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Joosten SC, Odeh SNO, Koch A, Buekers N, Aarts MJB, Baldewijns MMLL, Van Neste L, van Kuijk S, Schouten LJ, van den Brandt PA, Tjan-Heijnen VC, van Engeland M, Smits KM. Development of a prognostic risk model for clear cell renal cell carcinoma by systematic evaluation of DNA methylation markers. Clin Epigenetics 2021; 13:103. [PMID: 33947447 PMCID: PMC8094610 DOI: 10.1186/s13148-021-01084-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 04/19/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Current risk models for renal cell carcinoma (RCC) based on clinicopathological factors are sub-optimal in accurately identifying high-risk patients. Here, we perform a head-to-head comparison of previously published DNA methylation markers and propose a potential prognostic model for clear cell RCC (ccRCC). PATIENTS AND METHODS Promoter methylation of PCDH8, BNC1, SCUBE3, GREM1, LAD1, NEFH, RASSF1A, GATA5, SFRP1, CDO1, and NEURL was determined by nested methylation-specific PCR. To identify clinically relevant methylated regions, The Cancer Genome Atlas (TCGA) was used to guide primer design. Formalin-fixed paraffin-embedded (FFPE) tissue samples from 336 non-metastatic ccRCC patients from the prospective Netherlands Cohort Study (NLCS) were used to develop a Cox proportional hazards model using stepwise backward elimination and bootstrapping to correct for optimism. For validation purposes, FFPE ccRCC tissue of 64 patients from the University Hospitals Leuven and a series of 232 cases from The Cancer Genome Atlas (TCGA) were used. RESULTS Methylation of GREM1, GATA5, LAD1, NEFH, NEURL, and SFRP1 was associated with poor ccRCC-specific survival, independent of age, sex, tumor size, TNM stage or tumor grade. Moreover, the association between GREM1, NEFH, and NEURL methylation and outcome was shown to be dependent on the genomic region. A prognostic biomarker model containing GREM1, GATA5, LAD1, NEFH and NEURL methylation in combination with clinicopathological characteristics, performed better compared to the model with clinicopathological characteristics only (clinical model), in both the NLCS and the validation population with a c-statistic of 0.71 versus 0.65 and a c-statistic of 0.95 versus 0.86 consecutively. However, the biomarker model had limited added prognostic value in the TCGA series with a c-statistic of 0.76 versus 0.75 for the clinical model. CONCLUSION In this study we performed a head-to-head comparison of potential prognostic methylation markers for ccRCC using a novel approach to guide primers design which utilizes the optimal location for measuring DNA methylation. Using this approach, we identified five methylation markers that potentially show prognostic value in addition to currently known clinicopathological factors.
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Affiliation(s)
- S C Joosten
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands
- Department of Medical Oncology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - S N O Odeh
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands
| | - A Koch
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands
| | - N Buekers
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands
| | - M J B Aarts
- Department of Medical Oncology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | | | - L Van Neste
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands
| | - S van Kuijk
- Department of Clinical Epidemiology and Medical Technology Assessment, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - L J Schouten
- Department of Epidemiology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - P A van den Brandt
- Department of Epidemiology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - V C Tjan-Heijnen
- Department of Medical Oncology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - M van Engeland
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands
| | - K M Smits
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands.
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Deckers IAG, van den Brandt PA, van Engeland M, Soetekouw PMMB, Baldewijns MMLL, Goldbohm RA, Schouten LJ. Long-term dietary sodium, potassium and fluid intake; exploring potential novel risk factors for renal cell cancer in the Netherlands Cohort Study on diet and cancer. Br J Cancer 2013; 110:797-801. [PMID: 24327014 PMCID: PMC3915132 DOI: 10.1038/bjc.2013.771] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2013] [Revised: 11/05/2013] [Accepted: 11/17/2013] [Indexed: 01/20/2023] Open
Abstract
Background: As sodium, potassium and fluid intake are related to hypertension, an established risk factor for renal cell cancer (RCC), they may be independent risk factors for RCC. Methods: The Netherlands Cohort Study (NLCS) with case-cohort design included 120 852 participants aged 55–69 years. At baseline, diet and lifestyle were assessed with questionnaires. After 17.3 years of follow-up, 485 RCC cases and 4438 subcohort members were available for analyses. Results: Sodium intake increased RCC risk (P-trend=0.03), whereas fluid and potassium intake did not. For high sodium and low fluid intake, the RCC risk additionally increased (P-interaction=0.02). Conclusion: Sodium intake is a potential risk factor for RCC, particularly if fluid consumption is low.
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Affiliation(s)
- I A G Deckers
- Department of Epidemiology, School for Oncology and Developmental Biology (GROW), Maastricht University Medical Centre, Peter Debyeplein 1, Maastricht 6229 HA, The Netherlands
| | - P A van den Brandt
- Department of Epidemiology, School for Oncology and Developmental Biology (GROW), Maastricht University Medical Centre, Peter Debyeplein 1, Maastricht 6229 HA, The Netherlands
| | - M van Engeland
- Department of Pathology, School for Oncology and Developmental Biology (GROW), Maastricht University Medical Centre, Peter Debyelaan 25, Maastricht 6229 HX, The Netherlands
| | - P M M B Soetekouw
- Division of Medical Oncology, Department of Internal Medicine, School for Oncology and Developmental Biology (GROW), Maastricht University Medical Center, Peter Debyelaan 25, Maastricht 6229 HX, The Netherlands
| | - M M L L Baldewijns
- Department of Pathology, School for Oncology and Developmental Biology (GROW), Maastricht University Medical Centre, Peter Debyelaan 25, Maastricht 6229 HX, The Netherlands
| | - R A Goldbohm
- TNO Quality of Life, Wassenaarseweg 56, Leiden 2333 AL, The Netherlands
| | - L J Schouten
- Department of Epidemiology, School for Oncology and Developmental Biology (GROW), Maastricht University Medical Centre, Peter Debyeplein 1, Maastricht 6229 HA, The Netherlands
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