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Govers T, Resnick MJ, Trooskens G, Van Criekinge W, Schalken JA. Cost-effectiveness of a two-gene urine biomarker assay in MRI strategies for the initial detection of prostate cancer. J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.7_suppl.91] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
91 Background: MRI is increasingly used in men with a suspicion for prostate cancer (PCa) to target abnormal areas next to systematic biopsy. Although, MRI increases the detection of clinically significant PCa compared to systematic biopsy alone, overdiagnosis and overtreatment of insignificant disease still exists. The 2-gene mRNA PCR urine test combined with traditional risk factors SelectMDx (MDxhealth Irvine Ca) predicts clinically significant PCa, and can be used to reduce overdiagnosis and overtreatment. We assessed the cost-effectiveness of SelectMDx in a population of U.S. men who in the current situation undergo initial MRI and biopsies. Methods: We developed a decision-analytic model to simulate the downstream outcomes in the current MRI strategy, i.e. systematic biopsy plus targeted biopsy in case of a positive MRI. SelectMDx was assessed in two different diagnostic pathways: 1) before MRI to select patients for MRI and biopsy, 2) after a negative MRI to select patients for systematic biopsy. Outcomes were quality-adjusted life years (QALYs) and costs. Model parameters were informed by literature. Two scenarios regarding the mortality of missed PCa were used, using SPCG trial data and using data from the PIVOT trial. Results: Using SelectMDx before MRI (1) resulted in a health gain of 0.003 and 0.030 QALY per patient compared to the current MRI strategy, using the SPCG and PIVOT data, respectively. Cost savings were $1590 per patient and about $496 million for the yearly population of men at risk in the U.S. (n = 311,879). SelectMDx after negative MRI (2) resulted in a health gain of 0.008 and 0,011 QALY per patient using the SPCG and PIVOT data.. Cost savings were $436 per patient and about $136 million for the yearly population. Conclusions: The use of SelectMDx to guide prostate biopsy decision-making can improve health outcomes and lower costs. Cost savings were highest when SelectMDx was used before MRI to select patients for MRI and biopsy. With respect to health gain, the use of SelectMDx after negative MRI was most beneficial when assuming higher mortality for missed PCa (SPCG). When the mortality was assumed to be lower (PIVOT) SelectMDx should be used before MRI to result in the highest health gain.
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Affiliation(s)
- Tim Govers
- MedValue Radboud University Medical Center, Nijmegen, Netherlands
| | | | | | - Wim Van Criekinge
- Mathematical Modeling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium
| | - Jack A. Schalken
- Radboud University Nijmegen Medical Center, Nijmegen, Netherlands
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2
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Tilki D, Hessels D, Trooskens G, Mulders S, Brawer M, Van Criekinge W, Groskopf J, Haese A. Validation of a two-gene mRNA urine test for detection of high-grade prostate cancer in German men. J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.7_suppl.96] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
96 Background: There is an unmet need for non-invasive methods that can accurately identify patients at increased risk for clinically significant prostate cancer (PCa). SelectMDx is a urine-based molecular test that has been clinically validated for the detection of high-grade PCa. We evaluated SelectMDx clinical performance in a cohort of German men undergoing initial prostate biopsy. Methods: The study population consisted of 443 men sequentially enrolled men who underwent initial prostate biopsy between July 2009 and December 2014 due to suspected PCa. Post-DRE urine was collected from all subjects prior to biopsy, and samples stored at -70C. Urinary HOXC6 and DLX-1 mRNAs were quantified by PCR in May 2018, and RNA results combined with clinical risk factors to determine the likelihood that biopsy would identify ISUP grade group (GG) ≥ 2 (Gleason Score ≥ 7) PCa. We assessed SelectMDx performance for detection of GG ≥ 2 PCa, compared to the PCPT Risk Calculator Version 2.0 (PCPTRC, http://myprostatecancerrisk.com , accessed Oct 7, 2018). Results: For the 443 subjects enrolled, average age was 66 years (median 66, interquartile range 61 to 71), and average serum PSA level 8.8 ng/mL (6.4, 4.8 to 9.7). Cancer was detected in 243/443 (55%) men biopsied (43% GG1, 36% GG2, 9% GG3 and 12% GG4-5). The prevalence of GG2-5 PCa in this population was 31.4% (139/443). For detection of GG2 or higher PCa versus GG1 or no PCa at biopsy, SelectMDx AUC was 0.82 (95% C.I. 0.78-0.86) and the PCPTRC yielded AUC 0.75 (0.70-0.80), P < 0.001. SelectMDx sensitivity was 94% (89-98%), specificity 46% (40-52%), positive predictive value 45% (42-47%) and negative predictive value (NPV) 95% (90-97%). If the initial biopsy had been performed based on SelectMDx results alone, 46% of potentially unnecessary biopsies and 34% of all biopsies would have been avoided, while 5.8% of men with biopsy-detectable high-grade PCa (seven GG2, one GG3) may have had their diagnosis delayed. Conclusions: In this first validation study of SelectMDx in German men, the test’s clinical performance was comparable to the published EU validation study, showing a high NPV for detection of GG2 or higher PCa. These results provide further evidence for the clinical validity of SelectMDx.
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Affiliation(s)
- Derya Tilki
- Martini-Klinik Prostate Cancer Center and Department of Urology, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | | | | | | | | | - Wim Van Criekinge
- Mathematical Modeling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium
| | | | - Alexander Haese
- Martini-Klinik Prostate Cancer Center, University Hospital Hamburg-Eppendorf, Hamburg, Germany
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3
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Coussement L, Bolca S, Van Criekinge W, Trooskens G, Mensaert K, Poels K, Roche N, Blondeel P, Godderis L, Depypere H, De Meyer T. Exploratory analysis of the human breast DNA methylation profile upon soymilk exposure. Sci Rep 2018; 8:13617. [PMID: 30206342 PMCID: PMC6133922 DOI: 10.1038/s41598-018-31767-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 08/24/2018] [Indexed: 12/17/2022] Open
Abstract
Upon soy consumption, isoflavone metabolites attain bioactive concentrations in breast tissue possibly affecting health. Though in vitro epigenetic activity of soy metabolites has been described, the in vivo impact on the epigenome is largely unknown. Therefore, in this case-control study, the breast glandular tissue DNA methylome was explored in women undergoing an aesthetic breast reduction. After a run-in phase, 10 generally healthy Belgian or Dutch women received soymilk for 5 days. MethylCap-seq methylation profiles were compared with those of 10 matched controls. Isoflavones and their microbial metabolites were quantified in urine, serum, and glandular breast tissue (liquid chromatography-mass spectrometry) and 17β-estradiol in glandular breast tissue (immunoassay). Global DNA methylation levels were obtained for 6 cases and 5 controls using liquid chromatography-mass spectrometry. Although lower MethylCap-seq coverages were observed, mass spectrometry results and computational LINE-1 methylation analysis did not provide evidence supporting global methylation alterations upon treatment. At a false discovery rate of 0.05, no differentially methylated loci were identified. Moreover, a set of previously identified loci was specifically tested, but earlier reported results could not be validated. In conclusion, after a 5-day soymilk treatment, no major general epigenetic reprogramming in breast tissue could be found in this exploratory study.
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Affiliation(s)
- Louis Coussement
- Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Belgium, Coupure Links 653, B-9000, Ghent, Belgium
| | - Selin Bolca
- Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Belgium, Coupure Links 653, B-9000, Ghent, Belgium
| | - Wim Van Criekinge
- Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Belgium, Coupure Links 653, B-9000, Ghent, Belgium.,Bioinformatics Institute Ghent: from Nucleotides 2 Networks (BIG-N2N), Ghent University, Belgium, Ghent University - VIB, Technologiepark 927, B-9052, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University (Hospital), Belgium, Ghent University Hospital MRB, Corneel Heymanslaan 10, B-9000, Ghent, Belgium
| | - Geert Trooskens
- Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Belgium, Coupure Links 653, B-9000, Ghent, Belgium
| | - Klaas Mensaert
- Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Belgium, Coupure Links 653, B-9000, Ghent, Belgium
| | - Katrien Poels
- Department of Public Health and Primary Care, Centre for Environment and Health, KU Leuven, Belgium, Kapucijnenvoer 35 blok d, box 7001, B-3000, Leuven, Belgium
| | - Nathalie Roche
- Department of Plastic and Reconstructive Surgery, Ghent University Hospital, Belgium, University Hospital 2K12 IC, De Pintelaan 185, B-9000, Ghent, Belgium
| | - Phillip Blondeel
- Department of Plastic and Reconstructive Surgery, Ghent University Hospital, Belgium, University Hospital 2K12 IC, De Pintelaan 185, B-9000, Ghent, Belgium
| | - Lode Godderis
- Department of Public Health and Primary Care, Centre for Environment and Health, KU Leuven, Belgium, Kapucijnenvoer 35 blok d, box 7001, B-3000, Leuven, Belgium
| | - Herman Depypere
- Department of Uro-Gynaecology, Ghent University Hospital, Belgium, Corneel Heymanslaan 10, P3, B-9000, Ghent, Belgium
| | - Tim De Meyer
- Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Belgium, Coupure Links 653, B-9000, Ghent, Belgium. .,Bioinformatics Institute Ghent: from Nucleotides 2 Networks (BIG-N2N), Ghent University, Belgium, Ghent University - VIB, Technologiepark 927, B-9052, Ghent, Belgium. .,Cancer Research Institute Ghent (CRIG), Ghent University (Hospital), Belgium, Ghent University Hospital MRB, Corneel Heymanslaan 10, B-9000, Ghent, Belgium.
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4
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Trooskens G, Yantisetiasti A, Hendriks R, Van Oort I, Mulders P, Hulsbergen-van de Kaa C, Van Criekinge W, Schalken J. MP46-11 EVALUATION OF TWO URINARY RNA BIOMARKER TESTS WITH AN EPIGENETIC DNA ASSAY FOR THE IDENTIFICATION OF MEN WITH HIGH-GRADE PROSTATE CANCER. J Urol 2018. [DOI: 10.1016/j.juro.2018.02.1470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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5
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Stewart GD, Powles T, Van Neste C, Meynert A, O'Mahony F, Laird A, Deforce D, Van Nieuwerburgh F, Trooskens G, Van Criekinge W, De Meyer T, Harrison DJ. Dynamic epigenetic changes to VHL occur with sunitinib in metastatic clear cell renal cancer. Oncotarget 2018; 7:25241-50. [PMID: 27029034 PMCID: PMC5041900 DOI: 10.18632/oncotarget.8308] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 03/10/2016] [Indexed: 11/25/2022] Open
Abstract
Background Genetic intratumoral heterogeneity (ITH) hinders biomarker development in metastatic clear cell renal cancer (mccRCC). Epigenetic relative to genetic ITH or the presence of consistent epigenetic changes following targeted therapy in mccRCC have not been evaluated. The aim of this study was to determine methylome/genetic ITH and to evaluate specific epigenetic and genetic changes associated with sunitinib therapy. Patients and methods Multi-region DNA sampling performed on sequential frozen pairs of primary tumor tissue from 14 metastatic ccRCC patients, in the Upfront Sunitinib (SU011248) Therapy Followed by Surgery in Patients with Metastatic Renal Cancer: a Pilot Phase II Study (SuMR; ClinicalTrials.gov identifier: NCT01024205), at presentation (biopsy) and after 3-cycles of 50mg sunitinib (nephrectomy). Untreated biopsy and nephrectomy samples before and after renal artery ligation were controls. Ion Proton sequencing of 48 key ccRCC genes, and MethylCap-seq DNA methylation analysis was performed, data was analysed using the statistical computing environment R. Results Unsupervised hierarchical clustering revealed complete methylome clustering of biopsy and three nephrectomy samples for each patient (14/14 patients). For mutational status, untreated biopsy and all treated nephrectomy samples clustered together in 8/13 (61.5%) patients. The only methylation target significantly altered following sunitinib therapy was VHL promoter region 7896829 which was hypermethylated with treatment (FDR=0.077, P<0.001) and consistent for all patients (pre-treatment 50% patients had VHL mutations, 14% patients VHL hypermethylation). Renal artery ligation did not affect this result. No significant differences in driver or private mutation count was found with sunitinib treatment. Conclusions Demonstration of relative methylome homogeneity and consistent VHL hypermethylation, after sunitinib, may overcome the hurdle of ITH present at other molecular levels for biomarker research.
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Affiliation(s)
- Grant D Stewart
- Edinburgh Urological Cancer Group, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.,Scottish Collaboration On Translational Research into Renal Cell Cancer (SCOTRRCC), Scotland, UK.,Academic Urology Group, University of Cambridge, Addenbrooke's Hospital, Cambridge Biomedical Campus, Cambridge, UK
| | - Thomas Powles
- Renal Cancer Unit, The Royal Free Hospital, London, UK.,Centre for Experimental Cancer Medicine, Bart's Cancer Institute, Queen Mary University of London, London, UK
| | - Christophe Van Neste
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Alison Meynert
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Fiach O'Mahony
- Edinburgh Urological Cancer Group, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.,Scottish Collaboration On Translational Research into Renal Cell Cancer (SCOTRRCC), Scotland, UK
| | - Alexander Laird
- Edinburgh Urological Cancer Group, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.,Scottish Collaboration On Translational Research into Renal Cell Cancer (SCOTRRCC), Scotland, UK.,MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Geert Trooskens
- Biobix: Laboratory of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium
| | - Wim Van Criekinge
- Biobix: Laboratory of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium
| | - Tim De Meyer
- Biobix: Laboratory of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium
| | - David J Harrison
- Scottish Collaboration On Translational Research into Renal Cell Cancer (SCOTRRCC), Scotland, UK.,School of Medicine, University of St Andrews, Fife, UK
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6
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Bosch LJW, Trooskens G, Snaebjornsson P, Coupé VMH, Mongera S, Haan JC, Richman SD, Koopman M, Tol J, de Meyer T, Louwagie J, Dehaspe L, van Grieken NCT, Ylstra B, Verheul HMW, van Engeland M, Nagtegaal ID, Herman JG, Quirke P, Seymour MT, Punt CJA, van Criekinge W, Carvalho B, Meijer GA. Decoy receptor 1 ( DCR1) promoter hypermethylation and response to irinotecan in metastatic colorectal cancer. Oncotarget 2017; 8:63140-63154. [PMID: 28968978 PMCID: PMC5609910 DOI: 10.18632/oncotarget.18702] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 05/23/2017] [Indexed: 12/11/2022] Open
Abstract
Diversity in colorectal cancer biology is associated with variable responses to standard chemotherapy. We aimed to identify and validate DNA hypermethylated genes as predictive biomarkers for irinotecan treatment of metastatic CRC patients. Candidate genes were selected from 389 genes involved in DNA Damage Repair by correlation analyses between gene methylation status and drug response in 32 cell lines. A large series of samples (n=818) from two phase III clinical trials was used to evaluate these candidate genes by correlating methylation status to progression-free survival after treatment with first-line single-agent fluorouracil (Capecitabine or 5-fluorouracil) or combination chemotherapy (Capecitabine or 5-fluorouracil plus irinotecan (CAPIRI/FOLFIRI)). In the discovery (n=185) and initial validation set (n=166), patients with methylated Decoy Receptor 1 (DCR1) did not benefit from CAPIRI over Capecitabine treatment (discovery set: HR=1.2 (95%CI 0.7-1.9, p=0.6), validation set: HR=0.9 (95%CI 0.6-1.4, p=0.5)), whereas patients with unmethylated DCR1 did (discovery set: HR=0.4 (95%CI 0.3-0.6, p=0.00001), validation set: HR=0.5 (95%CI 0.3-0.7, p=0.0008)). These results could not be replicated in the external data set (n=467), where a similar effect size was found in patients with methylated and unmethylated DCR1 for FOLFIRI over 5FU treatment (methylated DCR1: HR=0.7 (95%CI 0.5-0.9, p=0.01), unmethylated DCR1: HR=0.8 (95%CI 0.6-1.2, p=0.4)). In conclusion, DCR1 promoter hypermethylation status is a potential predictive biomarker for response to treatment with irinotecan, when combined with capecitabine. This finding could not be replicated in an external validation set, in which irinotecan was combined with 5FU. These results underline the challenge and importance of extensive clinical evaluation of candidate biomarkers in multiple trials.
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Affiliation(s)
- Linda J W Bosch
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands.,Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Geert Trooskens
- Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium
| | - Petur Snaebjornsson
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands.,Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Veerle M H Coupé
- Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, The Netherlands
| | - Sandra Mongera
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | - Josien C Haan
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | - Susan D Richman
- Pathology and Tumour Biology, University of Leeds, Leeds, UK
| | - Miriam Koopman
- Department of Medical Oncology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jolien Tol
- Department of Internal Medicine, Jeroen Bosch Hospital, 's-Hertogenbosch, The Netherlands
| | - Tim de Meyer
- Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium
| | | | - Luc Dehaspe
- MDxHealth, SA, Liège, Belgium.,Genomics Core Facility, UZ Leuven, Leuven, Belgium
| | | | - Bauke Ylstra
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | - Henk M W Verheul
- Department of Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Manon van Engeland
- Department of Pathology, GROW - School for Oncology and Developmental Biology and Maastricht University Medical Center, Maastricht, The Netherlands
| | - Iris D Nagtegaal
- Department of Pathology, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - James G Herman
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Philip Quirke
- Pathology and Tumour Biology, University of Leeds, Leeds, UK
| | - Matthew T Seymour
- St James's Institute of Oncology, St James's University Hospital, Leeds, UK
| | - Cornelis J A Punt
- Department of Medical Oncology, Academic Medical Center, Amsterdam, The Netherlands
| | - Wim van Criekinge
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands.,Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium.,MDxHealth, SA, Liège, Belgium
| | - Beatriz Carvalho
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands.,Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Gerrit A Meijer
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands.,Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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7
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Van Neste L, Hendriks RJ, Dijkstra S, Trooskens G, Cornel EB, Jannink SA, de Jong H, Hessels D, Smit FP, Melchers WJ, Leyten GH, de Reijke TM, Vergunst H, Kil P, Knipscheer BC, Hulsbergen-van de Kaa CA, Mulders PF, van Oort IM, Van Criekinge W, Schalken JA. Detection of High-grade Prostate Cancer Using a Urinary Molecular Biomarker–Based Risk Score. Eur Urol 2016; 70:740-748. [DOI: 10.1016/j.eururo.2016.04.012] [Citation(s) in RCA: 196] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 04/07/2016] [Indexed: 10/21/2022]
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8
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Bosch LJW, Luo Y, Lao VV, Snaebjornsson P, Trooskens G, Vlassenbroeck I, Mongera S, Tang W, Welcsh P, Herman JG, Koopman M, Nagtegaal ID, Punt CJA, van Criekinge W, Meijer GA, Monnat RJ, Carvalho B, Grady WM. WRN Promoter CpG Island Hypermethylation Does Not Predict More Favorable Outcomes for Patients with Metastatic Colorectal Cancer Treated with Irinotecan-Based Therapy. Clin Cancer Res 2016; 22:4612-22. [PMID: 27121793 DOI: 10.1158/1078-0432.ccr-15-2703] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 03/26/2016] [Indexed: 01/28/2023]
Abstract
PURPOSE WRN promoter CpG island hypermethylation in colorectal cancer has been reported to increase sensitivity to irinotecan-based therapies. We aimed to characterize methylation of the WRN promoter, determine the effect of WRN promoter hypermethylation upon expression, and validate a previous report that WRN promoter hypermethylation predicts improved outcomes for patients with metastatic colorectal cancer (mCRC) treated with irinotecan-based therapy. EXPERIMENTAL DESIGN WRN methylation status was assessed using methylation-specific PCR and bisulfite sequencing assays. WRN expression was determined using qRT-PCR and Western blotting. WRN methylation status was correlated with overall survival (OS) and progression-free survival (PFS) in 183 patients with mCRC. Among these patients, 90 received capecitabine monotherapy as first-line therapy, and 93 received capecitabine plus irinotecan (CAPIRI) therapy as part of the CAIRO phase III clinical trial. RESULTS WRN mRNA and WRN protein expression levels were low in colorectal cancer cell lines and in primary colorectal cancer and were largely independent of WRN methylation status. Patients with methylated WRN colorectal cancer had a shorter OS compared with patients who had unmethylated WRN colorectal cancer (HR = 1.6; 95% confidence interval [CI], 1.2-2.2; P = 0.003). Patients with unmethylated WRN showed a significantly longer PFS when treated with CAPIRI compared with capecitabine alone (HR = 0.48; 95% CI, 0.32-0.70; P = 0.0001). In contrast, patients did not benefit from adding irinotecan to capecitabine when WRN was methylated (HR = 1.1; 95% CI, 0.69-1.77; P = 0.7). CONCLUSIONS WRN expression is largely independent of WRN promoter hypermethylation in colorectal cancer. Moreover, we could not validate the previous finding that WRN promoter hypermethylation predicts improved clinical outcomes of mCRC treated with irinotecan-based therapy and found instead the opposite result. Clin Cancer Res; 22(18); 4612-22. ©2016 AACR.
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Affiliation(s)
- Linda J W Bosch
- Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands. Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Yanxin Luo
- Clinical Research Division, Department of Medicine, Fred Hutchinson Cancer Research Center, University of Washington, Seattle, Washington. Department of Colorectal Surgery, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Victoria V Lao
- Clinical Research Division, Department of Medicine, Fred Hutchinson Cancer Research Center, University of Washington, Seattle, Washington
| | - Petur Snaebjornsson
- Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands. Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Geert Trooskens
- Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium
| | | | - Sandra Mongera
- Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands
| | - Weiliang Tang
- Department of Pathology, University of Washington, Seattle Washington
| | - Piri Welcsh
- Department of Pathology, University of Washington, Seattle Washington
| | - James G Herman
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Miriam Koopman
- Department of Medical Oncology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Iris D Nagtegaal
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Cornelis J A Punt
- Department of Medical Oncology, Academic Medical Center, Amsterdam, the Netherlands
| | - Wim van Criekinge
- Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands. Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands. Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium. MDxHealth SA, Liège, Belgium
| | - Gerrit A Meijer
- Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands. Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Raymond J Monnat
- Department of Pathology, University of Washington, Seattle Washington. Department of Genome Sciences, University of Washington, Seattle, Washington
| | - Beatriz Carvalho
- Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands. Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands.
| | - William M Grady
- Clinical Research Division, Department of Medicine, Fred Hutchinson Cancer Research Center, University of Washington, Seattle, Washington.
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9
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Trivedi MS, Hodgson NW, Walker SJ, Trooskens G, Nair V, Deth RC. Epigenetic effects of casein-derived opioid peptides in SH-SY5Y human neuroblastoma cells. Nutr Metab (Lond) 2015; 12:54. [PMID: 26664459 PMCID: PMC4673759 DOI: 10.1186/s12986-015-0050-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Accepted: 12/03/2015] [Indexed: 12/18/2022] Open
Abstract
Background Casein-free, gluten-free diets have been reported to mitigate some of the inflammatory gastrointestinal and behavioral traits associated with autism, but the mechanism for this palliative effect has not been elucidated. We recently showed that the opioid peptide beta-casomorphin-7, derived from bovine (bBCM7) milk, decreases cysteine uptake, lowers levels of the antioxidant glutathione (GSH) and decreases the methyl donor S-adenosylmethionine (SAM) in both Caco-2 human GI epithelial cells and SH-SY5Y human neuroblastoma cells. While human breast milk can also release a similar peptide (hBCM-7), the bBCM7 and hBCM-7 vary greatly in potency; as the bBCM-7 is highly potent and similar to morphine in it's effects. Since SAM is required for DNA methylation, we wanted to further investigate the epigenetic effects of these food-derived opioid peptides. In the current study the main objective was to characterize functional pathways and key genes responding to DNA methylation effects of food-derived opioid peptides. Methods SH-SY5Y neuroblastoma cells were treated with 1 μM hBCM7 and bBCM7 and RNA and DNA were isolated after 4 h with or without treatment. Transcriptional changes were assessed using a microarray approach and CpG methylation status was analyzed at 450,000 CpG sites. Functional implications from both endpoints were evaluated via Ingenuity Pathway Analysis 4.0 and KEGG pathway analysis was performed to identify biological interactions between transcripts that were significantly altered at DNA methylation or transcriptional levels (p < 0.05, FDR <0.1). Results Here we show that hBCM7 and bBCM7, as well as morphine, cause epigenetic changes affecting gene pathways related to gastrointestinal disease and inflammation. These epigenetic consequences exhibited the same potency order as opiate inhibition of cysteine uptake insofar as hBCM7 was less potent than bBCM7, which was less potent than morphine. Conclusion Our findings indicate that epigenetic effects of milk-derived opiate peptides may contribute to GI dysfunction and inflammation in sensitive individuals. While the current study was performed using SH-SY5Y neuronal cellular models, similar actions on other cells types might combine to cause symptoms of intolerance. These actions may provide a potential contributing mechanism for the beneficial effects of a casein-free diet in alleviating gastrointestinal symptoms in neurological conditions including autism and other conditions. Lastly, our study also contributes to the evolving awareness of a “gut-brain connection”. Electronic supplementary material The online version of this article (doi:10.1186/s12986-015-0050-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Malav S Trivedi
- Department of Pharmaceutical Sciences, Nova Southeastern University, Rm # 3103, HPD building, Fort Lauderdale, FL USA
| | - Nathaniel W Hodgson
- Department of Molecular and Cellular Biology, Harvard Medical School, Boston, MA USA
| | - Stephen J Walker
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston Salem, NC USA
| | - Geert Trooskens
- Department of Mathematical Modelling, Statistics and Bioinformatics, University of Ghent, Ghent, Belgium
| | - Vineeth Nair
- Department of Pharmaceutical Sciences, Nova Southeastern University, Rm # 3103, HPD building, Fort Lauderdale, FL USA
| | - Richard C Deth
- Department of Pharmaceutical Sciences, Nova Southeastern University, Rm # 3103, HPD building, Fort Lauderdale, FL USA
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10
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Noehammer C, Pulverer W, Hassler MR, Hofner M, Wielscher M, Vierlinger K, Liloglou T, McCarthy D, Jensen TJ, Nygren A, Gohlke H, Trooskens G, Braspenning M, Van Criekinge W, Egger G, Weinhaeusel A. Strategies for validation and testing of DNA methylation biomarkers. Epigenomics 2015; 6:603-22. [PMID: 25531255 DOI: 10.2217/epi.14.43] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
DNA methylation is a stable covalent epigenetic modification of primarily CpG dinucleotides that has recently gained considerable attention for its use as a biomarker in different clinical settings, including disease diagnosis, prognosis and therapeutic response prediction. Although the advent of genome-wide DNA methylation profiling in primary disease tissue has provided a manifold resource for biomarker development, only a tiny fraction of DNA methylation-based assays have reached clinical testing. Here, we provide a critical overview of different analytical methods that are suitable for biomarker validation, including general study design considerations, which might help to streamline epigenetic marker development. Furthermore, we highlight some of the recent marker validation studies and established markers that are currently commercially available for assisting in clinical management of different cancers.
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Affiliation(s)
- Christa Noehammer
- Health & Environment Department, Molecular Diagnostics, AIT Austrian Institute of Technology, Vienna, Austria
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11
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Stewart G, Van Neste C, Meynert A, Semple C, O'Mahony F, Laird A, Mackay A, Trooskens G, Van Criekinge W, De Meyer T, Powles T, Harrison DJ. Effect of sunitinib treatment on mutations and methylation in metastatic renal cancer. J Clin Oncol 2015. [DOI: 10.1200/jco.2015.33.7_suppl.492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
492 Background: The effect of VEGF targeted agents on DNA mutations and epigenetic expression in metastatic clear cell renal cancer (mccRCC) has not been reported. We hypothesise that significant DNA mutations and methylation changes occur with treatment which may be associated with resistance. Methods: DNA was extracted from sequential frozen pairs of primary tumour tissue from 14 mccRCC patients, in the SuMR clinical trial (NCT01024205), at presentation (biopsy) and after 3-cycles of sunitinib (nephrectomy). Multiple biopsies were taken to assess for heterogeneity. Biopsy and nephrectomy samples were compared in untreated tumours as controls. Array CGH, Ion Torrent sequencing (48 key ccRCC genes were assessed [Table]), and methylCap-seq DNA methylation analysis were performed. Results: aCGH hierarchical clustering showed that samples from 2/14 patients clustered together (13%). There were no significant increase in copy number variations (CNVs) following treatment with sunitinib. For somatic mutations of the 48 key genes, there were no patients in whom all samples clustered together. Conversely, at methylation level, all samples for each patient clustered. Mean frequency of mutations in the key genes relative to normal kidney was identical for biopsy and nephrectomy samples (n=14 mutations). 12/48 genes had CNVs or mutations in ≥2 patients following treatment with sunitinib (table). VHL was the only gene with significant difference in methylation pre- and post-sunitinib therapy (FDR=0.077; logFC=-0.8734, hypermethylated following sunitinib therapy); there was no difference in VHL methylation pre- and post-renal artery clamping. Conclusions: Intratumoral heterogeneity was not apparent in DNA methylation, unlike DNA. This may facilitate in biomarker research. The significant increase in VHL methylation following sunitinib gives insight into possible mechanisms of resistance at an epigenetic level. [Table: see text]
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Affiliation(s)
| | | | | | - Colin Semple
- University of Edinburgh, Edinburgh, United Kingdom
| | | | | | - Alan Mackay
- The Institute of Cancer Research, The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Geert Trooskens
- Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium
| | | | | | - Thomas Powles
- Barts Cancer Institute, Barts Health and the Royal Free NHS Trust, London, United Kingdom
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12
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Sante T, Vergult S, Volders PJ, Kloosterman WP, Trooskens G, De Preter K, Dheedene A, Speleman F, De Meyer T, Menten B. ViVar: a comprehensive platform for the analysis and visualization of structural genomic variation. PLoS One 2014; 9:e113800. [PMID: 25503062 PMCID: PMC4264741 DOI: 10.1371/journal.pone.0113800] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 10/20/2014] [Indexed: 01/06/2023] Open
Abstract
Structural genomic variations play an important role in human disease and phenotypic diversity. With the rise of high-throughput sequencing tools, mate-pair/paired-end/single-read sequencing has become an important technique for the detection and exploration of structural variation. Several analysis tools exist to handle different parts and aspects of such sequencing based structural variation analyses pipelines. A comprehensive analysis platform to handle all steps, from processing the sequencing data, to the discovery and visualization of structural variants, is missing. The ViVar platform is built to handle the discovery of structural variants, from Depth Of Coverage analysis, aberrant read pair clustering to split read analysis. ViVar provides you with powerful visualization options, enables easy reporting of results and better usability and data management. The platform facilitates the processing, analysis and visualization, of structural variation based on massive parallel sequencing data, enabling the rapid identification of disease loci or genes. ViVar allows you to scale your analysis with your work load over multiple (cloud) servers, has user access control to keep your data safe and is easy expandable as analysis techniques advance. URL: https://www.cmgg.be/vivar/
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Affiliation(s)
- Tom Sante
- Center for Medical Genetics, Faculty of Medicine and Health Sciences, Ghent University, Gent, Belgium
| | - Sarah Vergult
- Center for Medical Genetics, Faculty of Medicine and Health Sciences, Ghent University, Gent, Belgium
| | - Pieter-Jan Volders
- Center for Medical Genetics, Faculty of Medicine and Health Sciences, Ghent University, Gent, Belgium
| | - Wigard P. Kloosterman
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Geert Trooskens
- BioBix, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Katleen De Preter
- Center for Medical Genetics, Faculty of Medicine and Health Sciences, Ghent University, Gent, Belgium
| | - Annelies Dheedene
- Center for Medical Genetics, Faculty of Medicine and Health Sciences, Ghent University, Gent, Belgium
| | - Frank Speleman
- Center for Medical Genetics, Faculty of Medicine and Health Sciences, Ghent University, Gent, Belgium
| | - Tim De Meyer
- BioBix, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Björn Menten
- Center for Medical Genetics, Faculty of Medicine and Health Sciences, Ghent University, Gent, Belgium
- * E-mail:
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13
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Steyaert S, Van Criekinge W, De Paepe A, Denil S, Mensaert K, Vandepitte K, Vanden Berghe W, Trooskens G, De Meyer T. SNP-guided identification of monoallelic DNA-methylation events from enrichment-based sequencing data. Nucleic Acids Res 2014; 42:e157. [PMID: 25237057 PMCID: PMC4227762 DOI: 10.1093/nar/gku847] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Monoallelic gene expression is typically initiated early in the development of an organism. Dysregulation of monoallelic gene expression has already been linked to several non-Mendelian inherited genetic disorders. In humans, DNA-methylation is deemed to be an important regulator of monoallelic gene expression, but only few examples are known. One important reason is that current, cost-affordable truly genome-wide methods to assess DNA-methylation are based on sequencing post-enrichment. Here, we present a new methodology based on classical population genetic theory, i.e. the Hardy–Weinberg theorem, that combines methylomic data from MethylCap-seq with associated SNP profiles to identify monoallelically methylated loci. Applied on 334 MethylCap-seq samples of very diverse origin, this resulted in the identification of 80 genomic regions featured by monoallelic DNA-methylation. Of these 80 loci, 49 are located in genic regions of which 25 have already been linked to imprinting. Further analysis revealed statistically significant enrichment of these loci in promoter regions, further establishing the relevance and usefulness of the method. Additional validation was done using both 14 whole-genome bisulfite sequencing data sets and 16 mRNA-seq data sets. Importantly, the developed approach can be easily applied to other enrichment-based sequencing technologies, like the ChIP-seq-based identification of monoallelic histone modifications.
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Affiliation(s)
- Sandra Steyaert
- Department of Mathematical Modelling, Statistics and Bioinformatics, University of Ghent, Ghent 9000, Belgium
| | - Wim Van Criekinge
- Department of Mathematical Modelling, Statistics and Bioinformatics, University of Ghent, Ghent 9000, Belgium
| | - Ayla De Paepe
- Department of Mathematical Modelling, Statistics and Bioinformatics, University of Ghent, Ghent 9000, Belgium
| | - Simon Denil
- Department of Mathematical Modelling, Statistics and Bioinformatics, University of Ghent, Ghent 9000, Belgium
| | - Klaas Mensaert
- Department of Mathematical Modelling, Statistics and Bioinformatics, University of Ghent, Ghent 9000, Belgium
| | | | - Wim Vanden Berghe
- PPES, Department of Biomedical Sciences, University of Antwerp, Wilrijk 2610, Belgium
| | - Geert Trooskens
- Department of Mathematical Modelling, Statistics and Bioinformatics, University of Ghent, Ghent 9000, Belgium
| | - Tim De Meyer
- Department of Mathematical Modelling, Statistics and Bioinformatics, University of Ghent, Ghent 9000, Belgium
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14
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Mensaert K, Denil S, Trooskens G, Van Criekinge W, Thas O, De Meyer T. Next-generation technologies and data analytical approaches for epigenomics. Environ Mol Mutagen 2014; 55:155-70. [PMID: 24327356 DOI: 10.1002/em.21841] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 11/27/2013] [Accepted: 11/27/2013] [Indexed: 05/18/2023]
Abstract
Epigenetics refers to the collection of heritable features that modulate the genome-environment interaction without being encoded in the actual DNA sequence. While being mitotically and sometimes even meiotically transmitted, epigenetic traits often demonstrate extensive flexibility. This allows cells to acquire diverse gene expression patterns during differentiation, but also to adapt to a changing environment. However, epigenetic alterations are not always beneficial to the organism, as they are, for example, frequently identified in human diseases such as cancer. Accurate and cost-efficient genome-scale profiling of epigenetic features is thus of major importance to pinpoint these "epimutations," for example, to monitor the epigenetic impact of environmental exposure. Over the last decade, the field of epigenetics has been revolutionized by several innovative "epigenomics" technologies exactly addressing this need. In this review, we discuss and compare widely used next-generation methods to assess DNA methylation and hydroxymethylation, noncoding RNA expression, histone modifications, and nucleosome positioning. Although recent methods are typically based on "second-generation" sequencing, we also pay attention to still commonly used array- and PCR-based methods, and look forward to the additional advantages of single-molecule sequencing. As the current bottleneck in epigenomics research is the analysis rather than generation of data, the basic difficulties and problem-solving strategies regarding data preprocessing and statistical analysis are introduced for the different technologies. Finally, we also consider the complications associated with epigenomic studies of species with yet unsequenced genomes and possible solutions.
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Affiliation(s)
- Klaas Mensaert
- Department of Mathematical Modelling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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15
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Pérez-Novo CA, Zhang Y, Denil S, Trooskens G, De Meyer T, Van Criekinge W, Van Cauwenberge P, Zhang L, Bachert C. Staphylococcal enterotoxin B influences the DNA methylation pattern in nasal polyp tissue: a preliminary study. Allergy Asthma Clin Immunol 2013; 9:48. [PMID: 24341752 PMCID: PMC3867657 DOI: 10.1186/1710-1492-9-48] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 12/09/2013] [Indexed: 01/08/2023] Open
Abstract
Staphylococcal enterotoxins may influence the pro-inflammatory pattern of chronic sinus diseases via epigenetic events. This work intended to investigate the potential of staphylococcal enterotoxin B (SEB) to induce changes in the DNA methylation pattern. Nasal polyp tissue explants were cultured in the presence and absence of SEB; genomic DNA was then isolated and used for whole genome methylation analysis. Results showed that SEB stimulation altered the methylation pattern of gene regions when compared with non stimulated tissue. Data enrichment analysis highlighted two genes: the IKBKB and STAT-5B, both playing a crucial role in T- cell maturation/activation and immune response.
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Affiliation(s)
- Claudina A Pérez-Novo
- Upper Airways Research Laboratory, Department of Otorhinolaryngology, Ghent University Hospital, De Pintelaan 185, Ghent B-9000, Belgium
| | - Yuan Zhang
- Department of Otolaryngology, Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, PR China.,Key Laboratory of Otolaryngology, Head and Neck Surgery (Ministry of Education of China), Beijing Institute of Otorhinolaryngology, Beijing 100005, PR China
| | - Simon Denil
- Department of Mathematical Modelling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Geert Trooskens
- Department of Mathematical Modelling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Tim De Meyer
- Department of Mathematical Modelling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Wim Van Criekinge
- Department of Mathematical Modelling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Paul Van Cauwenberge
- Upper Airways Research Laboratory, Department of Otorhinolaryngology, Ghent University Hospital, De Pintelaan 185, Ghent B-9000, Belgium
| | - Luo Zhang
- Department of Otolaryngology, Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, PR China
| | - Claus Bachert
- Upper Airways Research Laboratory, Department of Otorhinolaryngology, Ghent University Hospital, De Pintelaan 185, Ghent B-9000, Belgium.,Karolinska Institutet, Division of ENT Diseases, CLINTEC, Stockholm, Sweden
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16
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Ji H, Gheysen G, Denil S, Lindsey K, Topping JF, Nahar K, Haegeman A, De Vos WH, Trooskens G, Van Criekinge W, De Meyer T, Kyndt T. Transcriptional analysis through RNA sequencing of giant cells induced by Meloidogyne graminicola in rice roots. J Exp Bot 2013; 64:3885-98. [PMID: 23881398 PMCID: PMC3745741 DOI: 10.1093/jxb/ert219] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
One of the reasons for the progressive yield decline observed in aerobic rice production is the rapid build-up of populations of the rice root knot nematode Meloidogyne graminicola. These nematodes induce specialized feeding cells inside root tissue, called giant cells. By injecting effectors in and sipping metabolites out of these cells, they reprogramme normal cell development and deprive the plant of its nutrients. In this research we have studied the transcriptome of giant cells in rice, after isolation of these cells by laser-capture microdissection. The expression profiles revealed a general induction of primary metabolism inside the giant cells. Although the roots were shielded from light induction, we detected a remarkable induction of genes involved in chloroplast biogenesis and tetrapyrrole synthesis. The presence of chloroplast-like structures inside these dark-grown cells was confirmed by confocal microscopy. On the other hand, genes involved in secondary metabolism and more specifically, the majority of defence-related genes were strongly suppressed in the giant cells. In addition, significant induction of transcripts involved in epigenetic processes was detected inside these cells 7 days after infection.
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Affiliation(s)
- Hongli Ji
- Department of Molecular Biotechnology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Godelieve Gheysen
- Department of Molecular Biotechnology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
- * To whom correspondence should be addressed. E-mail:
| | - Simon Denil
- Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Keith Lindsey
- School of Biological and Biomedical Sciences, Durham University, South Road, Durham DH1 3LE, UK
| | - Jennifer F. Topping
- School of Biological and Biomedical Sciences, Durham University, South Road, Durham DH1 3LE, UK
| | - Kamrun Nahar
- Department of Molecular Biotechnology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Annelies Haegeman
- Department of Molecular Biotechnology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Winnok H. De Vos
- Department of Molecular Biotechnology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
- Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Geert Trooskens
- Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Wim Van Criekinge
- Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
- NXTGNT, Ghent University, Medical Research Building, Ghent University Hospital, De Pintelaan 185, B-9000 Ghent, Belgium
| | - Tim De Meyer
- Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Tina Kyndt
- Department of Molecular Biotechnology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
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17
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Steenbergen RDM, Ongenaert M, Snellenberg S, Trooskens G, van der Meide WF, Pandey D, Bloushtain-Qimron N, Polyak K, Meijer CJLM, Snijders PJF, Van Criekinge W. Methylation-specific digital karyotyping of HPV16E6E7-expressing human keratinocytes identifies novel methylation events in cervical carcinogenesis. J Pathol 2013; 231:53-62. [DOI: 10.1002/path.4210] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Revised: 04/17/2013] [Accepted: 05/07/2013] [Indexed: 12/12/2022]
Affiliation(s)
| | - Maté Ongenaert
- BioBix, Department of Mathematical Modelling, Statistics and Bioinformatics; Ghent University; Belgium
- Centre for Medical Genetics; Ghent University; Belgium
| | - Suzanne Snellenberg
- Department of Pathology; VU University Medical Centre; Amsterdam The Netherlands
| | - Geert Trooskens
- BioBix, Department of Mathematical Modelling, Statistics and Bioinformatics; Ghent University; Belgium
| | | | - Deeksha Pandey
- Department of Pathology; VU University Medical Centre; Amsterdam The Netherlands
| | - Noga Bloushtain-Qimron
- Department of Medical Oncology; Dana-Farber Cancer Institute, Harvard Medical School; Boston MA USA
| | - Kornelia Polyak
- Department of Medical Oncology; Dana-Farber Cancer Institute, Harvard Medical School; Boston MA USA
| | - Chris JLM Meijer
- Department of Pathology; VU University Medical Centre; Amsterdam The Netherlands
| | - Peter JF Snijders
- Department of Pathology; VU University Medical Centre; Amsterdam The Netherlands
| | - Wim Van Criekinge
- BioBix, Department of Mathematical Modelling, Statistics and Bioinformatics; Ghent University; Belgium
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18
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Van Criekinge W, Bosch LJW, Trooskens G, Snaebjornsson P, Haan J, Pelosof LC, Koopman M, Tol J, Louwagie J, Dehaspe L, van Grieken NC, Ylstra B, Verheul HM, van Engeland M, Nagtegaal ID, Herman JG, Punt CJA, Carvalho B, Meijer GA. Association of DNA promoter hypermethylation of decoy receptor 1 (DCR1) with poor response to irinotecan in metastatic colorectal cancer. J Clin Oncol 2013. [DOI: 10.1200/jco.2013.31.15_suppl.3552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
3552 Background: Heterogeneity in the biology of colorectal cancer (CRC) is associated with variable responses to standard chemotherapy. We aimed to identify DNA hypermethylated genes as predictive biomarkers for irinotecan treatment of patients with metastatic CRC. Methods: The presence of DNA methylation for a selected panel of 22 genes was assessed by methylation specific PCR (MSP) on primary tumors of 185 patients with metastatic CRC treated with first-line capecitabine (CAP, n=90) or a combination of capecitabine and irinotecan (CAPIRI, n=95) in the phase 3 CAIRO trial. Methylation status of each gene was correlated to progression free survival (PFS) by treatment regimen. Genes for which methylation status associated with response to irinotecan, were validated in 166 patients treated with first-line CAP (n=78) or CAPIRI (n=88). Results: Decoy Receptor 1 (DCR1) was identified as a novel hypermethylated gene in CRC. In CAPIRI treated patients, DCR1 methylation was correlated to a shorter PFS compared to patients with unmethylated DCR1 (hazard ratio [HR]=0.4 (95%CI =0.3-0.7), p = 0.0009). In patients with methylated DCR1 PFS did not improve with CAPIRI treatment, compared to treatment with CAP (discovery set: HR=0.8 (95%CI=0.5-1.3, p=0.4); validation set: HR=1.1 (95%CI 0.7-1.7, p=0.6)), in contrast to patients with unmethylated DCR1 (discovery set: HR=2.5 (95%CI 1.7-3.3, p=0.00004); validation set: HR=1.7 (95%CI 1.1-2.0, p=0.004)). Conclusions: CRC patients with methylated DCR1 did not benefit from adding irinotecan to capecitabine therapy, indicating that DCR1 methylation status may guide selecting metastatic CRC patients for irinotecan-based therapy.
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Affiliation(s)
| | - Linda JW Bosch
- DNA promoter hypermethylation of Decoy Receptor 1 (DCR1) is associated with poor response to irinotecan in metastatic colorectal cancer, Amsterdam, Netherlands
| | - Geert Trooskens
- Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium, Gent, Belgium
| | - Petur Snaebjornsson
- Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands, Amsterdam, Netherlands
| | - Josien Haan
- Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands, Amsterdam, Netherlands
| | | | | | - Jolien Tol
- Radboud University Medical Centre, Nijmegen, Netherlands
| | | | | | | | - Bauke Ylstra
- Department of Pathology, VU University Medical Center, Amsterdam, Netherlands
| | - Henk M.W. Verheul
- Department of Medical Oncology, VU University Medical Center, Amsterdam, Netherlands
| | - Manon van Engeland
- Department of Pathology, GROW - School for Oncology and Developmental Biology and Maastricht University Medical Center, Maastricht, the Netherlands, Maastricht, Netherlands
| | | | | | | | - Beatriz Carvalho
- Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands, Amsterdam, Netherlands
| | - Gerrit A. Meijer
- Department of Pathology, VU University Medical Center, Amsterdam, Netherlands
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19
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De Meyer T, Trooskens G, Wibbe MK, Bartmann SB, van Engeland M, Van Criekinge W, Tjan-Heijnen VC, Knüchel R, Veeck J. Abstract 3458: An epigenomic next-generation sequencing approach to identify predictive markers for PARP inhibitor response in breast cancer cells. Cancer Res 2013. [DOI: 10.1158/1538-7445.am2013-3458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Inhibition of poly(ADP-ribose)-polymerase-1 (PARP1) leads to synthetic lethality in BRCA-associated breast cancer cells, and is a promising novel treatment strategy for hereditary BRCA-mutated tumors. Since BRCA1/2 germline mutations are relatively infrequent, our study aims at a systematic identification of epigenetic aberrations that may predict PARP inhibitor (PARib) response in sporadic breast cancer cells.
Methods: Genome-wide DNA methylation was assessed in nine malignant and one non-malignant (MCF10A) breast cell line (BCL) by MBD-isolated genome sequencing (MiGS). Sensitivity to the PARib AG14361 was determined by viability and clonogenicity assays before and after global DNA demethylation in vitro, and confirmed with the PARib AZD-2281 (olaparib). Correlation analyses of DNA methylation with PARib sensitivity identified potentially predictive candidate genes and microRNAs. By incubation with increasing concentrations of AG14361 we generated an isogenic PARib resistant BCL originally sensitive to AG14361.
Results: BCL clustered in three sensitivity groups (sensitive, intermediate, resistant) independent of hormone receptor status, but associated with PARP1 level (p=0.042). BRCA1 mutated (MDA-MB-436) and BRCA1 methylated (UACC3199) BCL were most sensitive to PARib. After global DNA demethylation sensitive BCL acquired resistance while resistant BCL were modestly sensitized. MCF10A cells did not shift PARib resistance after DNA demethylation. Correlation of MiGS profiles with PARib sensitivity identified 382 genes and seven microRNAs with exclusive promoter/exon1 methylation in sensitive BCL, while 313 genes and one microRNA were affected in resistant BCL. Artificially mediating resistance to BRCA1 methylated cells did neither hypomethylate the BRCA1 promoter nor induce BRCA1 expression, but significantly reduce cell proliferation. Gene ontology analyses revealed that methylation of WNT, ErbB, SHH, and mTOR signaling genes was significantly enriched in PARib resistant cells, while PARib sensitive cells exhibited methylation in DNA repair genes.
Conclusions: Aberrant DNA methylation seems to be involved in PARib sensitivity/resistance in BCL. By epigenomic analyses we identified several potential candidate genes beyond BRCA1 that might modulate PARib sensitivity/resistance in breast cancer, implying that more patients than currently anticipated may benefit from this drug class. Their expression, DNA methylation and net effect on cancer pathways are currently validated in BCL and explored in primary breast cancer tissues.
Citation Format: Tim De Meyer, Geert Trooskens, Mascha K. Wibbe, Sebastian B. Bartmann, Manon van Engeland, Wim Van Criekinge, Vivianne C. Tjan-Heijnen, Ruth Knüchel, Jürgen Veeck. An epigenomic next-generation sequencing approach to identify predictive markers for PARP inhibitor response in breast cancer cells. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3458. doi:10.1158/1538-7445.AM2013-3458
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Affiliation(s)
- Tim De Meyer
- 1Gent University, Department of Mathematical Modelling, Gent, Belgium
| | - Geert Trooskens
- 1Gent University, Department of Mathematical Modelling, Gent, Belgium
| | - Mascha K. Wibbe
- 2RWTH Aachen University Hospital, Institute of Pathology, Aachen, Germany
| | | | - Manon van Engeland
- 3Maastricht University Medical Centre, Department of Pathology, Maastricht, Netherlands
| | - Wim Van Criekinge
- 1Gent University, Department of Mathematical Modelling, Gent, Belgium
| | | | - Ruth Knüchel
- 2RWTH Aachen University Hospital, Institute of Pathology, Aachen, Germany
| | - Jürgen Veeck
- 2RWTH Aachen University Hospital, Institute of Pathology, Aachen, Germany
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Bosch LJW, Trooskens G, Snaebjornsson P, Haan JC, Pelosof L, Koopman M, Tol J, Louwagie J, Dehaspe L, Ylstra B, Verheul H, van Engeland M, Nagtegaal ID, Herman JG, Punt CJA, van Criekinge W, Carvalho B, Meijer GA. Abstract 1155: Promoter CpG island hypermethylation of Decoy Receptor 1 (DCR1) is associated with poor response to irinotecan in colorectal cancer. Cancer Res 2013. [DOI: 10.1158/1538-7445.am2013-1155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background
Heterogeneity in the biology of colorectal cancer (CRC) is associated with variable responses to standard chemotherapy. We aimed to identify DNA hypermethylated genes as predictive biomarkers for irinotecan treatment of patients with metastatic CRC.
Material and Methods
The presence of DNA methylation for a selected panel of 22 genes was assessed by methylation specific PCR (MSP) on primary tumors of 185 patients with metastatic CRC treated with first-line capecitabine (CAP, n=90) or a combination of capecitabine and irinotecan (CAPIRI, n=95) in the phase III CAIRO trial. Methylation status of each gene was correlated to progression free survival (PFS) by treatment regimen. Genes for which methylation status associated with response to irinotecan, were validated in 166 patients treated with first-line CAP (n=78) or CAPIRI (n=88).
Results
Decoy Receptor 1 (DCR1) was identified as a novel hypermethylated gene in CRC. In CAPIRI treated patients, DCR1 methylation was correlated to a shorter PFS compared to patients with unmethylated DCR1 (hazard ratio [HR]=0.4 (95%CI =0.3-0.7), p = 0.0009). In patients with methylated DCR1 PFS did not improve with CAPIRI treatment, compared to treatment with CAP (discovery set: HR=0.8 (95%CI=0.5-1.3, p=0.4); validation set: HR=1.1 (95%CI 0.7-1.7, p=0.6)), in contrast to patients with unmethylated DCR1 (discovery set: HR=2.5 (95%CI 1.7-3.3, p=0.00004); validation set: HR=1.7 (95%CI 1.1-2.0, p=0.004)).
Conclusion
CRC patients with methylated DCR1 did not benefit from adding irinotecan to capecitabine therapy, indicating that DCR1 methylation status may guide selecting metastatic CRC patients for irinotecan-based therapy.
Citation Format: Linda JW Bosch, Geert Trooskens, Petur Snaebjornsson, Josien C. Haan, Lorraine Pelosof, Miriam Koopman, Jolien Tol, Joost Louwagie, Luc Dehaspe, Bauke Ylstra, Henk Verheul, Manon van Engeland, Iris D. Nagtegaal, James G. Herman, Cornelis JA Punt, Wim van Criekinge, Beatriz Carvalho, Gerrit A. Meijer. Promoter CpG island hypermethylation of Decoy Receptor 1 (DCR1) is associated with poor response to irinotecan in colorectal cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1155. doi:10.1158/1538-7445.AM2013-1155
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Affiliation(s)
| | | | | | | | - Lorraine Pelosof
- 3Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | | | | | | | | | - Bauke Ylstra
- 1VU University Medical center, Amsterdam, Netherlands
| | - Henk Verheul
- 1VU University Medical center, Amsterdam, Netherlands
| | - Manon van Engeland
- 8GROW - School for Oncology and Developmental Biology and Maastricht University Medical Center, Maastricht, Netherlands
| | | | - James G. Herman
- 3Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
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21
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Dehan P, Canon C, Trooskens G, Rehli M, Munaut C, Van Criekinge W, Delvenne P. Expression of type 2 orexin receptor in human endometrium and its epigenetic silencing in endometrial cancer. J Clin Endocrinol Metab 2013; 98:1549-57. [PMID: 23482607 DOI: 10.1210/jc.2012-3263] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
CONTEXT Orexins A and B are neuropeptides that bind and activate 2 types of receptors. In addition to direct action in the brain, the orexinergic system has broader implications in peripheral organs, and it has been proposed to have a role in the induction of apoptosis. There are very few data on the endometrium. OBJECTIVE The expression and epigenetic regulation of type 2 orexin receptor (OX2R) was investigated in the human endometrium as well as in endometrial endometrioid carcinoma (EEC). METHODS OX2R localization was studied by immunohistochemistry in normal endometrium (n = 24) and in EEC (n = 32). The DNA methylation status of a CpG island located in the first exon of OX2R was analyzed by bisulfite sequencing in normal (n = 18), EEC (n = 34), and 3 endometrial cell lines. On the latter, mRNA expression and Western blotting as well as in vitro induction with orexin were performed. RESULTS Expression of the OX2R protein was detected in normal endometrial epithelia, whereas it was frequently lacking in EEC. This loss was associated with hypermethylation of OX2R in EEC in comparison with normal endometrium (median CpG methylation percentages of 48.85% and 5.85%, respectively). In cell lines, hypermethylation correlated with weak OX2R expression. Additionally, in vitro treatment of the 3 EEC cell lines with orexins A and B did not result in proliferation change CONCLUSIONS Altogether our data provide evidence for the epigenetic silencing of OX2R in EEC. The implication of the OX2R loss in tumoral progression remains to be elucidated.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Carcinoma, Endometrioid/genetics
- Carcinoma, Endometrioid/metabolism
- Carcinoma, Endometrioid/pathology
- Case-Control Studies
- Cell Line, Tumor
- Endometrial Neoplasms/genetics
- Endometrial Neoplasms/metabolism
- Endometrial Neoplasms/pathology
- Endometrium/metabolism
- Endometrium/pathology
- Epigenesis, Genetic/physiology
- Female
- Gene Expression
- Gene Expression Regulation, Neoplastic
- Gene Silencing/physiology
- Humans
- Middle Aged
- Orexin Receptors
- Receptors, G-Protein-Coupled/genetics
- Receptors, G-Protein-Coupled/metabolism
- Receptors, Neuropeptide/genetics
- Receptors, Neuropeptide/metabolism
- Validation Studies as Topic
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Affiliation(s)
- P Dehan
- Department of Experimental Pathology, University of Liège, Tour de Pathologie (B23 + 4), Boulevard de l'Hôpital 1, B 4000 Liege Belgium.
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22
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De Meyer T, Mampaey E, Vlemmix M, Denil S, Trooskens G, Renard JP, De Keulenaer S, Dehan P, Menschaert G, Van Criekinge W. Quality evaluation of methyl binding domain based kits for enrichment DNA-methylation sequencing. PLoS One 2013; 8:e59068. [PMID: 23554971 PMCID: PMC3598902 DOI: 10.1371/journal.pone.0059068] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Accepted: 01/23/2013] [Indexed: 12/18/2022] Open
Abstract
DNA-methylation is an important epigenetic feature in health and disease. Methylated sequence capturing by Methyl Binding Domain (MBD) based enrichment followed by second-generation sequencing provides the best combination of sensitivity and cost-efficiency for genome-wide DNA-methylation profiling. However, existing implementations are numerous, and quality control and optimization require expensive external validation. Therefore, this study has two aims: 1) to identify a best performing kit for MBD-based enrichment using independent validation data, and 2) to evaluate whether quality evaluation can also be performed solely based on the characteristics of the generated sequences. Five commercially available kits for MBD enrichment were combined with Illumina GAIIx sequencing for three cell lines (HCT15, DU145, PC3). Reduced representation bisulfite sequencing data (all three cell lines) and publicly available Illumina Infinium BeadChip data (DU145 and PC3) were used for benchmarking. Consistent large-scale differences in yield, sensitivity and specificity between the different kits could be identified, with Diagenode's MethylCap kit as overall best performing kit under the tested conditions. This kit could also be identified with the Fragment CpG-plot, which summarizes the CpG content of the captured fragments, implying that the latter can be used as a tool to monitor data quality. In conclusion, there are major quality differences between kits for MBD-based capturing of methylated DNA, with the MethylCap kit performing best under the used settings. The Fragment CpG-plot is able to monitor data quality based on inherent sequence data characteristics, and is therefore a cost-efficient tool for experimental optimization, but also to monitor quality throughout routine applications.
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Affiliation(s)
- Tim De Meyer
- Department of Mathematical Modelling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.
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23
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Kyndt T, Denil S, Haegeman A, Trooskens G, Bauters L, Van Criekinge W, De Meyer T, Gheysen G. Transcriptional reprogramming by root knot and migratory nematode infection in rice. New Phytol 2012; 196:887-900. [PMID: 22985291 DOI: 10.1111/j.1469-8137.2012.04311.x] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 07/27/2012] [Indexed: 05/20/2023]
Abstract
Rice is one of the most important staple crops worldwide, but its yield is compromised by different pathogens, including plant-parasitic nematodes. In this study we have characterized specific and general responses of rice (Oryza sativa) roots challenged with two endoparasitic nematodes with very different modes of action. Local transcriptional changes in rice roots upon root knot (Meloidogyne graminicola) and root rot nematode (RRN, Hirschmanniella oryzae) infection were studied at two time points (3 and 7 d after infection, dai), using mRNA-seq. Our results confirm that root knot nematodes (RKNs), which feed as sedentary endoparasites, stimulate metabolic pathways in the root, and enhance nutrient transport towards the induced root gall. The migratory RRNs, on the other hand, induce programmed cell death and oxidative stress, and obstruct the normal metabolic activity of the root. While RRN infection causes up-regulation of biotic stress-related genes early in the infection, the sedentary RKNs suppress the local defense pathways (e.g. salicylic acid and ethylene pathways). Interestingly, hormone pathways mainly involved in plant development were strongly induced (gibberellin) or repressed (cytokinin) at 3 dai. These results uncover previously unrecognized nematode-induced expression profiles related to their specific infection strategy.
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Affiliation(s)
- Tina Kyndt
- Department of Molecular Biotechnology, Ghent University (UGent), Coupure Links 653, B-9000, Ghent, Belgium
| | - Simon Denil
- Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University (UGent), Coupure Links 653, B-9000, Ghent, Belgium
| | - Annelies Haegeman
- Department of Molecular Biotechnology, Ghent University (UGent), Coupure Links 653, B-9000, Ghent, Belgium
| | - Geert Trooskens
- Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University (UGent), Coupure Links 653, B-9000, Ghent, Belgium
| | - Lander Bauters
- Department of Molecular Biotechnology, Ghent University (UGent), Coupure Links 653, B-9000, Ghent, Belgium
| | - Wim Van Criekinge
- Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University (UGent), Coupure Links 653, B-9000, Ghent, Belgium
- NXTGNT, Ghent University, Medical Research Building, Ghent University Hospital, De Pintelaan 185, B-9000, Ghent, Belgium
| | - Tim De Meyer
- Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University (UGent), Coupure Links 653, B-9000, Ghent, Belgium
| | - Godelieve Gheysen
- Department of Molecular Biotechnology, Ghent University (UGent), Coupure Links 653, B-9000, Ghent, Belgium
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24
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Hamshou M, Van Damme EJM, Vandenborre G, Ghesquière B, Trooskens G, Gevaert K, Smagghe G. GalNAc/Gal-binding Rhizoctonia solani agglutinin has antiproliferative activity in Drosophila melanogaster S2 cells via MAPK and JAK/STAT signaling. PLoS One 2012; 7:e33680. [PMID: 22529896 PMCID: PMC3329507 DOI: 10.1371/journal.pone.0033680] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Accepted: 02/15/2012] [Indexed: 12/16/2022] Open
Abstract
Rhizoctonia solani agglutinin, further referred to as RSA, is a lectin isolated from the plant pathogenic fungus Rhizoctonia solani. Previously, we reported a high entomotoxic activity of RSA towards the cotton leafworm Spodoptera littoralis. To better understand the mechanism of action of RSA, Drosophila melanogaster Schneider S2 cells were treated with different concentrations of the lectin and FITC-labeled RSA binding was examined using confocal fluorescence microscopy. RSA has antiproliferative activity with a median effect concentration (EC(50)) of 0.35 µM. In addition, the lectin was typically bound to the cell surface but not internalized. In contrast, the N-acetylglucosamine-binding lectin WGA and the galactose-binding lectin PNA, which were both also inhibitory for S2 cell proliferation, were internalized whereas the mannose-binding lectin GNA did not show any activity on these cells, although it was internalized. Extracted DNA and nuclei from S2 cells treated with RSA were not different from untreated cells, confirming inhibition of proliferation without apoptosis. Pre-incubation of RSA with N-acetylgalactosamine clearly inhibited the antiproliferative activity by RSA in S2 cells, demonstrating the importance of carbohydrate binding. Similarly, the use of MEK and JAK inhibitors reduced the activity of RSA. Finally, RSA affinity chromatography of membrane proteins from S2 cells allowed the identification of several cell surface receptors involved in both signaling transduction pathways.
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Affiliation(s)
- Mohamad Hamshou
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Laboratory of Biochemistry and Glycobiology, Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Els J. M. Van Damme
- Laboratory of Biochemistry and Glycobiology, Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Gianni Vandenborre
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Laboratory of Biochemistry and Glycobiology, Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Bart Ghesquière
- Department of Medical Protein Research, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Geert Trooskens
- Department of Mathematical Modelling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Kris Gevaert
- Department of Medical Protein Research, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Guy Smagghe
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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Kyndt T, Denil S, Haegeman A, Trooskens G, De Meyer T, Van Criekinge W, Gheysen G. Transcriptome analysis of rice mature root tissue and root tips in early development by massive parallel sequencing. J Exp Bot 2012; 63:2141-57. [PMID: 22213813 DOI: 10.1093/jxb/err435] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Despite the major physiological dissimilarities between mature root regions and their tips, differences in their gene expression profiles remain largely unexplored. In this research, the transcriptome of rice (Oryza sativa L. subsp. japonica) mature root tissue and root tips was monitored using mRNA-Seq at two time points. Almost 50 million 76 bp reads were mapped onto the rice genome sequence, expression patterns for different tissues and time points were investigated, and at least 1106 novel transcriptionally active regions (nTARs) expressed in rice root tissue were detected. More than 30 000 genes were found to be expressed in rice roots, among which were 1761 root-enriched and 306 tip-enriched transcripts. Mature root tissue appears to respond more strongly to external stimuli than tips, showing a higher expression of, for instance, auxin-responsive and abscisic acid-responsive genes, as well as the phenylpropanoid pathway and photosynthesis upon light. The root tip-enriched transcripts are mainly involved in mitochondrial electron transport, organelle development, secondary metabolism, DNA replication and metabolism, translation, and cellular component organization. During root maturation, genes involved in cell wall biosynthesis and modification, response to oxidative stress, and secondary metabolism were activated. For some nTARs, a potential role in root development can be put forward based on homology to genes involved in CLAVATA signalling, cell cycle regulators, and hormone signalling. A subset of differentially expressed genes and novel transcripts was confirmed using (quantitative) reverse transcription-PCR. These results uncover previously unrecognized tissue-specific expression profiles and provide an interesting starting point to study the different regulation of transcribed regions of these tissues.
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Affiliation(s)
- Tina Kyndt
- Department of Molecular Biotechnology, Ghent University, Coupure Links 653, Ghent, Belgium
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26
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Schouppe D, Ghesquière B, Menschaert G, De Vos WH, Bourque S, Trooskens G, Proost P, Gevaert K, Van Damme EJ. Interaction of the tobacco lectin with histone proteins. Plant Physiol 2011; 155:1091-102. [PMID: 21224338 PMCID: PMC3046571 DOI: 10.1104/pp.110.170134] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Accepted: 01/10/2011] [Indexed: 05/04/2023]
Abstract
The tobacco (Nicotiana tabacum) agglutinin or Nictaba is a member of a novel class of plant lectins residing in the nucleus and the cytoplasm of tobacco cells. Since tobacco lectin expression is only observed after the plant has been subjected to stress situations such as jasmonate treatment or insect attack, Nictaba is believed to act as a signaling protein involved in the stress physiology of the plant. In this paper, a nuclear proteomics approach was followed to identify the binding partners for Nictaba in the nucleus and the cytoplasm of tobacco cv Xanthi cells. Using lectin affinity chromatography and pull-down assays, it was shown that Nictaba interacts primarily with histone proteins. Binding of Nictaba with histone H2B was confirmed in vitro using affinity chromatography of purified calf thymus histone proteins on a Nictaba column. Elution of Nictaba-interacting histone proteins was achieved with 1 m N-acetylglucosamine (GlcNAc). Moreover, mass spectrometry analyses indicated that the Nictaba-interacting histone proteins are modified by O-GlcNAc. Since the lectin-histone interaction was shown to be carbohydrate dependent, it is proposed that Nictaba might fulfill a signaling role in response to stress by interacting with O-GlcNAcylated proteins in the plant cell nucleus.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Els J.M. Van Damme
- Laboratory of Biochemistry and Glycobiology, Department of Molecular Biotechnology, Faculty of Bioscience Engineering (D.S., E.J.M.V.D.), Department of Biochemistry (B.G., K.G.), Laboratory for Bioinformatics and Computational Genomics, Faculty of Bioscience Engineering (G.M., G.T.), and Bioimaging and Cytometry Unit, Faculty of Bioscience Engineering (W.H.D.V.), Ghent University, B–9000 Ghent, Belgium; Department of Medical Protein Research, VIB, B–9000 Ghent, Belgium (B.G., K.G.); UMR INRA 1088-CNRS 5184-Université de Bourgogne Plant-Microbe-Environnement, 21065 Dijon cedex, France (S.B.); Rega Institute for Medical Research, Laboratory of Molecular Immunology, Katholieke Universiteit Leuven, 3000 Leuven, Belgium (P.P.)
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Abstract
SUMMARY TreeIllustrator is a user-friendly application to visualize and customize phylogenetic trees. It has a broad range of functions and capabilities, such as dragging of nodes, different tree shapes, zooming and searching capabilities, and support for large trees. It acts as a solution that integrates the specificity of visualizing phylogenetic trees and the customization options of a drawing program. It also contains a simple and effective method that compares a custom tree with the Tree of Life, by detecting incongruence.
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Affiliation(s)
- Geert Trooskens
- Laboratorium for Bioinformatics and Computational Genomics (BioBix), Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Ghent University Ghent, Belgium
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