medical Center, Tel Hashomer 52621, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Amy B. Heimberger
- Department of Neurosurgery, Brain Tumor Center, University of Texas M.D. Anderson Cancer Center, Houston 77030, Texas, USA
| | - Zvi Ram
- Department of Neurosurgery, Sourasky Medical Center, Tel Aviv 64239, Israel
| | - Shlomi Constantini
- Department of Pediatric Neurosurgery, Dana Children’s Hospital, Sourasky Medical Center, Tel Aviv 64239, Israel
| | - Zohar S. Barbash
- Cancer Research Center, Chaim Sheba Medical Center, Tel Hashomer 52621, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Konstantin Adamsky
- Cancer Research Center, Chaim Sheba Medical Center, Tel Hashomer 52621, Israel
| | - Michal Safran
- Cancer Research Center, Chaim Sheba Medical Center, Tel Hashomer 52621, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Avi Hirschberg
- Cancer Research Center, Chaim Sheba Medical Center, Tel Hashomer 52621, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Meir Krupsky
- Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Department of Internal Medicine, Chaim Sheba Medical Center, Tel Hashomer 52621, Israel
| | - Issachar Ben-Dov
- Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Pulmonary Institute, Chaim Sheba Medical Center, Tel Hashomer 52621, Israel
| | - Simona Cazacu
- Hermelin Brain Tumor Center, Department of Neurosurgery, Henry Ford Hospital, Detroit, Michigan 48202, USA
| | - Tom Mikkelsen
- Hermelin Brain Tumor Center, Department of Neurosurgery, Henry Ford Hospital, Detroit, Michigan 48202, USA
| | - Chaya Brodie
- Hermelin Brain Tumor Center, Department of Neurosurgery, Henry Ford Hospital, Detroit, Michigan 48202, USA
- Neuro-Oncology Branch, NCI/NINDS, NIH, Bethesda 20892, Maryland, USA
| | - Eli Eisenberg
- School of Physics and Astronomy, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University 69978 Israel
| | - Gideon Rechavi
- Cancer Research Center, Chaim Sheba Medical Center, Tel Hashomer 52621, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Corresponding author.E-mail ; fax 972-3-5302377
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Bartoletti R, Cai T, Nesi G, Roberta Girardi L, Baroni G, Dal Canto M. Loss of P16 expression and chromosome 9p21 LOH in predicting outcome of patients affected by superficial bladder cancer. J Surg Res 2007; 143:422-7. [PMID: 17612565 DOI: 10.1016/j.jss.2007.01.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2006] [Revised: 01/16/2007] [Accepted: 01/18/2007] [Indexed: 11/28/2022]
Abstract
OBJECTIVES To evaluate the prognostic role of p16 expression and loss of heterozygosity (LOH) on chromosome 9p21 in patients affected by low-grade (G1-G2) urothelial bladder cancer. METHODS Fifty-six consecutive patients with diagnosis of urothelial bladder cancer were enrolled in this prospective study. LOH analysis was performed on a blood/tumor pair sample of each patient, by using polymerase chain reaction analysis. The D9S171 (9p21) locus on chromosome 9 was investigated. All tumors were stained immunohistochemically for p16. Data from p16 and LOH analyses were compared with follow-up data to evaluate the prognostic role of these molecular markers. RESULTS Loss of p16 expression was found in 33 patients (58.9%) and was significantly associated with the reduced recurrence-free probability (P < 0.0001). No correlations were reported with stage (P = 0.162) or grade (P = 0.051). Forty-three patients (76.7%) showed LOH on chromosome 9p21 (D9S171). A significant association was observed between loss of p16 expression and LOH on chromosome 9p21 (P = 0.005). The Kaplan-Meier curves showed a significant correlation between recurrence-free status and p16 expression (P = 0.0001). By multivariate analysis, p16 expression (P = 0.002) and number of lesions (P = 0.002) were identified as independent tumor recurrence factors. CONCLUSIONS Our study highlights the prognostic role of p16 in predicting the recurrence-free probability in patients affected by low-grade urothelial bladder and highlights the fact that this method could be used in everyday urologic clinical practice to better characterize the natural history of urothelial bladder carcinomas.
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Mitra AP, Datar RH, Cote RJ. Molecular Pathways in Invasive Bladder Cancer: New Insights Into Mechanisms, Progression, and Target Identification. J Clin Oncol 2006; 24:5552-64. [PMID: 17158541 DOI: 10.1200/jco.2006.08.2073] [Citation(s) in RCA: 204] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Papillary and invasive cancers of the urinary bladder appear to evolve and progress through distinct molecular pathways. Invasion in bladder cancer forebodes a graver prognosis, and these tumors are generally characterized by alterations in the p53 and retinoblastoma (RB) pathways that normally regulate the cell cycle by interacting with the Ras–mitogen activated protein kinase signal transduction pathway. Tumor angiogenesis further contributes to the neoplastic growth by providing a constant supply of oxygen and nutrients. Distinct epigenetic and genetic events characterize the interplay between the molecules involved in these pathways, thus affording their use as indicators of prognosis. Efforts are now underway to construct molecular panels comprising multiple markers that can serve as more robust predictors of outcome. While clinical trials for targeted chemotherapy for bladder cancer have commenced, novel genetic and pharmacologic agents that can target pathway-specific molecules are currently under development. The next generation of clinical management for urothelial carcinoma will witness the use of multimarker panels for prognostic prediction and combination therapy directed at novel molecular targets for treatment.
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Affiliation(s)
- Anirban P Mitra
- Department of Pathology, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA
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Rein T, Kobayashi T, Malott M, Leffak M, DePamphilis ML. DNA methylation at mammalian replication origins. J Biol Chem 1999; 274:25792-800. [PMID: 10464318 DOI: 10.1074/jbc.274.36.25792] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In Escherichia coli, DNA methylation regulates both origin usage and the time required to reassemble prereplication complexes at replication origins. In mammals, at least three replication origins are associated with a high density cluster of methylated CpG dinucleotides, and others whose methylation status has not yet been characterized have the potential to exhibit a similar DNA methylation pattern. One of these origins is found within the approximately 2-kilobase pair region upstream of the human c-myc gene that contains 86 CpGs. Application of the bisulfite method for detecting 5-methylcytosines at specific DNA sequences revealed that this region was not methylated in either total genomic DNA or newly synthesized DNA. Therefore, DNA methylation is not a universal component of mammalian replication origins. To determine whether or not DNA methylation plays a role in regulating the activity of origins that are methylated, the rate of remethylation and the effect of hypomethylation were determined at origin beta (ori-beta), downstream of the hamster DHFR gene. Remethylation at ori-beta did not begin until approximately 500 base pairs of DNA was synthesized, but it was then completed by the time that 4 kilobase pairs of DNA was synthesized (<3 min after release into S phase). Thus, DNA methylation cannot play a significant role in regulating reassembly of prereplication complexes in mammalian cells, as it does in E. coli. To determine whether or not DNA methylation plays any role in origin activity, hypomethylated hamster cells were examined for ori-beta activity. Cells that were >50% reduced in methylation at ori-beta no longer selectively activated ori-beta. Therefore, at some loci, DNA methylation either directly or indirectly determines where replication begins.
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Affiliation(s)
- T Rein
- NICHD, National Institutes of Health, Bethesda, Maryland 20892-2753, USA
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