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Zhong W, Wang D, Yao B, Chen X, Wang Z, Qu H, Ma B, Ye L, Qiu J. Integrative analysis of prognostic long non-coding RNAs with copy number variation in bladder cancer. J Zhejiang Univ Sci B 2021; 22:664-681. [PMID: 34414701 DOI: 10.1631/jzus.b2000494] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Copy number variations (CNVs), which can affect the role of long non-coding RNAs (lncRNAs), are important genetic changes seen in some malignant tumors. We analyzed lncRNAs with CNV to explore the relationship between lncRNAs and prognosis in bladder cancer (BLCA). Messenger RNA (mRNA) expression levels, DNA methylation, and DNA copy number data of 408 BLCA patients were subjected to integrative bioinformatics analysis. Cluster analysis was performed to obtain different subtypes and differently expressed lncRNAs and coding genes. Weighted gene co-expression network analysis (WGCNA) was performed to identify the co-expression gene and lncRNA modules. CNV-associated lncRNA data and their influence on cancer prognosis were assessed with Kaplan-Meier survival curve. Multi-omics integration analysis revealed five prognostic lncRNAs with CNV, namely NR2F1-AS1, LINC01138, THUMPD3-AS1, LOC101928489,and TMEM147-AS1,and a risk-score signature related to overall survival in BLCA was identified. Moreover, validated results in another independent Gene Expression Omnibus (GEO) dataset, GSE31684, were consistent with these results. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that the mitogen-activated protein kinase (MAPK) signaling pathway, focal adhesion pathway, and Janus kinase-signal transducers and activators of transcription (JAK-STAT) signaling pathway were enriched in a high-risk score pattern, suggesting that imbalance in these pathways is closely related to tumor development. We revealed the prognosis-related lncRNAs by analyzing the expression profiles of lncRNAs and CNVs, which can be used as prognostic biomarkers for BLCA.
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Affiliation(s)
- Wenwen Zhong
- Department of Urology, the Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou 510655, China
| | - Dejuan Wang
- Department of Urology, the Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou 510655, China
| | - Bing Yao
- Department of Urology, the Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou 510655, China
| | - Xiaoxia Chen
- Department of Medical Record Management Section, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510630, China
| | - Zhongyang Wang
- Department of Urology, the Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou 510655, China
| | - Hu Qu
- Department of Urology, the Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou 510655, China
| | - Bo Ma
- Department of Urology, the Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou 510655, China
| | - Lei Ye
- Department of Urology, the Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou 510655, China
| | - Jianguang Qiu
- Department of Urology, the Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou 510655, China.
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Gurung PMS, Barnett AR, Wilson JS, Hudson J, Ward DG, Messing EM, Bryan RT. Prognostic DNA Methylation Biomarkers in High-risk Non-muscle-invasive Bladder Cancer: A Systematic Review to Identify Loci for Prospective Validation. Eur Urol Focus 2019; 6:683-697. [PMID: 30803927 DOI: 10.1016/j.euf.2019.02.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 02/13/2019] [Indexed: 02/06/2023]
Abstract
CONTEXT High-risk non-muscle-invasive bladder cancer (HR-NMIBC) represents over 30% of all incident urothelial bladder cancers (BCs); patients are at risk of progression, and 20-30% will die from BC within 5 yr. Current guidelines recommend induction and maintenance of intravesical bacillus Calmette-Guérin (BCG) or upfront radical cystectomy for highest-risk disease, treatments with markedly different morbidity, mortality, and patient burden. There are no validated biomarkers to facilitate such treatment decisions. Alterations in DNA methylation are commonplace in BC; hence, measurable changes in DNA methylation represent an opportunity for the discovery of such biomarkers. OBJECTIVE To systematically assess the evidence regarding DNA methylation markers as prognosticators for HR-NMIBC. EVIDENCE ACQUISITION Standard systematic review methods were employed with searches undertaken in MEDLINE, EMBASE, and PubMed up to January 2019. Studies that included patients with HR-NMIBC and investigated the utility of DNA methylation biomarkers as prognostic tools were included. EVIDENCE SYNTHESIS Of 63 prognostic biomarker studies identified, 21 met the protocol-driven inclusion criteria and were directly relevant to HR-NMIBC patient outcomes: tumour recurrence (TR), tumour progression (TP), disease-specific survival (DSS), and overall survival (OS). These studies described 140 methylation markers; of these, the most promising were cadherin-13 (CDH13; hazard ratios [HRs]: 5.1 for TR, 6.6 for TP, 3.8-8.0 for OS), protocadherins (PCDHs; HRs: 4.7 for TR, 2.5 for TP, 3.0-4.8 for OS), Runt domain transcription factor 3 (RUNX3; HR: 5.1 for TP), Homeobox 9 (HOXA9; HR: 1.9 for TR), Islet-1 (ISL1; HRs: 1.7 for TR, 3.3 for TP), and PAX6 (HR: 2.2 for TR). CONCLUSIONS This systematic review identifies a number of potentially useful prognostic methylation markers for HR-NMIBC. These loci (CDH13, PCDHs, RUNX3, HOXA9, ISL1, and PAX6) should be validated in prospective studies in order to translate benefit to patients. PATIENT SUMMARY Early bladder cancer represents a more complex spectrum of disease than can be assessed by conventional methods Emerging studies on molecular markers will improve our understanding of this disease, and may enable more precise and personalised treatment.
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Affiliation(s)
- Pratik M S Gurung
- University of Rochester Medical Center, Rochester, New York, NY, USA
| | - Abigail R Barnett
- Institute of Cancer & Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Jayne S Wilson
- Institute of Cancer & Genomic Sciences, University of Birmingham, Birmingham, UK
| | | | - Douglas G Ward
- Institute of Cancer & Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Edward M Messing
- University of Rochester Medical Center, Rochester, New York, NY, USA
| | - Richard T Bryan
- Institute of Cancer & Genomic Sciences, University of Birmingham, Birmingham, UK.
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Yu Y, Cao H, Zhang M, Shi F, Wang R, Liu X. Prognostic value of DNA methylation for bladder cancer. Clin Chim Acta 2018; 484:207-212. [PMID: 29860035 DOI: 10.1016/j.cca.2018.05.056] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/29/2018] [Accepted: 05/29/2018] [Indexed: 12/26/2022]
Abstract
PURPOSE A growing number of researches manifest that DNA methylation has been considered as biomarker for the prognosis of bladder cancer (BC). However, the results are still in a discrepancy. MATERIALS AND METHODS This meta-analysis was conducted in accordance with PRISMA guidelines. Studies evaluating the practicability of methylated DNA as a prognostic marker for BC were thoroughly searched via the PubMed, Web of science and the Cochrane Library databases from January 1st, 2000 to May 5th, 2018. The association between DNA methylation and overall survival (OS) and progression-free survival (PFS) was analyzed. Hazard ratios (HRs) or odds ratios (ORs) with 95% confidence intervals (95% CIs) were calculated to assess the correlation between methylated DNA and prognostic value in BC by using multivariate survival analysis. RESULTS Nineteen studies were included. Patients with methylated DNA had poorer OS, compared with those with unmethylated DNA, the combined HR was 2.766 (95%CI: 2.099-3.806). Simultaneously, methylated DNA was considerably associated with shorter PFS (HR = 2.872, 95%CI: 1.971-4.185). Furthermore, DNA methylation had a significant association with gender (male vs female: OR = 1.486, 95% CI = 1.090-2.025), grade (3 vs 1-2: OR = 3.153, 95% CI = 2.006-4.955), tumor diameter (≤3 cm vs >3 cm: OR = 0.408, 95% CI = 0.277-0.602), number of tumors (single vs multiple: OR = 0.683, 95% CI = 0.501-0.932), stage (Ta vs T1: OR = 0.472, 95% CI = 0.342-0.654), (Ta-T1 vs T2-T4: OR = 0.338, 95% CI =0.210-0.543). CONCLUSIONS DNA methylation was negatively correlated with the prognosis of BC patients and might become a promising biomarker.
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Affiliation(s)
- Yinghui Yu
- Jilin University, School of Public Health, Epidemiology and Statistics, #1163, Xinmin Street, Changchun 130021, China
| | - Hui Cao
- Jilin University, School of Public Health, Epidemiology and Statistics, #1163, Xinmin Street, Changchun 130021, China
| | - Mengmeng Zhang
- Jilin University, School of Public Health, Epidemiology and Statistics, #1163, Xinmin Street, Changchun 130021, China
| | - Fang Shi
- Jilin University, School of Public Health, Epidemiology and Statistics, #1163, Xinmin Street, Changchun 130021, China
| | - Rui Wang
- Jilin University, School of Public Health, Epidemiology and Statistics, #1163, Xinmin Street, Changchun 130021, China
| | - Xin Liu
- Jilin University, School of Public Health, Epidemiology and Statistics, #1163, Xinmin Street, Changchun 130021, China.
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Khandelwal M, Anand V, Appunni S, Seth A, Singh P, Mathur S, Sharma A. Decitabine augments cytotoxicity of cisplatin and doxorubicin to bladder cancer cells by activating hippo pathway through RASSF1A. Mol Cell Biochem 2018; 446:105-114. [PMID: 29368096 DOI: 10.1007/s11010-018-3278-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 01/16/2018] [Indexed: 12/11/2022]
Abstract
Genetic abnormalities and epigenetic alterations both play vital role in initiation as well as progression of cancer. Whereas genetic mutations cannot be reversed, epigenetic alterations such as DNA methylation can be reversed by the application of DNA methyltransferase inhibitor decitabine. Epigenetic silencing of RASSF1A and involvement of hippo pathway both have been shown to involve in chemo-resistance. Purpose of this study was to observe the effect of combination treatment of decitabine with cisplatin or doxorubicin on bladder cancer cells involving hippo pathway through RASSF1A. Bladder cancer cells (HT1376 & T24) were treated with decitabine and its effect on RASSF1A expression, hippo pathway molecules (MST & YAP), and its downstream targets (CTGF, CYR61 & CTGF) was observed. Effect of decitabine pretreatment on sensitivity of bladder cancer cells towards chemotherapeutic drugs was also studied. Decitabine treatment leads to restoration of RASSF1A, activation of hippo pathway followed by decreased expression of its oncogenic downstream targets (CTGF & CYR61). Further pretreatment of decitabine enhanced cytotoxicity of cisplatin and doxorubicin to bladder cancer cells.
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Affiliation(s)
| | - Vivek Anand
- Department of Biochemistry, AIIMS, New Delhi, India
| | | | - Amlesh Seth
- Department of Urology, AIIMS, New Delhi, India
| | | | | | - Alpana Sharma
- Department of Biochemistry, AIIMS, New Delhi, India.
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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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Olkhov-Mitsel E, Savio AJ, Kron KJ, Pethe VV, Hermanns T, Fleshner NE, van Rhijn BW, van der Kwast TH, Zlotta AR, Bapat B. Epigenome-Wide DNA Methylation Profiling Identifies Differential Methylation Biomarkers in High-Grade Bladder Cancer. Transl Oncol 2017; 10:168-177. [PMID: 28167242 PMCID: PMC5293735 DOI: 10.1016/j.tranon.2017.01.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 12/23/2016] [Accepted: 01/05/2017] [Indexed: 01/22/2023] Open
Abstract
Epigenetic changes, including CpG island hypermethylation, occur frequently in bladder cancer (BC) and may be exploited for BC detection and distinction between high-grade (HG) and low-grade (LG) disease. Genome-wide methylation analysis was performed using Agilent Human CpG Island Microarrays to determine epigenetic differences between LG and HG cases. Pathway enrichment analysis and functional annotation determined that the most frequently methylated pathways in HG BC were enriched for anterior/posterior pattern specification, embryonic skeletal system development, neuron fate commitment, DNA binding, and transcription factor activity. We identified 990 probes comprising a 32-gene panel that completely distinguished LG from HG based on methylation. Selected genes from this panel, EOMES, GP5, PAX6, TCF4, and ZSCAN12, were selected for quantitative polymerase chain reaction–based validation by MethyLight in an independent series (n = 84) of normal bladder samples and LG and HG cases. GP5 and ZSCAN12, two novel methylated genes in BC, were significantly hypermethylated in HG versus LG BC (P ≤ .03). We validated our data in a second independent cohort of LG and HG BC cases (n = 42) from The Cancer Genome Atlas (TCGA). Probes representing our 32-gene panel were significantly differentially methylated in LG versus HG tumors (P ≤ .04). These results indicate the ability to distinguish normal tissue from cancer, as well as LG from HG, based on methylation and reveal important pathways dysregulated in HG BC. Our findings were corroborated using publicly available data sets from TCGA. Ultimately, the creation of a methylation panel, including GP5 and ZSCAN12, able to distinguish between disease phenotypes will improve disease management and patient outcomes.
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Affiliation(s)
- Ekaterina Olkhov-Mitsel
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 60 Murray St., Toronto, Ontario, Canada, M5T 3L9; Department of Laboratory Medicine and Pathobiology, University of Toronto, 27 King's College Circle, Toronto, Ontario, Canada, M5S 1A1.
| | - Andrea J Savio
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 60 Murray St., Toronto, Ontario, Canada, M5T 3L9; Department of Laboratory Medicine and Pathobiology, University of Toronto, 27 King's College Circle, Toronto, Ontario, Canada, M5S 1A1.
| | - Ken J Kron
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 60 Murray St., Toronto, Ontario, Canada, M5T 3L9; Department of Laboratory Medicine and Pathobiology, University of Toronto, 27 King's College Circle, Toronto, Ontario, Canada, M5S 1A1.
| | - Vaijayanti V Pethe
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 60 Murray St., Toronto, Ontario, Canada, M5T 3L9.
| | - Thomas Hermanns
- Department of Surgery and Surgical Oncology, Division of Urology, The Princess Margaret Cancer Centre, University Health Network, 610 University Ave., Toronto, Ontario, Canada, M5G 2M9.
| | - Neil E Fleshner
- Department of Surgery and Surgical Oncology, Division of Urology, The Princess Margaret Cancer Centre, University Health Network, 610 University Ave., Toronto, Ontario, Canada, M5G 2M9.
| | - Bas W van Rhijn
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 60 Murray St., Toronto, Ontario, Canada, M5T 3L9; Department of Surgery and Surgical Oncology, Division of Urology, The Princess Margaret Cancer Centre, University Health Network, 610 University Ave., Toronto, Ontario, Canada, M5G 2M9.
| | - Theodorus H van der Kwast
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 27 King's College Circle, Toronto, Ontario, Canada, M5S 1A1; Department of Pathology, University Health Network, 200 Elizabeth St., Toronto, Ontario, Canada, M5G 2C4.
| | - Alexandre R Zlotta
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 60 Murray St., Toronto, Ontario, Canada, M5T 3L9; Department of Surgery, Division of Urology, Sinai Health System, 600 University Ave., Toronto, Ontario, Canada, M5G 1X5.
| | - Bharati Bapat
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 60 Murray St., Toronto, Ontario, Canada, M5T 3L9; Department of Laboratory Medicine and Pathobiology, University of Toronto, 27 King's College Circle, Toronto, Ontario, Canada, M5S 1A1; Department of Pathology, University Health Network, 200 Elizabeth St., Toronto, Ontario, Canada, M5G 2C4.
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Zhan L, Zhang B, Tan Y, Yang C, Huang C, Wu Q, Zhang Y, Chen X, Zhou M, Shu A. Quantitative assessment of the relationship between RASSF1A gene promoter methylation and bladder cancer (PRISMA). Medicine (Baltimore) 2017; 96:e6097. [PMID: 28207521 PMCID: PMC5319510 DOI: 10.1097/md.0000000000006097] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Methylation of the Ras-association domain family 1 isoform A (RASSF1A) gene promoter region is thought to participate in the initiation and development of many different cancers. However, in bladder cancer the role of RASSF1A methylation was unclear. To evaluate the relationship between RASSF1A methylation and bladder cancer, a quantitative assessment of an independent meta-analysis was performed. In addition, a DNA methylation microarray database from the cancer genome atlas (TCGA) project was used to validate the results of the meta-analysis. METHODS We searched published articles from computerized databases, and DNA methylation data were extracted from TCGA project. All data were analyzed by R software. RESULTS The results of the meta-analysis indicated that the frequency of RASSF1A gene methylation in bladder cancer patients is significantly higher than in healthy controls. The hazard ratio (HR) was 2.24 (95% CI = [1.45; 3.48], P = 0.0003) for overall survival (OS), and the RASSF1A gene promoter methylation status was strongly associated with the TNM stage and differentiation grade of the tumor. The similar results were also found by the data from TCGA project. CONCLUSION There was a significant relationship between the methylation of the RASSF1A gene promoter and bladder cancer. Therefore, RASSF1A gene promoter methylation will be a potential biomarker for the clinical diagnosis of bladder cancer.
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Affiliation(s)
- Leyun Zhan
- Anesthesia department, People's Hospital of China Three Gorges University, The First People's Hospital of Yichang, Yichang, Hubei, P.R. China
| | - Bingyi Zhang
- Ultrasound department, People's Hospital of China Three Gorges University, The First People's Hospital of Yichang, Yichang, Hubei, P.R. China
| | - Yaojun Tan
- Anesthesia department, People's Hospital of China Three Gorges University, The First People's Hospital of Yichang, Yichang, Hubei, P.R. China
| | - Chengliang Yang
- Cardiothoracic surgery, People's Hospital of China Three Gorges University, The First People's Hospital of Yichang, Yichang, Hubei, P.R. China
| | - Chenhong Huang
- Anesthesia department, People's Hospital of China Three Gorges University, The First People's Hospital of Yichang, Yichang, Hubei, P.R. China
| | - Qiongya Wu
- Anesthesia department, People's Hospital of China Three Gorges University, The First People's Hospital of Yichang, Yichang, Hubei, P.R. China
| | - Yulin Zhang
- Department of science and education, People's Hospital of China Three Gorges University, The First People's Hospital of Yichang, Yichang, Hubei, P.R. China
| | - Xiaobo Chen
- Anesthesia department, People's Hospital of China Three Gorges University, The First People's Hospital of Yichang, Yichang, Hubei, P.R. China
| | - Mi Zhou
- Anesthesia department, People's Hospital of China Three Gorges University, The First People's Hospital of Yichang, Yichang, Hubei, P.R. China
| | - Aihua Shu
- Anesthesia department, People's Hospital of China Three Gorges University, The First People's Hospital of Yichang, Yichang, Hubei, P.R. China
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Amato E, Barbi S, Fassan M, Luchini C, Vicentini C, Brunelli M, Malleo G, Scarpa A, Malpeli G. RASSF1 tumor suppressor gene in pancreatic ductal adenocarcinoma: correlation of expression, chromosomal status and epigenetic changes. BMC Cancer 2016; 16:11. [PMID: 26754001 PMCID: PMC4710004 DOI: 10.1186/s12885-016-2048-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 01/06/2016] [Indexed: 12/13/2022] Open
Abstract
Background The Ras Association Domain Family Member 1 (RASSF1) is one of the most frequently reported methylation-inactivated tumor suppressor genes in primary pancreatic ductal adenocarcinomas (PDAC). Limited information is still available about the impact of RASSF1 gene silencing on the expression of its different isoforms in neoplastic cells. Methods A series of 96 primary PDAC, with known clinico-pathological parameters, was tested for RASSF1 methylation status by methylation-specific PCR, RASSF1 locus copy number alterations by fluorescence in situ hybridization, and Rassf1a protein expression by immunohistochemistry. A further series of 14 xenografted primary PDAC and 8 PDAC-derived cell lines were tested to obtain a detailed methylation mapping of CpG islands A and C of the RASSF1 locus by pyrosequencing and to evaluate the expression of Rassf1 variants by qRT-PCR. Results Methylation of CpG island A of the RASSF1 gene was observed in 35 % of the tumors and allelic loss of RASSF1 locus was seen in 30 disomic and in 20 polysomic cases (52 %). Rassf1a immunohistochemical expression was downregulated in half of primary PDAC, and this downregulation was neither correlated with methylation of RASSF1 promoter nor with RASSF1 copy number alterations. RASSF1 status did not influence patients’ prognosis. The expression of the seven RASSF1 isoforms in xenografts and cell lines showed that RASSF1A, RASSF1B, and RASSF1C isoforms were present in all xenografts and cell lines, whereas RASSF1D, RASSF1E, and RASSF1F isoforms were variably expressed among samples. RASSF1G was never expressed in either xenografts or cell lines. The variable expression of RASSF1 isoforms in PDAC xenografts and cell lines was not dependent on RASSF1 methylation status of CpG islands A and C. Conclusions RASSF1 alterations occurring in PDAC mainly consist in variations of expression of the different isoforms. Different genetic mechanisms seem to contribute to RASSF1 deregulation in this setting, but RASSF1 methylation does not seem to substantially affect RASSF1 isoforms expression. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2048-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Eliana Amato
- ARC-NET Centre for Applied Research on Cancer, Department of Pathology and Diagnostics, The Hospital and University of Verona, Verona, Italy.
| | - Stefano Barbi
- ARC-NET Centre for Applied Research on Cancer, Department of Pathology and Diagnostics, The Hospital and University of Verona, Verona, Italy.
| | - Matteo Fassan
- ARC-NET Centre for Applied Research on Cancer, Department of Pathology and Diagnostics, The Hospital and University of Verona, Verona, Italy.
| | - Claudio Luchini
- ARC-NET Centre for Applied Research on Cancer, Department of Pathology and Diagnostics, The Hospital and University of Verona, Verona, Italy. .,Department of Pathology, The Hospital and University of Verona, Verona, Italy.
| | - Caterina Vicentini
- ARC-NET Centre for Applied Research on Cancer, Department of Pathology and Diagnostics, The Hospital and University of Verona, Verona, Italy.
| | - Matteo Brunelli
- ARC-NET Centre for Applied Research on Cancer, Department of Pathology and Diagnostics, The Hospital and University of Verona, Verona, Italy.
| | - Giuseppe Malleo
- Department of Surgery and Oncology, The Hospital and University of Verona, Verona, Italy.
| | - Aldo Scarpa
- ARC-NET Centre for Applied Research on Cancer, Department of Pathology and Diagnostics, The Hospital and University of Verona, Verona, Italy. .,Department of Pathology, The Hospital and University of Verona, Verona, Italy.
| | - Giorgio Malpeli
- ARC-NET Centre for Applied Research on Cancer, Department of Pathology and Diagnostics, The Hospital and University of Verona, Verona, Italy. .,Department of Surgery and Oncology, The Hospital and University of Verona, Verona, Italy.
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Darwiche F, Parekh DJ, Gonzalgo ML. Biomarkers for non-muscle invasive bladder cancer: Current tests and future promise. Indian J Urol 2015; 31:273-82. [PMID: 26604437 PMCID: PMC4626910 DOI: 10.4103/0970-1591.166448] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The search continues for optimal markers that can be utilized to improve bladder cancer detection and to predict disease recurrence. Although no single marker has yet replaced the need to perform cystoscopy and urine cytology, many tests have been evaluated and are being developed. In the future, these promising markers may be incorporated into standard practice to address the challenge of screening in addition to long-term surveillance of patients who have or are at risk for developing bladder cancer.
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Affiliation(s)
- Fadi Darwiche
- Department of Urology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Dipen J Parekh
- Department of Urology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Mark L Gonzalgo
- Department of Urology, Miller School of Medicine, University of Miami, Miami, FL, USA
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10
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Grawenda AM, O'Neill E. Clinical utility of RASSF1A methylation in human malignancies. Br J Cancer 2015; 113:372-81. [PMID: 26158424 PMCID: PMC4522630 DOI: 10.1038/bjc.2015.221] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 05/11/2015] [Accepted: 05/13/2015] [Indexed: 02/06/2023] Open
Abstract
The high frequency of RASSF1A methylation has been noted in a vast number of patients in a broad spectrum of malignancies, suggesting that RASSF1A inactivation is associated with cancer pathogenesis. However, whether this recurrent incidence of RASSF1A hypermethylation in human malignancies and its association with more aggressive tumour phenotype is a frequent event across different cancer types has not yet been discussed. In this review, we interrogated existing evidence for association of RASSF1A hypermethylation with clinicopathological characteristics that can indicate more invasive lesions.
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Affiliation(s)
- A M Grawenda
- CRUK/MRC Oxford Institute, Department of Oncology, University of Oxford, Oxford, UK
| | - E O'Neill
- CRUK/MRC Oxford Institute, Department of Oncology, University of Oxford, Oxford, UK
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Zhang L, Xiong G, Fang D, Li X, Liu J, Ci W, Zhao W, Singla N, He Z, Zhou L. Contralateral upper tract urothelial carcinoma after nephroureterectomy: the predictive role of DNA methylation. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2015; 34:5. [PMID: 25613404 PMCID: PMC4307673 DOI: 10.1186/s13046-015-0120-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 01/04/2015] [Indexed: 01/26/2023]
Abstract
Background Aberrant methylation of genes is one of the most common epigenetic modifications involved in the development of urothelial carcinoma. However, it is unknown the predictive role of methylation to contralateral new upper tract urothelial carcinoma (UTUC) after radical nephroureterectomy (RNU). We retrospectively investigated the predictive role of DNA methylation and other clinicopathological factors in the contralateral upper tract urothelial carcinoma (UTUC) recurrence after radical nephroureterectomy (RNU) in a large single-center cohort of patients. Methods In a retrospective design, methylation of 10 genes was analyzed on tumor specimens belonging to 664 consecutive patients treated by RNU for primary UTUC. Median follow-up was 48 mo (range: 3–144 mo). Gene methylation was accessed by methylation-sensitive polymerase chain reaction, and we calculated the methylation index (MI), a reflection of the extent of methylation. The log-rank test and Cox regression were used to identify the predictor of contralateral UTUC recurrence. Results Thirty (4.5%) patients developed a subsequent contralateral UTUC after a median follow-up time of 27.5 (range: 2–139) months. Promoter methylation for at least one gene promoter locus was present in 88.9% of UTUC. Fewer methylation and lower MI (P = 0.001) were seen in the tumors with contralateral UTUC recurrence than the tumors without contralateral recurrence. High MI (P = 0.007) was significantly correlated with poor cancer-specific survival. Multivariate analysis indicated that unmethylated RASSF1A (P = 0.039), lack of bladder recurrence prior to contralateral UTUC (P = 0.009), history of renal transplantation (P < 0.001), and preoperative renal insufficiency (P = 0.002) are independent risk factors for contralateral UTUC recurrence after RNU. Conclusions Our data suggest a potential role of DNA methylation in predicting contralateral UTUC recurrence after RNU. Such information could help identify patients at high risk of new contralateral UTUC recurrence after RNU who need close surveillance during follow up.
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Affiliation(s)
- Lei Zhang
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, No. 8 Xishiku St, Xicheng District, Beijing, 100034, China.
| | - Gengyan Xiong
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, No. 8 Xishiku St, Xicheng District, Beijing, 100034, China.
| | - Dong Fang
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, No. 8 Xishiku St, Xicheng District, Beijing, 100034, China.
| | - Xuesong Li
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, No. 8 Xishiku St, Xicheng District, Beijing, 100034, China.
| | - Jin Liu
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, No. 8 Xishiku St, Xicheng District, Beijing, 100034, China.
| | - Weimin Ci
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Wei Zhao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Cell Biology, Peking University Cancer Hospital and Institute, Beijing, 100142, China.
| | - Nirmish Singla
- Department of Urology University of Texas Southwestern Medical Center, 5303 Harry Hines Blvd, Dallas, TX, 75390, USA.
| | - Zhisong He
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, No. 8 Xishiku St, Xicheng District, Beijing, 100034, China.
| | - Liqun Zhou
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, No. 8 Xishiku St, Xicheng District, Beijing, 100034, China.
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Zhang CY, Zhao YX, Xia RH, Han J, Wang BS, Tian Z, Wang LZ, Hu YH, Li J. RASSF1A promoter hypermethylation is a strong biomarker of poor survival in patients with salivary adenoid cystic carcinoma in a Chinese population. PLoS One 2014; 9:e110159. [PMID: 25302792 PMCID: PMC4193867 DOI: 10.1371/journal.pone.0110159] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 09/08/2014] [Indexed: 11/18/2022] Open
Abstract
In addition to the clinicopathological parameters, molecular biomarkers are becoming increasingly important in the prognostic evaluation of cancer patients. This study aimed to determine the molecular alterations in the RAS association domain family protein1A gene (RASSF1A) in salivary adenoid cystic carcinoma (ACC) and to evaluate the potential of such alterations as prognostic markers. One hundred and sixty-seven ACC tumor tissues and 50 samples of matched normal salivary gland tissues from the same patients were analyzed for RASSF1A promoter methylation status by bisulfite sequencing PCR (BSP) and/or methylation-specific PCR (MSP). Fifty ACC tumor tissues and matched normal salivary gland tissues were analyzed for loss of heterozygosity (LOH) by examining two microsatellite markers (D3S1478, D3S1621) at 3p21. RASSF1A gene mutations were detected by direct sequencing of all six exons in 50 tumor and normal tissue specimens. Over-all, RASSF1A promoter hypermethylation was detected in 35.3% (59/167) of ACC tissues and was associated with histologically solid tumor pattern (P = 0.002) and advanced TNM stage (P = 0.014). RASSF1A LOH was observed in 18.0% (9/50) of cases, and no somatic mutation of RASSF1A was detected in any cases. RASSF1A promoter methylation was associated with the poor over-all survival (Log-rank test, P <0.001) and disease-free survival (Log-rank test, P <0.001) and identified as an independent predicator of over-all patient survival (P = 0.009) and disease-free survival (P <0.001). It was concluded that RASSF1A methylation is involved in the development, differentiation and progression of ACC and is a strong independent biomarker of poor survival in ACC patients in a Chinese population.
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Affiliation(s)
- Chun-Ye Zhang
- Department of Oral Pathology, 9th People's Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai Key Laboratory of Stomatology, Shanghai, P. R. China
| | - Yang-Xing Zhao
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, P. R. China
| | - Rong-Hui Xia
- Department of Oral Pathology, 9th People's Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai Key Laboratory of Stomatology, Shanghai, P. R. China
| | - Jing Han
- Department of Oral Pathology, 9th People's Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai Key Laboratory of Stomatology, Shanghai, P. R. China
| | - Bing-Shun Wang
- Department of Biostatistics, Shanghai Jiao Tong University, School of Medicine, Shanghai, P. R. China
| | - Zhen Tian
- Department of Oral Pathology, 9th People's Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai Key Laboratory of Stomatology, Shanghai, P. R. China
| | - Li-Zhen Wang
- Department of Oral Pathology, 9th People's Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai Key Laboratory of Stomatology, Shanghai, P. R. China
| | - Yu-Hua Hu
- Department of Oral Pathology, 9th People's Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai Key Laboratory of Stomatology, Shanghai, P. R. China
| | - Jiang Li
- Department of Oral Pathology, 9th People's Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai Key Laboratory of Stomatology, Shanghai, P. R. China
- * E-mail:
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Tsao CK, Small A, Hall S, Oh WK, Galsky MD, Buckstein M, Stock R, Ali G, Morris GJ. T2 muscle-invasive bladder cancer. Semin Oncol 2014; 41:e11-8. [PMID: 24787300 DOI: 10.1053/j.seminoncol.2014.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Fu L, Zhang S. RASSF1A promotes apoptosis and suppresses the proliferation of ovarian cancer cells. Int J Mol Med 2014; 33:1153-60. [PMID: 24573512 DOI: 10.3892/ijmm.2014.1671] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 01/27/2014] [Indexed: 11/05/2022] Open
Abstract
As the most lethal gynecological malignancy, ovarian cancer has attracted much attention over the past few decades; however, the early detection of this malignancy has been largely unsuccessful. The aim of this study was to determine the effects of Ras-association domain family 1, isoform A (RASSF1A) on ovarian cancer and to elucidate the molecular mechanisms responsible for these effects. The expression of RASSF1A in different ovarian cancer cells was detected by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). The morphology, structure, apoptosis and proliferation of differently treated SKOV-3 cells were then analyzed using a fluorescence microscope, transmission electron microscope, flow cytometer and by western blot analysis, respectively. Moreover, the GSE14407 affymetrix microarray data were downloaded from the Gene Expression Omnibus database and the expression of RASSF1A was quantified by Spotfire DecisionSite software. A RASSF1A related protein-protein interaction (PPI) network was then constructed using STRING and Cytoscape software. Finally, DAVID was utilized to perform KEGG pathway enrichment analysis of the network. RASSF1A was expressed in the HO8910, HO8910PM cells and the SKOV-3 cells transfected with RASSF1A, whereas it was absent in the other SKOV-3 cells and OVCAR-3 cells. Additionally, compared with the other SKOV-3 cells, the nucleus of SKOV-3 cells transfected with RASSF1A was vacuolated, apoptosis was increased, and the expression of cyclin D1 and survivin was decreased (P<0.05), and that of p27 and caspase-3 was increased (P<0.01). Additionally, 10 genes, including serine/threonine kinase (STK)3, STK4, Harvey rat sarcoma viral oncogene homolog (HRAS) and cell division cycle 20 (CDC20), were found to have close interactions with RASSF1A in the PPI network. Finally, a total of 8 enriched pathways, such as bladder cancer, non-small cell lung cancer and pathways in cancer were identified. To our knowledge, this is the first study to explore the biological functions and the underlying mechanisms of action of RASSF1A in the development of ovarian cancer. Our findings may provide a novel therapeutic target for ovarian cancer.
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Affiliation(s)
- Lingjie Fu
- Department of Gynaecology and Obstetrics, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Shulan Zhang
- Department of Gynaecology and Obstetrics, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
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Current World Literature. Curr Opin Oncol 2013; 25:325-30. [DOI: 10.1097/cco.0b013e328360f591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Kandimalla R, van Tilborg AA, Zwarthoff EC. DNA methylation-based biomarkers in bladder cancer. Nat Rev Urol 2013; 10:327-35. [DOI: 10.1038/nrurol.2013.89] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Van De Voorde L, Speeckaert R, Van Gestel D, Bracke M, De Neve W, Delanghe J, Speeckaert M. DNA methylation-based biomarkers in serum of patients with breast cancer. Mutat Res 2012; 751:304-325. [PMID: 22698615 DOI: 10.1016/j.mrrev.2012.06.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Revised: 06/03/2012] [Accepted: 06/05/2012] [Indexed: 12/18/2022]
Abstract
Alterations of genetic and epigenetic features can provide important insights into the natural history of breast cancer. Although DNA methylation analysis is a rapidly developing field, a reproducible epigenetic blood-based assay for diagnosis and follow-up of breast cancer has yet to be successfully developed into a routine clinical test. The aim of this study was to review multiple serum DNA methylation assays and to highlight the value of those novel biomarkers in diagnosis, prognosis and prediction of therapeutic outcome. Serum is readily accessible for molecular diagnosis in all individuals from a peripheral blood sample. The list of hypermethylated genes in breast cancer is heterogeneous and no single gene is methylated in all breast cancer types. There is increasing evidence that a panel of epigenetic markers is essential to achieve a higher sensitivity and specificity in breast cancer detection. However, the reported percentages of methylation are highly variable, which can be partly explained by the different sensitivities and the different intra-/inter-assay coefficients of variability of the analysis methods. Moreover, there is a striking lack of receiver operating characteristic (ROC) curves of the proposed biomarkers. Another point of criticism is the fact that 'normal' patterns of DNA methylation of some tumor suppressor and other cancer-related genes are influenced by several factors and are often poorly characterized. A relatively frequent methylation of those genes has been observed in high-risk asymptomatic women. Finally, there is a call for larger prospective cohort studies to determine methylation patterns during treatment and follow-up. Identification of patterns specific for a differential response to therapeutic interventions should be useful. Only in this way, it will be possible to evaluate the predictive and prognostic characteristics of those novel promising biomarkers.
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Affiliation(s)
- Lien Van De Voorde
- Department of Radiation Oncology and Experimental Cancer Research, Ghent University Hospital, Ghent, Belgium
| | | | - Dirk Van Gestel
- Department of Radiation Oncology, Antwerp University Hospital, Antwerp, Belgium
| | - Marc Bracke
- Department of Radiation Oncology and Experimental Cancer Research, Ghent University Hospital, Ghent, Belgium
| | - Wilfried De Neve
- Department of Radiation Oncology and Experimental Cancer Research, Ghent University Hospital, Ghent, Belgium
| | - Joris Delanghe
- Department of Clinical Chemistry, Ghent University Hospital, Ghent, Belgium
| | - Marijn Speeckaert
- Department of Clinical Chemistry, Ghent University Hospital, Ghent, Belgium; Department of Internal Medicine, Ghent University Hospital, Ghent, Belgium.
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