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Mobaraki G, Shi S, Smits KM, Severens K, Lommen K, Rennspiess D, Chteinberg E, Winnepenninckx V, Samarska I, Klufah F, zur Hausen A. Bovine Meat and Milk Factor-like Sequences Are Frequently Detected in Renal Cell Carcinoma Tissues. Cancers (Basel) 2024; 16:1746. [PMID: 38730698 PMCID: PMC11083248 DOI: 10.3390/cancers16091746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 04/14/2024] [Accepted: 04/18/2024] [Indexed: 05/13/2024] Open
Abstract
Previous studies have indicated a potential role of diet in the pathogenesis of renal cell carcinoma (RCC). Recently, circular bovine meat and milk factor (BMMF) DNAs have been identified in peritumoral tissues of human colon and breast cancers. Here, we investigated the prevalence of the DNA of these novel human pathogenic infectious agents in RCC and adjacent peritumoral renal tissues. DNA was extracted from formalin-fixed and paraffin-embedded (FFPE) RCC and peritumoral kidney tissues, including a test (n = 11) and a validation (n = 152) collection. BMMF1 and BMMF2 consensus primers were designed to screen for the presence of BMMF1- and BMMF2-like DNA. In addition, BMMF-specific PCR was performed on selected cases to test for the presence of additional regions of BMMF1 and BMMF2 genomes. A reference collection of hepatocellular carcinomas (HCCs; n = 60) and adjacent peritumoral liver tissues (n = 50) was also included. Our results demonstrated that BMMF1 and BMMF2 DNAs are frequently found in human RCC tissues and are particularly more prevalent in peritumoral kidney tissues. Of note, BMMF1 and BMMF2 genotype heterogeneity was higher in peritumoral kidney tissues compared to RCC tissues. This is the first study to directly test human FFPE tissues for BMMF1- and BMMF2-like DNA using consensus PCR and demonstrate BMMF DNA in neoplastic and peritumoral kidney tissues. The findings are in line with the recently proposed indirect etiopathogenetic role of BMMFs in, e.g., colorectal carcinogenesis. Follow-up studies are needed to explore the potential role of BMMFs in the etiopathogenesis of RCC.
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Affiliation(s)
- Ghalib Mobaraki
- Department of Pathology, GROW—Institute for Oncology & Reproduction, Maastricht University Medical Centre+, 6229 HX Maastricht, The Netherlands; (G.M.); (S.S.); (K.M.S.); (K.S.); (K.L.); (D.R.); (V.W.); (I.S.); (F.K.)
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Jazan University, Jazan 45142, Saudi Arabia
| | - Shuai Shi
- Department of Pathology, GROW—Institute for Oncology & Reproduction, Maastricht University Medical Centre+, 6229 HX Maastricht, The Netherlands; (G.M.); (S.S.); (K.M.S.); (K.S.); (K.L.); (D.R.); (V.W.); (I.S.); (F.K.)
| | - Kim M. Smits
- Department of Pathology, GROW—Institute for Oncology & Reproduction, Maastricht University Medical Centre+, 6229 HX Maastricht, The Netherlands; (G.M.); (S.S.); (K.M.S.); (K.S.); (K.L.); (D.R.); (V.W.); (I.S.); (F.K.)
| | - Kim Severens
- Department of Pathology, GROW—Institute for Oncology & Reproduction, Maastricht University Medical Centre+, 6229 HX Maastricht, The Netherlands; (G.M.); (S.S.); (K.M.S.); (K.S.); (K.L.); (D.R.); (V.W.); (I.S.); (F.K.)
| | - Kim Lommen
- Department of Pathology, GROW—Institute for Oncology & Reproduction, Maastricht University Medical Centre+, 6229 HX Maastricht, The Netherlands; (G.M.); (S.S.); (K.M.S.); (K.S.); (K.L.); (D.R.); (V.W.); (I.S.); (F.K.)
| | - Dorit Rennspiess
- Department of Pathology, GROW—Institute for Oncology & Reproduction, Maastricht University Medical Centre+, 6229 HX Maastricht, The Netherlands; (G.M.); (S.S.); (K.M.S.); (K.S.); (K.L.); (D.R.); (V.W.); (I.S.); (F.K.)
| | - Emil Chteinberg
- Institute of Human Genetics, Ulm University Medical Center, 89081 Ulm, Germany
| | - Véronique Winnepenninckx
- Department of Pathology, GROW—Institute for Oncology & Reproduction, Maastricht University Medical Centre+, 6229 HX Maastricht, The Netherlands; (G.M.); (S.S.); (K.M.S.); (K.S.); (K.L.); (D.R.); (V.W.); (I.S.); (F.K.)
| | - Iryna Samarska
- Department of Pathology, GROW—Institute for Oncology & Reproduction, Maastricht University Medical Centre+, 6229 HX Maastricht, The Netherlands; (G.M.); (S.S.); (K.M.S.); (K.S.); (K.L.); (D.R.); (V.W.); (I.S.); (F.K.)
| | - Faisal Klufah
- Department of Pathology, GROW—Institute for Oncology & Reproduction, Maastricht University Medical Centre+, 6229 HX Maastricht, The Netherlands; (G.M.); (S.S.); (K.M.S.); (K.S.); (K.L.); (D.R.); (V.W.); (I.S.); (F.K.)
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Al-Baha University, Al Baha 65528, Saudi Arabia
| | - Axel zur Hausen
- Department of Pathology, GROW—Institute for Oncology & Reproduction, Maastricht University Medical Centre+, 6229 HX Maastricht, The Netherlands; (G.M.); (S.S.); (K.M.S.); (K.S.); (K.L.); (D.R.); (V.W.); (I.S.); (F.K.)
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Offermans K, Jenniskens JCA, Simons CCJM, Samarska I, Fazzi GE, Smits KM, Schouten LJ, Weijenberg MP, Grabsch HI, van den Brandt PA. Association between adjuvant therapy and survival in colorectal cancer patients according to metabolic Warburg-subtypes. J Cancer Res Clin Oncol 2023; 149:6271-6282. [PMID: 36723668 PMCID: PMC10356897 DOI: 10.1007/s00432-023-04581-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 01/08/2023] [Indexed: 02/02/2023]
Abstract
PURPOSE Tumor location and tumor node metastasis (TNM) stage guide treatment decisions in colorectal cancer (CRC) patients. However, patients with the same disease stage do not benefit equally from adjuvant therapy. Hence, there remains an urgent clinical need to identify prognostic and/or predictive biomarker(s) to personalize treatment decisions. In this exploratory study, we investigated whether our previously defined metabolic Warburg-subtypes can predict which CRC patients might derive survival benefit from adjuvant therapy. METHODS Information regarding treatment (surgery only: n = 1451; adjuvant radiotherapy: n = 82; or adjuvant chemotherapy: n = 260) and Warburg-subtype (Warburg-low: n = 485, -moderate: n = 641, or -high: n = 667) was available for 1793 CRC patients from the Netherlands Cohort Study (NLCS). Kaplan-Meier curves and Cox regression models were used to investigate survival benefit from adjuvant therapy compared to surgery-only for the different Warburg-subtypes. RESULTS Patients with Warburg-moderate CRC (HRCRC-specific 0.64; 95% CI 0.47-0.86, HRoverall 0.61; 95% CI 0.47-0.80), and possibly Warburg-high CRC (HRCRC-specific 0.86; 95% CI 0.65-1.14, HRoverall 0.82; 95% CI 0.64-1.05), had survival benefit from adjuvant therapy. No survival benefit was observed for patients with Warburg-low CRC (HRCRC-specific 1.07; 95% CI 0.76-1.52, HRoverall 0.95; 95% CI 0.70-1.30). There was a significant interaction between Warburg-subtype and adjuvant therapy for CRC-specific survival (p = 0.049) and overall survival (p = 0.035). CONCLUSION Our results suggest that Warburg-subtypes may predict survival benefit from adjuvant therapy in CRC patients. A survival benefit from adjuvant therapy was observed for patients with Warburg-moderate and possibly Warburg-high CRC, but not for patients with Warburg-low CRC. Future prospective studies are necessary to validate our findings.
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Affiliation(s)
- Kelly Offermans
- Department of Epidemiology, GROW School for Oncology and Reproduction, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Josien C A Jenniskens
- Department of Epidemiology, GROW School for Oncology and Reproduction, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Colinda C J M Simons
- Department of Epidemiology, GROW School for Oncology and Reproduction, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Iryna Samarska
- Department of Pathology, GROW School for Oncology and Reproduction, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Gregorio E Fazzi
- Department of Pathology, GROW School for Oncology and Reproduction, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Kim M Smits
- Department of Pathology, GROW School for Oncology and Reproduction, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Leo J Schouten
- Department of Epidemiology, GROW School for Oncology and Reproduction, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Matty P Weijenberg
- Department of Epidemiology, GROW School for Oncology and Reproduction, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Heike I Grabsch
- Department of Pathology, GROW School for Oncology and Reproduction, Maastricht University Medical Center+, Maastricht, The Netherlands.
- Pathology and Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK.
| | - Piet A van den Brandt
- Department of Epidemiology, GROW School for Oncology and Reproduction, Maastricht University Medical Center+, Maastricht, The Netherlands.
- Department of Epidemiology, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Center+, Maastricht, The Netherlands.
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Jenniskens JCA, Offermans K, Simons CCJM, Samarska I, Fazzi GE, van der Meer JRM, Smits KM, Schouten LJ, Weijenberg MP, Grabsch HI, van den Brandt PA. Energy balance-related factors in childhood and adolescence and risk of colorectal cancer based on KRAS, PIK3CA, and BRAF mutations and MMR status. Mol Carcinog 2022; 61:1099-1115. [PMID: 36177801 PMCID: PMC9828509 DOI: 10.1002/mc.23459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 08/02/2022] [Accepted: 08/25/2022] [Indexed: 01/12/2023]
Abstract
KRAS mutations (KRASmut ), PIK3CAmut , BRAFmut , and deficient DNA mismatch repair (dMMR) have been associated with the Warburg effect. We previously reported differential associations between early-life energy balance-related factors (height, energy restriction, body mass index [BMI]) and colorectal cancer (CRC) subtypes based on the Warburg effect. We now investigated associations of early-life energy balance-related factors and the risk of CRC subgroups based on mutation and MMR status. Data from the Netherlands Cohort Study was used. KRASmut , PIK3CAmut, BRAFmut, and MMR status were available for 2349 CRC cases, and complete covariate data for 1934 cases and 3911 subcohort members. Multivariable-adjusted Cox regression was used to estimate associations of height, energy restriction proxies (exposure to Dutch Hunger Winter, Second World War, Economic Depression), and early adult BMI (age 20 years) with risk of CRC based on individual molecular features and combinations thereof (all-wild-type+MMR-proficient [pMMR]; any-mutation/dMMR). Height was positively associated with any-mutation/dMMR CRC but not all-wild-type+pMMR CRC, with the exception of rectal cancer in men, and with heterogeneity in associations observed for colon cancer in men (p-heterogeneity = 0.049) and rectal cancer in women (p-heterogeneity = 0.014). Results on early-life energy restriction proxies in relation to the risk of CRC subgroups did not show clear patterns. Early adult BMI was positively, but not significantly, associated with KRASmut colon cancer in men and with BRAFmut and dMMR colon cancer in women. Our results suggest a role of KRASmut , PIK3CAmut , BRAFmut , and dMMR in the etiological pathway between height and CRC risk. KRASmut might potentially play a role in associations of early adult BMI with colon cancer risk in men, and BRAFmut and dMMR in women.
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Affiliation(s)
- Josien C. A. Jenniskens
- Department of Epidemiology, GROW School for Oncology and ReproductionMaastricht University Medical Center+MaastrichtThe Netherlands
| | - Kelly Offermans
- Department of Epidemiology, GROW School for Oncology and ReproductionMaastricht University Medical Center+MaastrichtThe Netherlands
| | - Colinda C. J. M. Simons
- Department of Epidemiology, GROW School for Oncology and ReproductionMaastricht University Medical Center+MaastrichtThe Netherlands
| | - Iryna Samarska
- Department of Pathology, GROW School for Oncology and ReproductionMaastricht University Medical Center+MaastrichtThe Netherlands
| | - Gregorio E. Fazzi
- Department of Pathology, GROW School for Oncology and ReproductionMaastricht University Medical Center+MaastrichtThe Netherlands
| | - Jaleesa R. M. van der Meer
- Department of Pathology, GROW School for Oncology and ReproductionMaastricht University Medical Center+MaastrichtThe Netherlands
| | - Kim M. Smits
- Department of Pathology, GROW School for Oncology and ReproductionMaastricht University Medical Center+MaastrichtThe Netherlands
| | - Leo J. Schouten
- Department of Epidemiology, GROW School for Oncology and ReproductionMaastricht University Medical Center+MaastrichtThe Netherlands
| | - Matty P. Weijenberg
- Department of Epidemiology, GROW School for Oncology and ReproductionMaastricht University Medical Center+MaastrichtThe Netherlands
| | - Heike I. Grabsch
- Department of Pathology, GROW School for Oncology and ReproductionMaastricht University Medical Center+MaastrichtThe Netherlands,Pathology and Data Analytics, Leeds Institute of Medical Research at St James'sUniversity of LeedsLeedsUK
| | - Piet A. van den Brandt
- Department of Epidemiology, GROW School for Oncology and ReproductionMaastricht University Medical Center+MaastrichtThe Netherlands,Department of Epidemiology, Care and Public Health Research Institute (CAPHRI)Maastricht University Medical Center+MaastrichtThe Netherlands
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Offermans K, Jenniskens JCA, Simons CCJM, Samarska I, Fazzi GE, van der Meer JRM, Smits KM, Schouten LJ, Weijenberg MP, Grabsch HI, van den Brandt PA. Association between mutational subgroups, Warburg-subtypes, and survival in patients with colorectal cancer. Cancer Med 2022; 12:1137-1156. [PMID: 35785488 PMCID: PMC9883416 DOI: 10.1002/cam4.4968] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/24/2022] [Accepted: 06/11/2022] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Previous research suggests that Warburg-subtypes are related to potentially important survival differences in colorectal cancer (CRC) patients. In the present study, we investigated whether mutational subgroups based on somatic mutations in RAS, BRAF, PIK3CA, and MET, which are known to promote the Warburg-effect, as well as mismatch repair (MMR) status, hold prognostic value in CRC. In addition, we investigated whether Warburg-subtypes provide additional prognostic information, independent of known prognostic factors like TNM stage. METHODS CRC patients (n = 2344) from the prospective Netherlands Cohort Study (NLCS) were classified into eight mutually exclusive mutational subgroups, based on observed mutations in RAS, BRAF, PIK3CA, and MET, and MMR status: All-wild-type + MMRproficient , KRASmut + MMRproficient , KRASmut + PIK3CAmut + MMRproficient , PIK3CAmut + MMRproficient , BRAFmut + MMRproficient , BRAFmut + MMRdeficient , other + MMRproficient , and other + MMRdeficient . Kaplan-Meier curves and Cox regression models were used to investigate associations between mutational subgroups and survival, as well as associations between our previously established Warburg-subtypes and survival within these mutational subgroups. RESULTS Compared to patients with all-wild-type + MMRproficient CRC, patients with KRASmut + MMRproficient , KRASmut + PIK3CAmut + MMRproficient , BRAFmut + MMRproficient , or other + MMRproficient CRC had a statistically significant worse survival (HRCRC-specific ranged from 1.29 to 1.88). In contrast, patients with other + MMRdeficient CRC had the most favorable survival (HRCRC-specific 0.48). No statistically significant survival differences were observed for the Warburg-subtypes within mutational subgroups. CONCLUSION Our results highlight the prognostic potential of mutational subgroups in CRC. Warburg-subtypes did not provide additional prognostic information within these mutational subgroups. Future larger-scale prospective studies are necessary to validate our findings and to examine the potential clinical utility of CRC subtyping based on mutational subgroups.
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Affiliation(s)
- Kelly Offermans
- Department of Epidemiology, GROW School for Oncology and ReproductionMaastricht University Medical Center+MaastrichtThe Netherlands
| | - Josien C. A. Jenniskens
- Department of Epidemiology, GROW School for Oncology and ReproductionMaastricht University Medical Center+MaastrichtThe Netherlands
| | - Colinda C. J. M. Simons
- Department of Epidemiology, GROW School for Oncology and ReproductionMaastricht University Medical Center+MaastrichtThe Netherlands
| | - Iryna Samarska
- Department of Pathology, GROW School for Oncology and ReproductionMaastricht University Medical Center+MaastrichtThe Netherlands
| | - Gregorio E. Fazzi
- Department of Pathology, GROW School for Oncology and ReproductionMaastricht University Medical Center+MaastrichtThe Netherlands
| | - Jaleesa R. M. van der Meer
- Department of Pathology, GROW School for Oncology and ReproductionMaastricht University Medical Center+MaastrichtThe Netherlands
| | - Kim M. Smits
- Department of Pathology, GROW School for Oncology and ReproductionMaastricht University Medical Center+MaastrichtThe Netherlands
| | - Leo J. Schouten
- Department of Epidemiology, GROW School for Oncology and ReproductionMaastricht University Medical Center+MaastrichtThe Netherlands
| | - Matty P. Weijenberg
- Department of Epidemiology, GROW School for Oncology and ReproductionMaastricht University Medical Center+MaastrichtThe Netherlands
| | - Heike I. Grabsch
- Department of Pathology, GROW School for Oncology and ReproductionMaastricht University Medical Center+MaastrichtThe Netherlands,Pathology and Data Analytics, Leeds Institute of Medical Research at St James'sUniversity of LeedsLeedsUK
| | - Piet A. van den Brandt
- Department of Epidemiology, GROW School for Oncology and ReproductionMaastricht University Medical Center+MaastrichtThe Netherlands,Department of Epidemiology, Care and Public Health Research Institute (CAPHRI)Maastricht University Medical Center+MaastrichtThe Netherlands
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Feng Z, Oberije CJG, van de Wetering AJP, Koch A, Wouters KAD, Vaes N, Masclee AAM, Carvalho B, Meijer GA, Zeegers MP, Herman JG, Melotte V, van Engeland M, Smits KM. Lessons From a Systematic Literature Search on Diagnostic DNA Methylation Biomarkers for Colorectal Cancer: How to Increase Research Value and Decrease Research Waste? Clin Transl Gastroenterol 2022; 13:e00499. [PMID: 35584320 PMCID: PMC9236597 DOI: 10.14309/ctg.0000000000000499] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 04/22/2022] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVES To improve colorectal cancer (CRC) survival and lower incidence rates, colonoscopy and/or fecal immunochemical test screening are widely implemented. Although candidate DNA methylation biomarkers have been published to improve or complement the fecal immunochemical test, clinical translation is limited. We describe technical and methodological problems encountered after a systematic literature search and provide recommendations to increase (clinical) value and decrease research waste in biomarker research. In addition, we present current evidence for diagnostic CRC DNA methylation biomarkers. METHODS A systematic literature search identified 331 diagnostic DNA methylation marker studies published before November 2020 in PubMed, EMBASE, Cochrane Library, and Google Scholar. For 136 bodily fluid studies, extended data extraction was performed. STARD criteria and level of evidence were registered to assess reporting quality and strength for clinical translation. RESULTS Our systematic literature search revealed multiple issues that hamper the development of DNA methylation biomarkers for CRC diagnosis, including methodological and technical heterogeneity and lack of validation or clinical translation. For example, clinical translation and independent validation were limited, with 100 of 434 markers (23%) studied in bodily fluids, 3 of 434 markers (0.7%) translated into clinical tests, and independent validation for 92 of 411 tissue markers (22%) and 59 of 100 bodily fluids markers (59%). DISCUSSION This systematic literature search revealed that major requirements to develop clinically relevant diagnostic CRC DNA methylation markers are often lacking. To avoid the resulting research waste, clinical needs, intended biomarker use, and independent validation should be better considered before study design. In addition, improved reporting quality would facilitate meta-analysis, thereby increasing the level of evidence and enabling clinical translation.
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Affiliation(s)
- Zheng Feng
- Department of Pathology, GROW – School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, the Netherlands;
| | - Cary J. G. Oberije
- Department of Pathology, GROW – School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, the Netherlands;
- The D-Lab, Department of Precision Medicine, GROW—School for Oncology and Reproduction, Maastricht University Medical Centre, Maastricht, the Netherlands;
| | - Alouisa J. P. van de Wetering
- Department of Pathology, GROW – School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, the Netherlands;
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Maastricht University Medical Center, Maastricht, the Netherlands;
| | - Alexander Koch
- Department of Pathology, GROW – School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, the Netherlands;
| | - Kim. A. D. Wouters
- Department of Pathology, GROW – School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, the Netherlands;
| | - Nathalie Vaes
- Department of Pathology, GROW – School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, the Netherlands;
| | - Ad A. M. Masclee
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Maastricht University Medical Center, Maastricht, the Netherlands;
- Division of Gastroenterology-Hepatology, Department of Internal Medicine, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre, Maastricht, the Netherlands;
| | - Beatriz Carvalho
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands;
| | - Gerrit A. Meijer
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands;
| | - Maurice P. Zeegers
- Department of Complex Genetics, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center, Maastricht, the Netherlands;
- Department of Complex Genetics, CAPHRI – Care and Public Health Research Institute, Maastricht University Medical Center, Maastricht, the Netherlands;
| | - James G. Herman
- Division of Hematology/Oncology, University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania, USA
| | - Veerle Melotte
- Department of Pathology, GROW – School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, the Netherlands;
- Department of Clinical Genetics, Erasmus University Medical Center, University of Rotterdam, Rotterdam, the Netherlands;
| | - Manon van Engeland
- Department of Pathology, GROW – School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, the Netherlands;
| | - Kim M. Smits
- Department of Pathology, GROW – School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, the Netherlands;
- Division of Medical Oncology, Department of Internal Medicine, GROW – School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, the Netherlands.
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Jenniskens JCA, Offermans K, Simons CCJM, Samarska I, Fazzi GE, van der Meer JRM, Smits KM, Schouten LJ, Weijenberg MP, Grabsch HI, van den Brandt PA. Energy balance-related factors and risk of colorectal cancer based on KRAS, PIK3CA, and BRAF mutations and MMR status. J Cancer Res Clin Oncol 2022; 148:2723-2742. [PMID: 35546360 PMCID: PMC9470639 DOI: 10.1007/s00432-022-04019-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 01/13/2022] [Accepted: 04/06/2022] [Indexed: 11/26/2022]
Abstract
Introduction KRAS mutations (KRASmut), PIK3CAmut, BRAFmut, and mismatch repair deficiency (dMMR) have been associated with the Warburg-effect. We previously observed differential associations between energy balance-related factors (BMI, clothing-size, physical activity) and colorectal cancer (CRC) subtypes based on the Warburg-effect. We now investigated whether associations between energy balance-related factors and risk of CRC differ between subgroups based on mutation and MMR status. Methods Information on molecular features was available for 2349 incident CRC cases within the Netherlands Cohort Study (NLCS), with complete covariate data available for 1934 cases and 3911 subcohort members. Multivariable-adjusted Cox-regression was used to estimate associations of energy balance-related factors with risk of CRC based on individual molecular features (KRASmut; PIK3CAmut; BRAFmut; dMMR) and combinations thereof (all-wild-type + MMR-proficient (pMMR); any-mutation/dMMR). Results In men, BMI and clothing-size were positively associated with risk of colon, but not rectal cancer, regardless of molecular features subgroups; the strongest associations were observed for PIK3CAmut colon cancer. In women, however, BMI and clothing-size were only associated with risk of KRASmut colon cancer (p-heterogeneityKRASmut versus all-wild-type+pMMR = 0.008). Inverse associations of non-occupational physical activity with risk of colon cancer were strongest for any-mutation/dMMR tumors in men and women, and specifically for PIK3CAmut tumors in women. Occupational physical activity was inversely associated with both combination subgroups of colon cancer in men. Conclusion In men, associations did not vary according to molecular features. In women, a role of KRAS mutations in the etiological pathway between adiposity and colon cancer is suggested, and of PIK3CA mutations between physical activity and colon cancer. Supplementary Information The online version contains supplementary material available at 10.1007/s00432-022-04019-9.
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Affiliation(s)
- Josien C A Jenniskens
- Department of Epidemiology, GROW School for Oncology and Reproduction, Maastricht University Medical Center+, P.O. BOX 616, 6200 MD, Maastricht, The Netherlands
| | - Kelly Offermans
- Department of Epidemiology, GROW School for Oncology and Reproduction, Maastricht University Medical Center+, P.O. BOX 616, 6200 MD, Maastricht, The Netherlands
| | - Colinda C J M Simons
- Department of Epidemiology, GROW School for Oncology and Reproduction, Maastricht University Medical Center+, P.O. BOX 616, 6200 MD, Maastricht, The Netherlands
| | - Iryna Samarska
- Department of Pathology, GROW School for Oncology and Reproduction, Maastricht University Medical Center+, P.O. BOX 5800, 6202 AZ, Maastricht, The Netherlands
| | - Gregorio E Fazzi
- Department of Pathology, GROW School for Oncology and Reproduction, Maastricht University Medical Center+, P.O. BOX 5800, 6202 AZ, Maastricht, The Netherlands
| | - Jaleesa R M van der Meer
- Department of Pathology, GROW School for Oncology and Reproduction, Maastricht University Medical Center+, P.O. BOX 5800, 6202 AZ, Maastricht, The Netherlands
| | - Kim M Smits
- Department of Pathology, GROW School for Oncology and Reproduction, Maastricht University Medical Center+, P.O. BOX 5800, 6202 AZ, Maastricht, The Netherlands
| | - Leo J Schouten
- Department of Epidemiology, GROW School for Oncology and Reproduction, Maastricht University Medical Center+, P.O. BOX 616, 6200 MD, Maastricht, The Netherlands
| | - Matty P Weijenberg
- Department of Epidemiology, GROW School for Oncology and Reproduction, Maastricht University Medical Center+, P.O. BOX 616, 6200 MD, Maastricht, The Netherlands
| | - Heike I Grabsch
- Department of Pathology, GROW School for Oncology and Reproduction, Maastricht University Medical Center+, P.O. BOX 5800, 6202 AZ, Maastricht, The Netherlands.
- Pathology and Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK.
| | - Piet A van den Brandt
- Department of Epidemiology, GROW School for Oncology and Reproduction, Maastricht University Medical Center+, P.O. BOX 616, 6200 MD, Maastricht, The Netherlands.
- Department of Epidemiology, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Center+, Maastricht, The Netherlands.
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Massen M, Lommen K, Wouters KAD, Vandersmissen J, van Criekinge W, Herman JG, Melotte V, Schouten LJ, van Engeland M, Smits KM. Technical considerations in PCR-based assay design for diagnostic DNA methylation cancer biomarkers. Clin Epigenetics 2022; 14:56. [PMID: 35477541 PMCID: PMC9047347 DOI: 10.1186/s13148-022-01273-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 01/12/2022] [Accepted: 04/07/2022] [Indexed: 11/21/2022] Open
Abstract
Background DNA methylation biomarkers for early detection, risk stratification and treatment response in cancer have been of great interest over the past decades. Nevertheless, clinical implementation of these biomarkers is limited, as only < 1% of the identified biomarkers is translated into a clinical or commercial setting. Technical factors such as a suboptimal genomic location of the assay and inefficient primer or probe design have been emphasized as important pitfalls in biomarker research. Here, we use eleven diagnostic DNA methylation biomarkers for colorectal cancer (ALX4, APC, CDKN2A, MGMT, MLH1, NDRG4, SDC2, SFRP1, SFRP2, TFPI1 and VIM), previously described in a systematic literature search, to evaluate these pitfalls. Results To assess the genomic assay location, the optimal genomic locations according to TCGA data were extracted and compared to the genomic locations used in the published assays for all eleven biomarkers. In addition, all primers and probes were technically evaluated according to several criteria, based on literature and expert opinion. Both assay location and assay design quality varied widely among studies. Conclusions Large variation in both assay location and design hinders the development of future DNA methylation biomarkers as well as inter-study comparability.
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Affiliation(s)
- Maartje Massen
- Department of Pathology, GROW - School for Oncology and Reproduction, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Kim Lommen
- Department of Pathology, GROW - School for Oncology and Reproduction, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Kim A D Wouters
- Department of Pathology, GROW - School for Oncology and Reproduction, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | | | - Wim van Criekinge
- Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, 9000, Ghent, Belgium
| | - James G Herman
- The Hillman Cancer Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA, 15232, USA
| | - Veerle Melotte
- Department of Pathology, GROW - School for Oncology and Reproduction, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands.,Department of Clinical Genetics, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Leo J Schouten
- Department of Epidemiology, GROW - School for Oncology and Reproduction, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Manon van Engeland
- Department of Pathology, GROW - School for Oncology and Reproduction, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Kim M Smits
- Department of Pathology, GROW - School for Oncology and Reproduction, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands.
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8
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Jenniskens JCA, Offermans K, Simons CCJM, Samarska I, Fazzi GE, Smits KM, Schouten LJ, Weijenberg MP, Grabsch HI, Brandt PA. Energy balance‐related factors in childhood and adolescence and risk of colorectal cancer expressing different levels of proteins involved in the Warburg‐effect. Int J Cancer 2022; 150:1812-1824. [PMID: 35064924 PMCID: PMC9304212 DOI: 10.1002/ijc.33941] [Citation(s) in RCA: 5] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 12/22/2021] [Accepted: 01/13/2022] [Indexed: 11/15/2022]
Abstract
Early‐life (childhood to adolescence) energy balance‐related factors (height, energy restriction, BMI) have been associated with adult colorectal cancer (CRC) risk. Warburg‐effect activation via PI3K/Akt‐signaling might explain this link. We investigated whether early‐life energy balance‐related factors were associated with risk of Warburg‐subtypes in CRC. We used immunohistochemistry for six proteins involved in the Warburg‐effect (LDHA, GLUT1, MCT4, PKM2, P53, and PTEN) on tissue microarrays of 2399 incident CRC cases from the prospective Netherlands Cohort Study (NLCS). Expression levels of all proteins were combined into a pathway‐based sum score and categorized into three Warburg‐subtypes (Warburg‐low/‐moderate/‐high). Multivariable Cox‐regression analyses were used to estimate associations of height, energy restriction proxies (exposure to Dutch Hunger Winter; Second World War [WWII]; Economic Depression) and adolescent BMI with Warburg‐subtypes in CRC. Height was positively associated with colon cancer in men, regardless of Warburg‐subtypes, and with Warburg‐low colon and Warburg‐moderate rectal cancer in women. Energy restriction during the Dutch Hunger Winter was inversely associated with colon cancer in men, regardless of Warburg‐subtypes. In women, energy restriction during the Hunger Winter and WWII was inversely associated with Warburg‐low colon cancer, whereas energy restriction during the Economic Depression was positively associated with Warburg‐high colon cancer. Adolescent BMI was positively associated with Warburg‐high colon cancer in men, and Warburg‐moderate rectal cancer in women. In conclusion, the Warburg‐effect seems to be involved in associations of adolescent BMI with colon cancer in men, and of energy restriction during the Economic Depression with colon cancer in women. Further research is needed to validate these results.
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Affiliation(s)
- Josien C. A. Jenniskens
- Department of Epidemiology GROW School for Oncology and Developmental Biology, Maastricht University Medical Center+, Maastricht the Netherlands
| | - Kelly Offermans
- Department of Epidemiology GROW School for Oncology and Developmental Biology, Maastricht University Medical Center+, Maastricht the Netherlands
| | - Colinda C. J. M. Simons
- Department of Epidemiology GROW School for Oncology and Developmental Biology, Maastricht University Medical Center+, Maastricht the Netherlands
| | - Iryna Samarska
- Department of Pathology GROW School for Oncology and Developmental Biology, Maastricht University Medical Center+, Maastricht the Netherlands
| | - Gregorio E. Fazzi
- Department of Pathology GROW School for Oncology and Developmental Biology, Maastricht University Medical Center+, Maastricht the Netherlands
| | - Kim M. Smits
- Department of Pathology GROW School for Oncology and Developmental Biology, Maastricht University Medical Center+, Maastricht the Netherlands
| | - Leo J. Schouten
- Department of Epidemiology GROW School for Oncology and Developmental Biology, Maastricht University Medical Center+, Maastricht the Netherlands
| | - Matty P. Weijenberg
- Department of Epidemiology GROW School for Oncology and Developmental Biology, Maastricht University Medical Center+, Maastricht the Netherlands
| | - Heike I. Grabsch
- Department of Pathology GROW School for Oncology and Developmental Biology, Maastricht University Medical Center+, Maastricht the Netherlands
- Pathology and Data Analytics, Leeds Institute of Medical Research at St James's University of Leeds Leeds United Kingdom
| | - Piet A. Brandt
- Department of Epidemiology GROW School for Oncology and Developmental Biology, Maastricht University Medical Center+, Maastricht the Netherlands
- Department of Epidemiology Care and Public Health Research Institute (CAPHRI) , Maastricht University Medical Center+, Maastricht the Netherlands
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9
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Jenniskens JC, Offermans K, Simons CCJM, Samarska I, Fazzi GE, Smits KM, Schouten LJ, Weijenberg MP, Grabsch HI, van den Brandt PA. Energy balance-related factors and risk of colorectal cancer expressing different levels of proteins involved in the Warburg-effect. Cancer Epidemiol Biomarkers Prev 2021; 31:633-646. [DOI: 10.1158/1055-9965.epi-21-0678] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 09/23/2021] [Accepted: 12/10/2021] [Indexed: 11/16/2022] Open
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10
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Offermans K, Jenniskens JC, Simons CC, Samarska I, Fazzi GE, Smits KM, Schouten LJ, Weijenberg MP, Grabsch HI, van den Brandt PA. Expression of proteins associated with the Warburg-effect and survival in colorectal cancer. J Pathol Clin Res 2021; 8:169-180. [PMID: 34791830 PMCID: PMC8822385 DOI: 10.1002/cjp2.250] [Citation(s) in RCA: 5] [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] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 09/17/2021] [Accepted: 09/30/2021] [Indexed: 12/23/2022]
Abstract
Previous research has suggested that the expression of proteins related to the Warburg effect may have prognostic value in colorectal cancer (CRC), but results remain inconsistent. Our objective was to investigate the relationship between Warburg-subtypes and patient survival in a large population-based series of CRC patients. In the present study, we investigated the expression of six proteins related to the Warburg effect (LDHA, GLUT1, MCT4, PKM2, p53, PTEN) by immunohistochemistry on tissue microarrays (TMAs) from 2,399 incident CRC patients from the prospective Netherlands Cohort Study. Expression levels of the six proteins were combined into a pathway-based sum-score and patients were categorised into three Warburg-subtypes (low/moderate/high). The associations between Warburg-subtypes and CRC-specific and overall survival were investigated using Kaplan-Meier curves and Cox regression models. CRC patients were classified as Warburg-low (n = 695, 29.0%), Warburg-moderate (n = 858, 35.8%) or Warburg-high (n = 841, 35.1%). Patients with Warburg-high CRC had the poorest CRC-specific [hazard ratio (HR) 1.17; 95% CI 1.00-1.38] and overall survival (HR 1.19; 95% CI 1.05-1.35), independent of known prognostic factors. In stratified analyses, this was particularly true for patients with tumour-node-metastasis (TNM) stage III CRC (HRCRC-specific 1.45; 95% CI 1.10-1.92 and HRoverall 1.47; 95% CI 1.15-1.87), and cancers located in the rectum (HRoverall 1.56; 95% CI 1.15-2.13). To our knowledge, this is the first study to identify the prognostic value of immunohistochemistry-based Warburg-subtypes in CRC. Our data suggest that Warburg-subtypes are related to potentially important differences in CRC survival. Further research is required to validate our findings and to investigate the potential clinical utility of these Warburg-subtypes in CRC.
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Affiliation(s)
- Kelly Offermans
- Department of Epidemiology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Josien Ca Jenniskens
- Department of Epidemiology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Colinda Cjm Simons
- Department of Epidemiology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Iryna Samarska
- Department of Pathology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Gregorio E Fazzi
- Department of Pathology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Kim M Smits
- Department of Pathology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Leo J Schouten
- Department of Epidemiology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Matty P Weijenberg
- Department of Epidemiology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Heike I Grabsch
- Department of Pathology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center+, Maastricht, The Netherlands.,Pathology and Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Piet A van den Brandt
- Department of Epidemiology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center+, Maastricht, The Netherlands.,Department of Epidemiology, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Center+, Maastricht, The Netherlands
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11
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Jenniskens JCA, Offermans K, Samarska I, Fazzi GE, Simons CCJM, Smits KM, Schouten LJ, Weijenberg MP, van den Brandt PA, Grabsch HI. Validity and Reproducibility of Immunohistochemical Scoring by Trained Non-Pathologists on Tissue Microarrays. Cancer Epidemiol Biomarkers Prev 2021; 30:1867-1874. [PMID: 34272264 DOI: 10.1158/1055-9965.epi-21-0295] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/04/2021] [Accepted: 07/12/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Scoring of immunohistochemistry (IHC) staining is often done by non-pathologists, especially in large-scale tissue microarray (TMA)-based studies. Studies on the validity and reproducibility of scoring results from non-pathologists are limited. Therefore, our main aim was to assess interobserver agreement between trained non-pathologists and an experienced histopathologist for three IHC markers with different subcellular localization (nucleus/membrane/cytoplasm). METHODS Three non-pathologists were trained in recognizing adenocarcinoma and IHC scoring by a senior histopathologist. Kappa statistics were used to analyze interobserver and intraobserver agreement for 6,249 TMA cores from a colorectal cancer series. RESULTS Interobserver agreement between non-pathologists (independently scored) and the histopathologist was "substantial" for nuclear and membranous IHC markers (κrange = 0.67-0.75 and κrange = 0.61-0.69, respectively), and "moderate" for the cytoplasmic IHC marker (κrange = 0.43-0.57). Scores of the three non-pathologists were also combined into a "combination score" (if at least two non-pathologists independently assigned the same score to a core, this was the combination score). This increased agreement with the pathologist (κnuclear = 0.74; κmembranous = 0.73; κcytopasmic = 0.57). Interobserver agreement between non-pathologists was "substantial" (κnuclear = 0.78; κmembranous = 0.72; κcytopasmic = 0.61). Intraobserver agreement of non-pathologists was "substantial" to "almost perfect" (κnuclear,range = 0.83-0.87; κmembranous,range = 0.75-0.82; κcytopasmic = 0.69). Overall, agreement was lowest for the cytoplasmic IHC marker. CONCLUSIONS This study shows that adequately trained non-pathologists are able to generate reproducible IHC scoring results, that are similar to those of an experienced histopathologist. A combination score of at least two non-pathologists yielded optimal results. IMPACT Non-pathologists can generate reproducible IHC results after appropriate training, making analyses of large-scale molecular pathological epidemiology studies feasible within an acceptable time frame.
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Affiliation(s)
- Josien C A Jenniskens
- Department of Epidemiology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center+, Maastricht, the Netherlands
| | - Kelly Offermans
- Department of Epidemiology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center+, Maastricht, the Netherlands
| | - Iryna Samarska
- Department of Pathology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center+, Maastricht, the Netherlands
| | - Gregorio E Fazzi
- Department of Pathology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center+, Maastricht, the Netherlands
| | - Colinda C J M Simons
- Department of Epidemiology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center+, Maastricht, the Netherlands
| | - Kim M Smits
- Department of Pathology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center+, Maastricht, the Netherlands
| | - Leo J Schouten
- Department of Epidemiology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center+, Maastricht, the Netherlands
| | - Matty P Weijenberg
- Department of Epidemiology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center+, Maastricht, the Netherlands
| | - Piet A van den Brandt
- Department of Epidemiology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center+, Maastricht, the Netherlands. .,Department of Epidemiology, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Center+, Maastricht, the Netherlands
| | - Heike I Grabsch
- Department of Pathology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center+, Maastricht, the Netherlands. .,Pathology and Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
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12
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Offermans K, Jenniskens JC, Samarska I, Fazzi GE, Simons CC, Smits KM, Schouten LJ, Weijenberg MP, van den Brandt PA, Grabsch HI. Abstract 830: Validity and reproducibility of immunohistochemical scoring by trained non-pathologists on Tissue MicroArrays. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-830] [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
Aims: Scoring of immunohistochemical (IHC) staining is often done by non-pathologists, especially in large-scale Tissue MicroArray (TMA)-based studies. Studies on the validity of scoring results from non-pathologists are very limited. Therefore, our main aim was to assess inter-observer agreement between trained non-pathologists and an experienced histopathologist for three IHC markers with different subcellular localisation (nucleus/membrane/cytoplasm).
Methods and results: Three non-pathologists were trained in recognizing adenocarcinoma and IHC scoring by a senior histopathologist. Kappa statistics were used to analyse inter- and intra-observer agreement for 6249 TMA cores from a colorectal cancer (CRC) series. Inter-observer agreement between non-pathologists (independently scored) and the histopathologist was “substantial” for nuclear and membranous IHC markers (κrange=0.67-0.75 and κrange=0.61-0.69, respectively), and “moderate” for the cytoplasmic IHC marker (κrange=0.43-0.57). Scores of the three non-pathologists were also combined into a combination score (if at least two non-pathologists independently assigned the same score to a core, this was the combination score). This increased agreement with the pathologist (κnuclear=0.74; κmembranous=0.73; κcytopasmic=0.56). Inter-observer agreement between non-pathologists was “substantial” (κnuclear=0.78; κmembranous=0.72; κcytopasmic=0.61). Intra-observer agreement of non-pathologists was “substantial” to “almost perfect” (κnuclear,range=0.83-0.87; κmembranous,range=0.75-0.82; κcytopasmic,range=0.69-0.69). Overall, agreement was lowest for the cytoplasmic IHC marker.
Conclusions: This study shows that adequately trained non-pathologists are able to produce similar IHC scoring results as an experienced histopathologist. Considering the histopathologist's score as the golden standard, we can conclude that trained non-pathologists can produce valid IHC results on TMA sections. A combination score of at least two non-pathologists yielded optimal results.
Citation Format: Kelly Offermans, Josien C. Jenniskens, Iryna Samarska, Gregorio E. Fazzi, Colinda C. Simons, Kim M. Smits, Leo J. Schouten, Matty P. Weijenberg, Piet A. van den Brandt, Heike I. Grabsch. Validity and reproducibility of immunohistochemical scoring by trained non-pathologists on Tissue MicroArrays [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 830.
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Affiliation(s)
- Kelly Offermans
- Maastricht University Medical Centre+, Maastricht, Netherlands
| | | | - Iryna Samarska
- Maastricht University Medical Centre+, Maastricht, Netherlands
| | | | | | - Kim M. Smits
- Maastricht University Medical Centre+, Maastricht, Netherlands
| | - Leo J. Schouten
- Maastricht University Medical Centre+, Maastricht, Netherlands
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13
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Vaes N, Schonkeren SL, Rademakers G, Holland AM, Koch A, Gijbels MJ, Keulers TG, de Wit M, Moonen L, Van der Meer JRM, van den Boezem E, Wolfs TGAM, Threadgill DW, Demmers J, Fijneman RJA, Jimenez CR, Vanden Berghe P, Smits KM, Rouschop KMA, Boesmans W, Hofstra RMW, Melotte V. Loss of enteric neuronal Ndrg4 promotes colorectal cancer via increased release of Nid1 and Fbln2. EMBO Rep 2021; 22:e51913. [PMID: 33890711 PMCID: PMC8183412 DOI: 10.15252/embr.202051913] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 10/16/2020] [Revised: 03/09/2021] [Accepted: 03/11/2021] [Indexed: 12/28/2022] Open
Abstract
The N-Myc Downstream-Regulated Gene 4 (NDRG4), a prominent biomarker for colorectal cancer (CRC), is specifically expressed by enteric neurons. Considering that nerves are important members of the tumor microenvironment, we here establish different Ndrg4 knockout (Ndrg4-/- ) CRC models and an indirect co-culture of primary enteric nervous system (ENS) cells and intestinal organoids to identify whether the ENS, via NDRG4, affects intestinal tumorigenesis. Linking immunostainings and gastrointestinal motility (GI) assays, we show that the absence of Ndrg4 does not trigger any functional or morphological GI abnormalities. However, combining in vivo, in vitro, and quantitative proteomics data, we uncover that Ndrg4 knockdown is associated with enlarged intestinal adenoma development and that organoid growth is boosted by the Ndrg4-/- ENS cell secretome, which is enriched for Nidogen-1 (Nid1) and Fibulin-2 (Fbln2). Moreover, NID1 and FBLN2 are expressed in enteric neurons, enhance migration capacities of CRC cells, and are enriched in human CRC secretomes. Hence, we provide evidence that the ENS, via loss of Ndrg4, is involved in colorectal pathogenesis and that ENS-derived Nidogen-1 and Fibulin-2 enhance colorectal carcinogenesis.
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Affiliation(s)
- Nathalie Vaes
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Simone L Schonkeren
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Glenn Rademakers
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Amy M Holland
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Alexander Koch
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Marion J Gijbels
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
- Department of Molecular GeneticsCardiovascular Research Institute Maastricht (CARIM)MaastrichtThe Netherlands
- Department of Medical BiochemistryAcademic Medical CenterAmsterdamThe Netherlands
| | - Tom G Keulers
- Department of RadiotherapyGROW‐School for Oncology and Developmental Biology and Comprehensive Cancer Center Maastricht MUMC+Maastricht UniversityMaastrichtThe Netherlands
| | - Meike de Wit
- Department of Medical Oncology and Oncoproteomics LaboratoryCancer Center AmsterdamVrije Universiteit AmsterdamAmsterdam UMCAmsterdamThe Netherlands
- Department of PathologyNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Laura Moonen
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Jaleesa R M Van der Meer
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Edith van den Boezem
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Tim G A M Wolfs
- Department of PediatricsGROW‐School for Oncology and Developmental BiologyMaastricht UniversityMaastrichtThe Netherlands
| | - David W Threadgill
- Department of Molecular and Cellular MedicineTexas A&M University Health Science CenterCollege StationTXUSA
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTXUSA
| | - Jeroen Demmers
- Proteomics CenterErasmus University Medical CenterRotterdamThe Netherlands
| | | | - Connie R Jimenez
- Department of Medical Oncology and Oncoproteomics LaboratoryCancer Center AmsterdamVrije Universiteit AmsterdamAmsterdam UMCAmsterdamThe Netherlands
| | - Pieter Vanden Berghe
- Laboratory for Enteric Neuroscience (LENS) and Translational Research Center for Gastrointestinal Disorders (TARGID)Department of Chronic Diseases, Metabolism and AgeingKU LeuvenLeuvenBelgium
| | - Kim M Smits
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Kasper M A Rouschop
- Department of RadiotherapyGROW‐School for Oncology and Developmental Biology and Comprehensive Cancer Center Maastricht MUMC+Maastricht UniversityMaastrichtThe Netherlands
| | - Werend Boesmans
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
- Biomedical Research Institute (BIOMED)Hasselt UniversityHasseltBelgium
| | - Robert M W Hofstra
- Department of Clinical GeneticsErasmus University Medical CenterRotterdamThe Netherlands
| | - Veerle Melotte
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
- Department of Clinical GeneticsErasmus University Medical CenterRotterdamThe Netherlands
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14
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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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15
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Rademakers G, Massen M, Koch A, Draht MX, Buekers N, Wouters KAD, Vaes N, De Meyer T, Carvalho B, Meijer GA, Herman JG, Smits KM, van Engeland M, Melotte V. Identification of DNA methylation markers for early detection of CRC indicates a role for nervous system-related genes in CRC. Clin Epigenetics 2021; 13:80. [PMID: 33858496 PMCID: PMC8048074 DOI: 10.1186/s13148-021-01067-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 03/05/2021] [Accepted: 04/04/2021] [Indexed: 12/17/2022] Open
Abstract
Purpose Colonoscopy and the fecal immunochemical test (FIT) are currently the most widely used screening modalities for colorectal cancer (CRC), however, both with their own limitations. Here we aim to identify and validate stool-based DNA methylation markers for the early detection of CRC and investigate the biological pathways prone to DNA methylation. Methods DNA methylation marker discovery was performed using The Cancer Genome Atlas (TCGA) colon adenocarcinoma data set consisting of normal and primary colon adenocarcinoma tissue. The performance of the five best candidate markers and a previously identified marker, NDRG4, was evaluated on tissues and whole stool samples of healthy subjects and CRC patients using quantitative MSP assays. The results were compared and combined with FIT data. Finally, pathway and gene ontology enrichment analyses were performed using ToppFun, GOrilla and clusterProfiler. Results GDNF, HAND2, SLC35F3, SNAP91 and SORCS1 were ranked as the best performing markers. Gene combinations of all five markers, NDRG4 and FIT were evaluated to establish the biomarker panel with the highest diagnostic potential, resulting in the identification of GDNF/SNAP91/NDRG4/FIT as the best performing marker panel. Pathway and gene ontology enrichment analyses revealed that genes associated with the nervous system were enriched in the set of best performing CRC-specific biomarkers. Conclusion In silico discovery analysis using TCGA-derived data yielded a novel DNA-methylation-based assay for the early detection of CRC, potentially improving current screening modalities. Additionally, nervous system-related pathways were enriched in the identified genes, indicating an epigenetic regulation of neuronal genes in CRC. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01067-9.
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Affiliation(s)
- Glenn Rademakers
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Maartje Massen
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Alexander Koch
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Muriel X Draht
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Nikkie Buekers
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Kim A D Wouters
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Nathalie Vaes
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Tim De Meyer
- Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium
| | - Beatriz Carvalho
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Gerrit A Meijer
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - James G Herman
- The Hillman Cancer Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
| | - Kim M Smits
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Manon van Engeland
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Veerle Melotte
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands. .,Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands.
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16
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de Ruijter TC, van der Heide F, Smits KM, Aarts MJ, van Engeland M, Heijnen VCG. Prognostic DNA methylation markers for hormone receptor breast cancer: a systematic review. Breast Cancer Res 2020; 22:13. [PMID: 32005275 PMCID: PMC6993426 DOI: 10.1186/s13058-020-1250-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [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: 08/07/2019] [Accepted: 01/15/2020] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND In patients with hormone receptor-positive breast cancer, differentiating between patients with a low and a high risk of recurrence is an ongoing challenge. In current practice, prognostic clinical parameters are used for risk prediction. DNA methylation markers have been proven to be of additional prognostic value in several cancer types. Numerous prognostic DNA methylation markers for breast cancer have been published in the literature. However, to date, none of these markers are used in clinical practice. METHODS We conducted a systematic review of PubMed and EMBASE to assess the number and level of evidence of published DNA methylation markers for hormone receptor-positive breast cancer. To obtain an overview of the reporting quality of the included studies, all were scored according to the REMARK criteria that were established as reporting guidelines for prognostic biomarker studies. RESULTS A total of 74 studies were identified reporting on 87 different DNA methylation markers. Assessment of the REMARK criteria showed variation in reporting quality of the studies. Eighteen single markers and one marker panel were studied in multiple independent populations. Hypermethylation of the markers RASSF1, BRCA, PITX2, CDH1, RARB, PCDH10 and PGR, and the marker panel GSTP1, RASSF1 and RARB showed a statistically significant correlation with poor disease outcome that was confirmed in at least one other, independent study. CONCLUSION This systematic review provides an overview on published prognostic DNA methylation markers for hormone receptor-positive breast cancer and identifies eight markers that have been independently validated. Analysis of the reporting quality of included studies suggests that future research on this topic would benefit from standardised reporting guidelines.
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Affiliation(s)
- Tim C. de Ruijter
- Division of Medical Oncology, Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
- GROW – School for Oncology and Developmental Biology, Maastricht University Medical Center, 6200 MD Maastricht, The Netherlands
| | - Frank van der Heide
- Division of Medical Oncology, Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Kim M. Smits
- Division of Medical Oncology, Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
- GROW – School for Oncology and Developmental Biology, Maastricht University Medical Center, 6200 MD Maastricht, The Netherlands
- Department of Pathology, Maastricht University Medical Centre, 6202 AZ Maastricht, The Netherlands
| | - Maureen J. Aarts
- Division of Medical Oncology, Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
- GROW – School for Oncology and Developmental Biology, Maastricht University Medical Center, 6200 MD Maastricht, The Netherlands
| | - Manon van Engeland
- GROW – School for Oncology and Developmental Biology, Maastricht University Medical Center, 6200 MD Maastricht, The Netherlands
- Department of Pathology, Maastricht University Medical Centre, 6202 AZ Maastricht, The Netherlands
| | - Vivianne C. G. Heijnen
- Division of Medical Oncology, Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
- GROW – School for Oncology and Developmental Biology, Maastricht University Medical Center, 6200 MD Maastricht, The Netherlands
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17
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de Ruijter TC, Smits KM, Aarts MJ, van Hellemond IEG, Van Neste L, de Vries B, Peer PGM, Veeck J, van Engeland M, Tjan-Heijnen VCG. The trans-DATA study: aims and design of a translational breast cancer prognostic marker identification study. Diagn Progn Res 2019; 3:20. [PMID: 31641693 PMCID: PMC6796450 DOI: 10.1186/s41512-019-0065-6] [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] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 08/12/2019] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The effect of extended adjuvant aromatase inhibition in hormone-positive breast cancer after sequential tamoxifen, aromatase inhibitor treatment of 5 years was recently investigated by the DATA study. This study found no statistically significant effect of prolonged aromatase therapy. However, subgroup analysis showed post hoc statistically significant benefits in certain sub-populations. The trans-DATA study is a translational sub-study aiming to identify DNA methylation markers prognostic of patient outcome. METHODS Patients from the DATA study are included in the trans-DATA study. Primary breast tumour tissue will be collected, subtyped and used for DNA isolation. A genome-wide DNA methylation discovery assay will be performed on 60 patients that had a distant recurrence and 60 patients that did not have a distant recurrence using the Infinium Methylation EPIC Bead Chip platform. Differentially methylated regions of interest will be selected based on Akaike's Information Criterion, Gene Ontology Analysis and correlation between methylation and expression levels. Selected candidate genes will subsequently be validated in the remaining patients using qMSP. DISCUSSION The trans-DATA study uses a cohort derived from a clinical randomised trial. This study was designed to avoid common pitfalls in marker discovery studies such as selection bias, confounding and lack of reproducibility. In addition to the usual clinical risk factors, the results of this study may identify predictors of high recurrence risk in hormone receptor-positive breast cancer patients treated with sequential tamoxifen and aromatase inhibitor therapy.
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Affiliation(s)
- Tim C. de Ruijter
- 0000 0004 0480 1382grid.412966.eDivision of Medical Oncology, Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
- 0000 0004 0480 1382grid.412966.eGROW – School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Kim M. Smits
- 0000 0004 0480 1382grid.412966.eDivision of Medical Oncology, Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
- 0000 0004 0480 1382grid.412966.eGROW – School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
- 0000 0004 0480 1382grid.412966.eDepartment of Pathology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Maureen J. Aarts
- 0000 0004 0480 1382grid.412966.eDivision of Medical Oncology, Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
- 0000 0004 0480 1382grid.412966.eGROW – School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Irene E. G. van Hellemond
- 0000 0004 0480 1382grid.412966.eDivision of Medical Oncology, Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
- 0000 0004 0480 1382grid.412966.eGROW – School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Leander Van Neste
- 0000 0004 0480 1382grid.412966.eGROW – School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
- 0000 0004 0480 1382grid.412966.eDepartment of Pathology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Bart de Vries
- Department of Pathology, Zuyderland Medical Centre, Heerlen, The Netherlands
| | - Petronella G. M. Peer
- 0000 0004 0444 9382grid.10417.33Biostatistics, Department for Health Evidence, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jürgen Veeck
- 0000 0004 0480 1382grid.412966.eDivision of Medical Oncology, Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
- 0000 0004 0480 1382grid.412966.eGROW – School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Manon van Engeland
- 0000 0004 0480 1382grid.412966.eGROW – School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
- 0000 0004 0480 1382grid.412966.eDepartment of Pathology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Vivianne C. G. Tjan-Heijnen
- 0000 0004 0480 1382grid.412966.eDivision of Medical Oncology, Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
- 0000 0004 0480 1382grid.412966.eGROW – School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
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Joosten SC, Deckers IA, Aarts MJ, Hoeben A, van Roermund JG, Smits KM, Melotte V, van Engeland M, Tjan-Heijnen VC. Prognostic DNA methylation markers for renal cell carcinoma: a systematic review. Epigenomics 2017; 9:1243-1257. [PMID: 28803494 DOI: 10.2217/epi-2017-0040] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [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: 02/06/2023] Open
Abstract
AIM Despite numerous published prognostic methylation markers for renal cell carcinoma (RCC), none of these have yet changed patient management. Our aim is to systematically review and evaluate the literature on prognostic DNA methylation markers for RCC. MATERIALS & METHODS We conducted an exhaustive search of PubMed, EMBASE and MEDLINE up to April 2017 and identified 49 publications. Studies were reviewed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement, assessed for their reporting quality using the Reporting Recommendations for Tumor Marker Prognostic Studies (REMARK) criteria, and were graded to determine the level of evidence (LOE) for each biomarker. RESULTS We identified promoter methylation of BNC1, SCUBE3, GATA5, SFRP1, GREM1, RASSF1A, PCDH8, LAD1 and NEFH as promising prognostic markers. Extensive methodological heterogeneity across the included studies was observed, which hampers comparability and reproducibility of results, providing a possible explanation why these biomarkers do not reach the clinic. CONCLUSION Potential prognostic methylation markers for RCC have been identified, but they require further validation in prospective studies to determine their true clinical value.
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Affiliation(s)
- Sophie C Joosten
- Division of Medical Oncology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Ivette Ag Deckers
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Maureen J Aarts
- Division of Medical Oncology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Ann Hoeben
- Division of Medical Oncology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Joep G van Roermund
- Department of Urology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Kim M Smits
- Division of Medical Oncology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands.,Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Veerle Melotte
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Manon 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
| | - Vivianne C Tjan-Heijnen
- Division of Medical Oncology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands
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19
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van Vlodrop IJH, Joosten SC, De Meyer T, Smits KM, Van Neste L, Melotte V, Baldewijns MMLL, Schouten LJ, van den Brandt PA, Jeschke J, Yi JM, Schuebel KE, Ahuja N, Herman JG, Aarts MJ, Bosman FT, Van Criekinge W, van Engeland M. A Four-Gene Promoter Methylation Marker Panel Consisting of GREM1, NEURL, LAD1, and NEFH Predicts Survival of Clear Cell Renal Cell Cancer Patients. Clin Cancer Res 2017; 23:2006-2018. [PMID: 27756787 DOI: 10.1158/1078-0432.ccr-16-1236] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 09/02/2016] [Accepted: 09/24/2016] [Indexed: 11/16/2022]
Abstract
Purpose: The currently used prognostic models for patients with nonmetastatic clear cell renal cell carcinoma (ccRCC) are based on clinicopathologic features and might be improved by adding molecular markers. Epigenetic alterations occur frequently in ccRCC and are promising biomarkers. The aim of this study is to identify prognostic promoter methylation markers for ccRCC.Experimental Design: We integrated data generated by massive parallel sequencing of methyl-binding domain enriched DNA and microarray-based RNA expression profiling of 5-aza-2'-deoxycytidine-treated ccRCC cell lines to comprehensively characterize the ccRCC methylome. A selection of the identified methylation markers was evaluated in two independent series of primary ccRCC (n = 150 and n = 185) by methylation-specific PCR. Kaplan-Meier curves and log-rank tests were used to estimate cause-specific survival. HRs and corresponding 95% confidence intervals (CI) were assessed using Cox proportional hazard models. To assess the predictive capacity and fit of models combining several methylation markers, HarrellC statistic and the Akaike Information Criterion were used.Results: We identified four methylation markers, that is, GREM1, NEURL, LAD1, and NEFH, that individually predicted prognosis of patients with ccRCC. The four markers combined were associated with poorer survival in two independent patient series (HR, 3.64; 95% CI, 1.02-13.00 and HR, 7.54; 95% CI, 2.68-21.19). These findings were confirmed in a third series of ccRCC cases from The Cancer Genome Atlas (HR, 3.60; 95% CI, 2.02-6.40).Conclusions: A four-gene promoter methylation marker panel consisting of GREM1, NEURL, LAD1, and NEFH predicts outcome of patients with ccRCC and might be used to improve current prognostic models. Clin Cancer Res; 23(8); 2006-18. ©2016 AACR.
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Affiliation(s)
- Iris J H van Vlodrop
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Sophie C Joosten
- Division of Medical Oncology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Tim De Meyer
- BioBix: Laboratory of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium
| | - Kim M Smits
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
- Department of Radiation Oncology (MAASTRO), GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Leander Van Neste
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Veerle Melotte
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Marcella M L L Baldewijns
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Leo J Schouten
- Department of Epidemiology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Piet A van den Brandt
- Department of Epidemiology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Jana Jeschke
- The Sidney Kimmel Comprehensive Cancer Center at the Johns Hopkins University School of Medicine, Baltimore, Maryland
- Laboratory of Cancer Epigenetics, Faculty of Medicine, Université Libre de Bruxelles, Brussels, Belgium
| | - Joo Mi Yi
- Research Institute, Dongnam Institute of Radiological and Medical Sciences (DIRAMS), Jangan-eup, Gijang-gun, Busan, Korea
| | - Kornel E Schuebel
- The Sidney Kimmel Comprehensive Cancer Center at the Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Nita Ahuja
- The Sidney Kimmel Comprehensive Cancer Center at the Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Maureen J Aarts
- Division of Medical Oncology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Fred T Bosman
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Wim Van Criekinge
- BioBix: Laboratory of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium
| | - Manon van Engeland
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands.
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Lambin P, Zindler J, Vanneste BGL, De Voorde LV, Eekers D, Compter I, Panth KM, Peerlings J, Larue RTHM, Deist TM, Jochems A, Lustberg T, van Soest J, de Jong EEC, Even AJG, Reymen B, Rekers N, van Gisbergen M, Roelofs E, Carvalho S, Leijenaar RTH, Zegers CML, Jacobs M, van Timmeren J, Brouwers P, Lal JA, Dubois L, Yaromina A, Van Limbergen EJ, Berbee M, van Elmpt W, Oberije C, Ramaekers B, Dekker A, Boersma LJ, Hoebers F, Smits KM, Berlanga AJ, Walsh S. Decision support systems for personalized and participative radiation oncology. Adv Drug Deliv Rev 2017; 109:131-153. [PMID: 26774327 DOI: 10.1016/j.addr.2016.01.006] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 12/08/2015] [Accepted: 01/06/2016] [Indexed: 12/12/2022]
Abstract
A paradigm shift from current population based medicine to personalized and participative medicine is underway. This transition is being supported by the development of clinical decision support systems based on prediction models of treatment outcome. In radiation oncology, these models 'learn' using advanced and innovative information technologies (ideally in a distributed fashion - please watch the animation: http://youtu.be/ZDJFOxpwqEA) from all available/appropriate medical data (clinical, treatment, imaging, biological/genetic, etc.) to achieve the highest possible accuracy with respect to prediction of tumor response and normal tissue toxicity. In this position paper, we deliver an overview of the factors that are associated with outcome in radiation oncology and discuss the methodology behind the development of accurate prediction models, which is a multi-faceted process. Subsequent to initial development/validation and clinical introduction, decision support systems should be constantly re-evaluated (through quality assurance procedures) in different patient datasets in order to refine and re-optimize the models, ensuring the continuous utility of the models. In the reasonably near future, decision support systems will be fully integrated within the clinic, with data and knowledge being shared in a standardized, dynamic, and potentially global manner enabling truly personalized and participative medicine.
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Affiliation(s)
- Philippe Lambin
- Department of Radiation Oncology (MAASTRO), GROW, School for Oncology and Developmental Biology, Maastricht University Medical Centre+, Maastricht, The Netherlands.
| | - Jaap Zindler
- Department of Radiation Oncology (MAASTRO), GROW, School for Oncology and Developmental Biology, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Ben G L Vanneste
- Department of Radiation Oncology (MAASTRO), GROW, School for Oncology and Developmental Biology, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Lien Van De Voorde
- Department of Radiation Oncology (MAASTRO), GROW, School for Oncology and Developmental Biology, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Daniëlle Eekers
- Department of Radiation Oncology (MAASTRO), GROW, School for Oncology and Developmental Biology, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Inge Compter
- Department of Radiation Oncology (MAASTRO), GROW, School for Oncology and Developmental Biology, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Kranthi Marella Panth
- Department of Radiation Oncology (MAASTRO), GROW, School for Oncology and Developmental Biology, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Jurgen Peerlings
- Department of Radiation Oncology (MAASTRO), GROW, School for Oncology and Developmental Biology, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Ruben T H M Larue
- Department of Radiation Oncology (MAASTRO), GROW, School for Oncology and Developmental Biology, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Timo M Deist
- Department of Radiation Oncology (MAASTRO), GROW, School for Oncology and Developmental Biology, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Arthur Jochems
- Department of Radiation Oncology (MAASTRO), GROW, School for Oncology and Developmental Biology, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Tim Lustberg
- Department of Radiation Oncology (MAASTRO), GROW, School for Oncology and Developmental Biology, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Johan van Soest
- Department of Radiation Oncology (MAASTRO), GROW, School for Oncology and Developmental Biology, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Evelyn E C de Jong
- Department of Radiation Oncology (MAASTRO), GROW, School for Oncology and Developmental Biology, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Aniek J G Even
- Department of Radiation Oncology (MAASTRO), GROW, School for Oncology and Developmental Biology, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Bart Reymen
- Department of Radiation Oncology (MAASTRO), GROW, School for Oncology and Developmental Biology, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Nicolle Rekers
- Department of Radiation Oncology (MAASTRO), GROW, School for Oncology and Developmental Biology, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Marike van Gisbergen
- Department of Radiation Oncology (MAASTRO), GROW, School for Oncology and Developmental Biology, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Erik Roelofs
- Department of Radiation Oncology (MAASTRO), GROW, School for Oncology and Developmental Biology, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Sara Carvalho
- Department of Radiation Oncology (MAASTRO), GROW, School for Oncology and Developmental Biology, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Ralph T H Leijenaar
- Department of Radiation Oncology (MAASTRO), GROW, School for Oncology and Developmental Biology, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Catharina M L Zegers
- Department of Radiation Oncology (MAASTRO), GROW, School for Oncology and Developmental Biology, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Maria Jacobs
- Department of Radiation Oncology (MAASTRO), GROW, School for Oncology and Developmental Biology, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Janita van Timmeren
- Department of Radiation Oncology (MAASTRO), GROW, School for Oncology and Developmental Biology, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Patricia Brouwers
- Department of Radiation Oncology (MAASTRO), GROW, School for Oncology and Developmental Biology, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Jonathan A Lal
- Department of Radiation Oncology (MAASTRO), GROW, School for Oncology and Developmental Biology, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Ludwig Dubois
- Department of Radiation Oncology (MAASTRO), GROW, School for Oncology and Developmental Biology, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Ala Yaromina
- Department of Radiation Oncology (MAASTRO), GROW, School for Oncology and Developmental Biology, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Evert Jan Van Limbergen
- Department of Radiation Oncology (MAASTRO), GROW, School for Oncology and Developmental Biology, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Maaike Berbee
- Department of Radiation Oncology (MAASTRO), GROW, School for Oncology and Developmental Biology, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Wouter van Elmpt
- Department of Radiation Oncology (MAASTRO), GROW, School for Oncology and Developmental Biology, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Cary Oberije
- Department of Radiation Oncology (MAASTRO), GROW, School for Oncology and Developmental Biology, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Bram Ramaekers
- Department of Radiation Oncology (MAASTRO), GROW, School for Oncology and Developmental Biology, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Andre Dekker
- Department of Radiation Oncology (MAASTRO), GROW, School for Oncology and Developmental Biology, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Liesbeth J Boersma
- Department of Radiation Oncology (MAASTRO), GROW, School for Oncology and Developmental Biology, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Frank Hoebers
- Department of Radiation Oncology (MAASTRO), GROW, School for Oncology and Developmental Biology, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Kim M Smits
- Department of Radiation Oncology (MAASTRO), GROW, School for Oncology and Developmental Biology, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Adriana J Berlanga
- Department of Radiation Oncology (MAASTRO), GROW, School for Oncology and Developmental Biology, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Sean Walsh
- Department of Radiation Oncology (MAASTRO), GROW, School for Oncology and Developmental Biology, Maastricht University Medical Centre+, Maastricht, The Netherlands
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21
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van Loon J, Even AJG, Aerts HJWL, Öllers M, Hoebers F, van Elmpt W, Dubois L, Dingemans AMC, Lalisang RI, Kempers P, Brans B, Winnepenninckx V, Speel EJ, Thunnissen E, Smits KM, Boellaard R, Vugts DJ, De Ruysscher D, Lambin P. PET imaging of zirconium-89 labelled cetuximab: A phase I trial in patients with head and neck and lung cancer. Radiother Oncol 2016; 122:267-273. [PMID: 28012793 DOI: 10.1016/j.radonc.2016.11.020] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 11/18/2016] [Accepted: 11/26/2016] [Indexed: 02/07/2023]
Abstract
BACKGROUND AND PURPOSE PET imaging of cetuximab uptake may help selecting cancer patients with the highest chance of benefit. The aim of this phase I trial was to determine the safety of the tracer 89Zr-cetuximab and to assess tumour uptake. METHODS Two dose schedules were used; two consecutive doses of 60MBq 89Zr-cetuximab or a single dose of 120MBq, both preceded by 400mg/m2 of unlabelled cetuximab. Toxicity (CTCAE 3.0) was scored twice weekly. PET-CT scans were acquired on days 4, 5 and 6 (step 1) or 5, 6, 7 (step 2). Because tumour uptake could not be assessed satisfactorily, a third step was added including EGFR overexpressing tumours. RESULTS Nine patients were included (6 NSCLC; 3 HNC). No additional toxicity was associated with administration of 89Zr-cetuximab compared to standard cetuximab. A tumour to blood ratio (TBR)>1 was observed in all but one patient, with a maximum of 4.56. TBR was not different between dose schedules. There was a trend for higher TBR at intervals>5days after injection. CONCLUSIONS Both presented 89Zr-cetuximab administration schedules are safe. The recommended dose for future trials is 60MBq, with a minimum time interval for scanning of 6days.
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Affiliation(s)
- Judith van Loon
- Department of Radiation Oncology (MAASTRO), GROW - School for Oncology and Developmental Biology, Maastricht University Medical Centre, The Netherlands.
| | - Aniek J G Even
- Department of Radiation Oncology (MAASTRO), GROW - School for Oncology and Developmental Biology, Maastricht University Medical Centre, The Netherlands
| | - Hugo J W L Aerts
- Department of Radiation Oncology (MAASTRO), GROW - School for Oncology and Developmental Biology, Maastricht University Medical Centre, The Netherlands; Departments of Radiation Oncology and Radiology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, USA
| | - Michel Öllers
- Department of Radiation Oncology (MAASTRO), GROW - School for Oncology and Developmental Biology, Maastricht University Medical Centre, The Netherlands
| | - Frank Hoebers
- Department of Radiation Oncology (MAASTRO), GROW - School for Oncology and Developmental Biology, Maastricht University Medical Centre, The Netherlands
| | - Wouter van Elmpt
- Department of Radiation Oncology (MAASTRO), GROW - School for Oncology and Developmental Biology, Maastricht University Medical Centre, The Netherlands
| | - Ludwig Dubois
- Department of Radiation Oncology (MAASTRO), GROW - School for Oncology and Developmental Biology, Maastricht University Medical Centre, The Netherlands
| | | | - Roy I Lalisang
- Department of Medical Oncology, Maastricht University Medical Centre, The Netherlands
| | - Pascal Kempers
- Department of Nuclear Medicine, Maastricht University Medical Centre, The Netherlands
| | - Boudewijn Brans
- Department of Nuclear Medicine, Maastricht University Medical Centre, The Netherlands
| | | | - Ernst-Jan Speel
- Department of Pathology, Maastricht University Medical Centre, The Netherlands
| | - Eric Thunnissen
- Department of Pathology, VU University Medical Centre, Amsterdam, The Netherlands
| | - Kim M Smits
- Department of Radiation Oncology (MAASTRO), GROW - School for Oncology and Developmental Biology, Maastricht University Medical Centre, The Netherlands
| | - Ronald Boellaard
- Department of Radiology and Nuclear Medicine, VU University Medical Centre, Amsterdam, The Netherlands
| | - Danielle J Vugts
- Department of Radiology and Nuclear Medicine, VU University Medical Centre, Amsterdam, The Netherlands
| | - Dirk De Ruysscher
- Department of Radiation Oncology (MAASTRO), GROW - School for Oncology and Developmental Biology, Maastricht University Medical Centre, The Netherlands; Department of Radiation Oncology, University Hospital Leuven, KU Leuven, Belgium
| | - Philippe Lambin
- Department of Radiation Oncology (MAASTRO), GROW - School for Oncology and Developmental Biology, Maastricht University Medical Centre, The Netherlands
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22
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Draht MXG, Smits KM, Jooste V, Tournier B, Vervoort M, Ramaekers C, Chapusot C, Weijenberg MP, van Engeland M, Melotte V. Analysis of RET promoter CpG island methylation using methylation-specific PCR (MSP), pyrosequencing, and methylation-sensitive high-resolution melting (MS-HRM): impact on stage II colon cancer patient outcome. Clin Epigenetics 2016; 8:44. [PMID: 27118999 PMCID: PMC4845472 DOI: 10.1186/s13148-016-0211-8] [Citation(s) in RCA: 16] [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: 12/10/2015] [Accepted: 04/14/2016] [Indexed: 12/20/2022] Open
Abstract
Background Already since the 1990s, promoter CpG island methylation markers have been considered promising diagnostic, prognostic, and predictive cancer biomarkers. However, so far, only a limited number of DNA methylation markers have been introduced into clinical practice. One reason why the vast majority of methylation markers do not translate into clinical applications is lack of independent validation of methylation markers, often caused by differences in methylation analysis techniques. We recently described RET promoter CpG island methylation as a potential prognostic marker in stage II colorectal cancer (CRC) patients of two independent series. Methods In the current study, we analyzed the RET promoter CpG island methylation of 241 stage II colon cancer patients by direct methylation-specific PCR (MSP), nested-MSP, pyrosequencing, and methylation-sensitive high-resolution melting (MS-HRM). All primers were designed as close as possible to the same genomic region. In order to investigate the effect of different DNA methylation assays on patient outcome, we assessed the clinical sensitivity and specificity as well as the association of RET methylation with overall survival for three and five years of follow-up. Results Using direct-MSP and nested-MSP, 12.0 % (25/209) and 29.6 % (71/240) of the patients showed RET promoter CpG island methylation. Methylation frequencies detected by pyrosequencing were related to the threshold for positivity that defined RET methylation. Methylation frequencies obtained by pyrosequencing (threshold for positivity at 20 %) and MS-HRM were 13.3 % (32/240) and 13.8 % (33/239), respectively. The pyrosequencing threshold for positivity of 20 % showed the best correlation with MS-HRM and direct-MSP results. Nested-MSP detected RET promoter CpG island methylation in deceased patients with a higher sensitivity (33.1 %) compared to direct-MSP (10.7 %), pyrosequencing (14.4 %), and MS-HRM (15.4 %). While RET methylation frequencies detected by nested-MSP, pyrosequencing, and MS-HRM varied, the prognostic effect seemed similar (HR 1.74, 95 % CI 0.97–3.15; HR 1.85, 95 % CI 0.93–3.86; HR 1.83, 95 % CI 0.92–3.65, respectively). Conclusions Our results show that upon optimizing and aligning four RET methylation assays with regard to primer location and sensitivity, differences in methylation frequencies and clinical sensitivities are observed; however, the effect on the marker’s prognostic outcome is minimal. Electronic supplementary material The online version of this article (doi:10.1186/s13148-016-0211-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Muriel X G Draht
- Department of Pathology, GROW - School for Oncology & Developmental Biology, Maastricht University Medical Center, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Kim M Smits
- Department of Radiation Oncology (MAASTRO), GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Valérie Jooste
- Registre Bourguignon des cancers digestifs, INSERM U866, Universite de Bourgogne, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | - Benjamin Tournier
- Service de Pathologie, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | - Martijn Vervoort
- Zuyd University of Applied Sciences, Heerlen, The Netherlands ; Chemelot Innovation and Learning Labs, Geleen, The Netherlands
| | | | - Caroline Chapusot
- Service de Pathologie, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | - Matty P Weijenberg
- Department of Epidemiology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Manon van Engeland
- Department of Pathology, GROW - School for Oncology & Developmental Biology, Maastricht University Medical Center, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Veerle Melotte
- Department of Pathology, GROW - School for Oncology & Developmental Biology, Maastricht University Medical Center, P.O. Box 616, 6200 MD Maastricht, The Netherlands
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23
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Cleven AHG, Derks S, Draht MXG, Smits KM, Melotte V, Van Neste L, Tournier B, Jooste V, Chapusot C, Weijenberg MP, Herman JG, de Bruïne AP, van Engeland M. CHFR promoter methylation indicates poor prognosis in stage II microsatellite stable colorectal cancer. Clin Cancer Res 2015; 20:3261-71. [PMID: 24928946 DOI: 10.1158/1078-0432.ccr-12-3734] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [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
PURPOSE Data on the prognostic significance of promoter CpG island methylation in colorectal cancer (CRC) are conflicting, possibly due to associations between methylation and other factors affecting survival such as genetic alterations and use of adjuvant therapy. Here, we examine the prognostic impact of promoter methylation in patients with CRC treated with surgery alone in the context of microsatellite instability (MSI), BRAF and KRAS mutations. EXPERIMENTAL METHODS One hundred and seventy-three CRCs were analyzed for promoter methylation of 19 tumor suppressor and DNA repair genes, the CpG island methylator phenotype (CIMP), MSI, the exon 15 V600E BRAF mutation and KRAS codon 12 and 13 mutations. RESULTS Unsupervised hierarchical clustering based on methylation status of 19 genes revealed three subgroups: cluster 1 [CL1, 57% (98/173) of CRCs], cluster 2 [CL2, 25% (43/173) of CRCs], and cluster 3 [CL3, 18% (32/173) of CRCs]. CL3 had the highest methylation index (0.25, 0.49, and 0.69, respectively, P = <0.01) and was strongly associated with CIMP (P < 0.01). Subgroup analysis for tumor stage, MSI, and BRAF status showed no statistically significant differences in survival between CL1, CL2, and CL3 nor between CIMP and non-CIMP CRCs. Analyzing genes separately revealed that CHFR promoter methylation was associated with a poor prognosis in stage II, microsatellite stability (MSS), BRAF wild-type (WT) CRCs: multivariate Cox proportional HR = 3.89 [95% confidence interval (CI), 1.58-9.60, P < 0.01; n = 66] and HR = 2.11 (95% CI, 0.95-4.69, P = 0.068, n = 136) in a second independent population-based study. CONCLUSIONS CHFR promoter CpG island methylation, which is associated with MSI, also occurs frequently in MSS CRCs and is a promising prognostic marker in stage II, MSS, BRAF WT CRCs.
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Affiliation(s)
- Arjen H G Cleven
- Authors' Affiliations: Departments of Pathology, Radiation Oncology (MAASTRO) and Epidemiology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands; Service de Pathologie; Registre des cancers digestifs, Université de Bourgogne, Centre Hospitalier Universitaire de Dijon, Dijon, France; and The Sidney Kimmel Comprehensive Cancer Center at the Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Sarah Derks
- Authors' Affiliations: Departments of Pathology, Radiation Oncology (MAASTRO) and Epidemiology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands; Service de Pathologie; Registre des cancers digestifs, Université de Bourgogne, Centre Hospitalier Universitaire de Dijon, Dijon, France; and The Sidney Kimmel Comprehensive Cancer Center at the Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Muriel X G Draht
- Authors' Affiliations: Departments of Pathology, Radiation Oncology (MAASTRO) and Epidemiology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands; Service de Pathologie; Registre des cancers digestifs, Université de Bourgogne, Centre Hospitalier Universitaire de Dijon, Dijon, France; and The Sidney Kimmel Comprehensive Cancer Center at the Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kim M Smits
- Authors' Affiliations: Departments of Pathology, Radiation Oncology (MAASTRO) and Epidemiology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands; Service de Pathologie; Registre des cancers digestifs, Université de Bourgogne, Centre Hospitalier Universitaire de Dijon, Dijon, France; and The Sidney Kimmel Comprehensive Cancer Center at the Johns Hopkins University School of Medicine, Baltimore, MarylandAuthors' Affiliations: Departments of Pathology, Radiation Oncology (MAASTRO) and Epidemiology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands; Service de Pathologie; Registre des cancers digestifs, Université de Bourgogne, Centre Hospitalier Universitaire de Dijon, Dijon, France; and The Sidney Kimmel Comprehensive Cancer Center at the Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Veerle Melotte
- Authors' Affiliations: Departments of Pathology, Radiation Oncology (MAASTRO) and Epidemiology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands; Service de Pathologie; Registre des cancers digestifs, Université de Bourgogne, Centre Hospitalier Universitaire de Dijon, Dijon, France; and The Sidney Kimmel Comprehensive Cancer Center at the Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Leander Van Neste
- Authors' Affiliations: Departments of Pathology, Radiation Oncology (MAASTRO) and Epidemiology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands; Service de Pathologie; Registre des cancers digestifs, Université de Bourgogne, Centre Hospitalier Universitaire de Dijon, Dijon, France; and The Sidney Kimmel Comprehensive Cancer Center at the Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Benjamin Tournier
- Authors' Affiliations: Departments of Pathology, Radiation Oncology (MAASTRO) and Epidemiology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands; Service de Pathologie; Registre des cancers digestifs, Université de Bourgogne, Centre Hospitalier Universitaire de Dijon, Dijon, France; and The Sidney Kimmel Comprehensive Cancer Center at the Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Valerie Jooste
- Authors' Affiliations: Departments of Pathology, Radiation Oncology (MAASTRO) and Epidemiology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands; Service de Pathologie; Registre des cancers digestifs, Université de Bourgogne, Centre Hospitalier Universitaire de Dijon, Dijon, France; and The Sidney Kimmel Comprehensive Cancer Center at the Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Caroline Chapusot
- Authors' Affiliations: Departments of Pathology, Radiation Oncology (MAASTRO) and Epidemiology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands; Service de Pathologie; Registre des cancers digestifs, Université de Bourgogne, Centre Hospitalier Universitaire de Dijon, Dijon, France; and The Sidney Kimmel Comprehensive Cancer Center at the Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Matty P Weijenberg
- Authors' Affiliations: Departments of Pathology, Radiation Oncology (MAASTRO) and Epidemiology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands; Service de Pathologie; Registre des cancers digestifs, Université de Bourgogne, Centre Hospitalier Universitaire de Dijon, Dijon, France; and The Sidney Kimmel Comprehensive Cancer Center at the Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - James G Herman
- Authors' Affiliations: Departments of Pathology, Radiation Oncology (MAASTRO) and Epidemiology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands; Service de Pathologie; Registre des cancers digestifs, Université de Bourgogne, Centre Hospitalier Universitaire de Dijon, Dijon, France; and The Sidney Kimmel Comprehensive Cancer Center at the Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Adriaan P de Bruïne
- Authors' Affiliations: Departments of Pathology, Radiation Oncology (MAASTRO) and Epidemiology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands; Service de Pathologie; Registre des cancers digestifs, Université de Bourgogne, Centre Hospitalier Universitaire de Dijon, Dijon, France; and The Sidney Kimmel Comprehensive Cancer Center at the Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Manon van Engeland
- Authors' Affiliations: Departments of Pathology, Radiation Oncology (MAASTRO) and Epidemiology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands; Service de Pathologie; Registre des cancers digestifs, Université de Bourgogne, Centre Hospitalier Universitaire de Dijon, Dijon, France; and The Sidney Kimmel Comprehensive Cancer Center at the Johns Hopkins University School of Medicine, Baltimore, Maryland
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24
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Derks S, Cleven AHG, Melotte V, Smits KM, Brandes JC, Azad N, van Criekinge W, de Bruïne AP, Herman JG, van Engeland M. Emerging evidence for CHFR as a cancer biomarker: from tumor biology to precision medicine. Cancer Metastasis Rev 2015; 33:161-71. [PMID: 24375389 PMCID: PMC3988518 DOI: 10.1007/s10555-013-9462-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Novel insights in the biology of cancer have switched the paradigm of a “one-size-fits-all” cancer treatment to an individualized biology-driven treatment approach. In recent years, a diversity of biomarkers and targeted therapies has been discovered. Although these examples accentuate the promise of personalized cancer treatment, for most cancers and cancer subgroups no biomarkers and effective targeted therapy are available. The great majority of patients still receive unselected standard therapies with no use of their individual molecular characteristics. Better knowledge about the underlying tumor biology will lead the way toward personalized cancer treatment. In this review, we summarize the evidence for a promising cancer biomarker: checkpoint with forkhead and ring finger domains (CHFR). CHFR is a mitotic checkpoint and tumor suppressor gene, which is inactivated in a diverse group of solid malignancies, mostly by promoter CpG island methylation. CHFR inactivation has shown to be an indicator of poor prognosis and sensitivity to taxane-based chemotherapy. Here we summarize the current knowledge of altered CHFR expression in cancer, the impact on tumor biology and implications for personalized cancer treatment.
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Affiliation(s)
- Sarah Derks
- Department of Medical Oncology, Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - Arjen H. G. Cleven
- Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, 6200 MD Maastricht, The Netherlands
| | - Veerle Melotte
- Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, 6200 MD Maastricht, The Netherlands
| | - Kim M. Smits
- Department of Radiation Oncology (MAASTRO Clinic), GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Johann C. Brandes
- Department of Hematology and Oncology, Atlanta VA Medical Center Winship Cancer Institute, Emory University, Atlanta, GA USA
| | - Nilofer Azad
- Department of Gastrointestinal Oncology, The Sidney Kimmel Comprehensive Cancer Center at the Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Wim van Criekinge
- Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium
- MDxHealth, Irvine, CA USA
| | - Adriaan P. de Bruïne
- Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, 6200 MD Maastricht, The Netherlands
| | - James G. Herman
- Department of Tumor Biology, The Sidney Kimmel Comprehensive Cancer Center at the Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Manon van Engeland
- Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, 6200 MD Maastricht, The Netherlands
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25
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Melotte V, Yi JM, Lentjes MHFM, Smits KM, Van Neste L, Niessen HEC, Wouters KAD, Louwagie J, Schuebel KE, Herman JG, Baylin SB, van Criekinge W, Meijer GA, Ahuja N, van Engeland M. Spectrin repeat containing nuclear envelope 1 and forkhead box protein E1 are promising markers for the detection of colorectal cancer in blood. Cancer Prev Res (Phila) 2014; 8:157-64. [PMID: 25538088 DOI: 10.1158/1940-6207.capr-14-0198] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Identifying biomarkers in body fluids may improve the noninvasive detection of colorectal cancer. Previously, we identified N-Myc downstream-regulated gene 4 (NDRG4) and GATA binding protein 5 (GATA5) methylation as promising biomarkers for colorectal cancer in stool DNA. Here, we examined the utility of NDRG4, GATA5, and two additional markers [Forkhead box protein E1 (FOXE1) and spectrin repeat containing nuclear envelope 1 (SYNE1)] promoter methylation as biomarkers in plasma DNA. Quantitative methylation-specific PCR was performed on plasma DNA from 220 patients with colorectal cancer and 684 noncancer controls, divided in a training set and a test set. Receiver operating characteristic analysis was performed to measure the area under the curve of GATA5, NDRG4, SYNE1, and FOXE1 methylation. Functional assays were performed in SYNE1 and FOXE1 stably transfected cell lines. The sensitivity of NDRG4, GATA5, FOXE1, and SYNE1 methylation in all stages of colorectal cancer (154 cases, 444 controls) was 27% [95% confidence interval (CI), 20%-34%), 18% (95% CI, 12%-24%), 46% (95% CI, 38%-54%), and 47% (95% CI, 39%-55%), with a specificity of 95% (95% CI, 93%-97%), 99% (95% CI, 98%-100%), 93% (95% CI, 91%-95%), and 96% (95% CI, 94%-98%), respectively. Combining SYNE1 and FOXE1, increased the sensitivity to 56% (95% CI, 48%-64%), while the specificity decreased to 90% (95% CI, 87%-93%) in the training set and to 58% sensitivity (95% CI, 46%-70%) and 91% specificity (95% CI, 80%-100%) in a test set (66 cases, 240 controls). SYNE1 overexpression showed no major differences in cell proliferation, migration, and invasion compared with controls. Overexpression of FOXE1 significantly decreased the number of colonies in SW480 and HCT116 cell lines. Overall, our data suggest that SYNE1 and FOXE1 are promising markers for colorectal cancer detection.
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Affiliation(s)
- Veerle Melotte
- Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Joo Mi Yi
- Dongnam Institute of Radiological and Medical Sciences (DIRAMS), Busan, South Korea
| | - Marjolein H F M Lentjes
- Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Kim M Smits
- Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands. Department of Radiation Oncology (MAASTRO), GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Leander Van Neste
- Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands. MDxHealth, Herstal, Belgium
| | - Hanneke E C Niessen
- Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Kim A D Wouters
- Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | | | - Kornel E Schuebel
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - James G Herman
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Stephen B Baylin
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Gerrit A Meijer
- Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands
| | - Nita Ahuja
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University School of Medicine, Baltimore, Maryland. Department of Surgery, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University School of Medicine, Baltimore, Maryland. Department of Urology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Manon van Engeland
- Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands.
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Smits KM, Melotte V, Niessen HE, Dubois L, Oberije C, Troost EG, Starmans MH, Boutros PC, Vooijs M, van Engeland M, Lambin P. Epigenetics in radiotherapy: Where are we heading? Radiother Oncol 2014; 111:168-77. [DOI: 10.1016/j.radonc.2014.05.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 03/17/2014] [Accepted: 05/01/2014] [Indexed: 12/20/2022]
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van Engeland M, Cleven A, Derks S, Draht MXG, Smits KM, Melotte V, Weijenberg MP, Herman JG, de Bruïne AP, Van Criekinge W. CHFR promoter methylation indicates poor prognosis in stage II microsatellite stable colorectal cancer. J Clin Oncol 2013. [DOI: 10.1200/jco.2013.31.15_suppl.e14503] [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
e14503 Background: Data on the prognostic significance of promoter CpG island methylation in colorectal cancer (CRC) are conflicting, possibly due to associations between methylation and other factors affecting survival such as genetic alterations and use of adjuvant therapy. Here we examine the prognostic impact of promoter methylation in CRC patients treated with surgery alone in the context of microsatellite instability (MSI), BRAF- and KRAS mutations. Methods: 173 CRCs were analyzed for promoter methylation of 19 tumor suppressor- and DNA repair genes, the CpG island methylator phenotype (CIMP), MSI, the exon 15 V600E BRAF mutation and KRAS codon 12 and 13 mutations. Results: Unsupervised hierarchical clustering based on methylation status of 19 genes revealed three subgroups: cluster 1 (CL1, 57% (98/173) of CRCs), cluster 2 (CL2, 25% (43/173) of CRCs) and cluster 3 (CL3, 18% (32/173) of CRCs). CL3 had the highest methylation index (0.25, 0.49 and 0.69 respectively, p=<0.01) and was strongly associated with CIMP (p<0.01). After stratification for tumor stage, MSI and BRAF status, no statistically significant differences in survival between CL1, CL2 and CL3 nor between CIMP and non-CIMP CRCs were detected. Analyzing genes separately revealed that CHFR promoter methylation was associated with a poor prognosis in stage II, MSS, BRAF wild-type CRCs: HR=3.89 (95% CI =1.58-9.60, p=0.003) and HR=2.21 (95% CI =1.09-4.48, p=0.03) in a second population-based study (n=151). Conclusions: CHFR promoter CpG island methylation, which is associated with MSI, also occurs frequently in MSS CRCs and is a promising prognostic marker in stage II, MSS, BRAF wild-type CRCs.
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Affiliation(s)
- Manon van Engeland
- Department of Pathology, GROW - School for Oncology and Developmental Biology and Maastricht University Medical Center, Maastricht, the Netherlands, Maastricht, Netherlands
| | - Arjen Cleven
- Departments of Pathology and Epidemiology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, Netherlands
| | - Sarah Derks
- Departments of Pathology and Epidemiology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, Netherlands
| | - Muriel XG Draht
- Departments of Pathology and Epidemiology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, Netherlands
| | - Kim M Smits
- Departments of Pathology and Epidemiology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, Netherlands
| | - Veerle Melotte
- Departments of Pathology and Epidemiology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, Netherlands
| | - Matty P Weijenberg
- Departments of Pathology and Epidemiology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, Netherlands
| | | | - Adriaan P de Bruïne
- Department of Pathology, Maastricht University Medical Center, Maastricht, Netherlands
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Simons CCJM, Hughes LAE, Smits KM, Khalid-de Bakker CA, de Bruïne AP, Carvalho B, Meijer GA, Schouten LJ, van den Brandt PA, Weijenberg MP, van Engeland M. A novel classification of colorectal tumors based on microsatellite instability, the CpG island methylator phenotype and chromosomal instability: implications for prognosis. Ann Oncol 2013; 24:2048-56. [PMID: 23532114 DOI: 10.1093/annonc/mdt076] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND We studied the overlap between the major (epi)genomic events microsatellite instability (MSI), the CpG island methylator phenotype (CIMP) and chromosomal instability (CIN) in colorectal cancer (CRC), and whether specific (epi)genotypes were associated with CRC-related deaths. PATIENTS AND METHODS Molecular analyses using tumor DNA were successful in 509 CRC cases identified within the Netherlands Cohort Study in the period 1989-1993. Follow-up for the vital status until May 2005 was 100%. RESULTS MSI (12.6%), CIMP-only (5.3%), CIMP + CIN (13.4%), CIN-only (58.2%) and triple-negative tumors (10.6%) differed significantly regarding tumor localization, differentiation grade, initial adjuvant therapy (AT) use and genetic characteristics (P ≤ 0.03). CIMP-only, CIMP + CIN and triple-negative tumors, compared with CIN-only tumors, were significantly associated with a 3.67, 2.44 and 3.78-fold risk of CRC-related deaths after 2-year follow-up (95% confidence intervals, CIs, 1.70-7.91, 1.35-4.41 and 1.97-7.25, respectively), but not after late follow-up. MSI tumors were borderline significantly associated with a 0.40-fold risk of CRC-related deaths after late follow-up (95% CI 0.15-1.03). CONCLUSION(S) This is the first study to show that specific (epi)genotypes may hold a differential prognostic value that may vary over time. Although no specific treatment data were available, an explanation for the differential findings over time might be that (epi)genotypes modify therapy response.
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Affiliation(s)
- C C J M Simons
- Department of Epidemiology, GROW-School for Oncology and Developmental Biology, Maastricht University, Maastricht, the Netherlands
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Draht MXG, Riedl RR, Niessen H, Carvalho B, Meijer GA, Herman JG, van Engeland M, Melotte V, Smits KM. Promoter CpG island methylation markers in colorectal cancer: the road ahead. Epigenomics 2012; 4:179-94. [PMID: 22449189 DOI: 10.2217/epi.12.9] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Despite increasing knowledge on the biology, detection and treatment of colorectal cancer (CRC), the disease is still a major health problem. Hypermethylation of promoter regions of genes has been studied extensively as a contributor in CRC carcinogenesis. In addition, it is the topic of many studies focusing on biomarkers for the early detection, prediction of prognosis and treatment outcome. Methylation markers may be preferred over current screening and test methods as they are stable and easy to detect. However, almost no methylation marker is currently being used in clinical practice, often due to a lack of sensitivity, specificity, or validation of the results. This review summarizes the current knowledge of hypermethylation biomarkers for CRC detection, progression and treatment outcome.
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Affiliation(s)
- Muriel X G Draht
- Department of Pathology, GROW-School for Oncology & Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
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Smits KM, Paranjape T, Nallur S, Wouters KA, Weijenberg MP, Schouten LJ, van den Brandt PA, Bosman FT, Weidhaas JB, van Engeland M. KRAS-LCS6 Genotype as a Prognostic Marker in Early-Stage CRC–Response. Clin Cancer Res 2012. [DOI: 10.1158/1078-0432.ccr-12-1023] [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: 11/16/2022]
Affiliation(s)
- Kim M. Smits
- Authors' Affiliations: Departments of 1Pathology and 2Epidemiology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands; and 3Department of Therapeutic Radiology, Yale University, New Haven, Connecticut
| | - Trupti Paranjape
- Authors' Affiliations: Departments of 1Pathology and 2Epidemiology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands; and 3Department of Therapeutic Radiology, Yale University, New Haven, Connecticut
| | - Sunitha Nallur
- Authors' Affiliations: Departments of 1Pathology and 2Epidemiology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands; and 3Department of Therapeutic Radiology, Yale University, New Haven, Connecticut
| | - Kim A.D. Wouters
- Authors' Affiliations: Departments of 1Pathology and 2Epidemiology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands; and 3Department of Therapeutic Radiology, Yale University, New Haven, Connecticut
| | - Matty P. Weijenberg
- Authors' Affiliations: Departments of 1Pathology and 2Epidemiology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands; and 3Department of Therapeutic Radiology, Yale University, New Haven, Connecticut
| | - Leo J. Schouten
- Authors' Affiliations: Departments of 1Pathology and 2Epidemiology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands; and 3Department of Therapeutic Radiology, Yale University, New Haven, Connecticut
| | - Piet A. van den Brandt
- Authors' Affiliations: Departments of 1Pathology and 2Epidemiology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands; and 3Department of Therapeutic Radiology, Yale University, New Haven, Connecticut
| | - Fred T. Bosman
- Authors' Affiliations: Departments of 1Pathology and 2Epidemiology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands; and 3Department of Therapeutic Radiology, Yale University, New Haven, Connecticut
| | - Joanne B. Weidhaas
- Authors' Affiliations: Departments of 1Pathology and 2Epidemiology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands; and 3Department of Therapeutic Radiology, Yale University, New Haven, Connecticut
| | - Manon van Engeland
- Authors' Affiliations: Departments of 1Pathology and 2Epidemiology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands; and 3Department of Therapeutic Radiology, Yale University, New Haven, Connecticut
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Hughes LAE, Khalid-de Bakker CAJ, Smits KM, van den Brandt PA, Jonkers D, Ahuja N, Herman JG, Weijenberg MP, van Engeland M. The CpG island methylator phenotype in colorectal cancer: progress and problems. Biochim Biophys Acta Rev Cancer 2011; 1825:77-85. [PMID: 22056543 DOI: 10.1016/j.bbcan.2011.10.005] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Revised: 10/21/2011] [Accepted: 10/23/2011] [Indexed: 12/15/2022]
Abstract
In recent years, attention has focused on the biology and potential clinical importance of the CpG island methylator phenotype (CIMP) in colorectal cancer (CRC). While it is generally well accepted that etiologically and clinically distinct subgroups exist in this disease, a precise definition of CIMP remains to be established. Here, we summarize existing literature that documents the prevalence of CIMP in CRC, with particular attention to the various methods and definitions used to classify a tumor as CIMP positive. Through a systematic review on both case-series and population based studies, we examined only original research articles reporting on sporadic CRC and/or adenomas in unselected cases. Forty-eight papers published between January 1999 and August 2011 met the inclusion criteria. We describe the use of multiple gene panels, marker threshold values, and laboratory techniques which results in a wide range in the prevalence of CIMP. Because there is no universal standard or consensus on quantifying the phenotype, establishing its true prevalence is a challenge. This bottleneck is becoming increasingly evident as molecular pathological epidemiology continues to offer possibilities for clear answers regarding environmental risk factors and disease trends. For the first time, large, unselected series of cases are available for analysis, but comparing populations and pooling data will remain a challenge unless a universal definition of CIMP and a consensus on analysis can be reached, and the primary cause of CIMP identified.
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Affiliation(s)
- Laura A E Hughes
- Dept. of Epidemiology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, 6200MD Maastricht, the Netherlands
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Huysentruyt CJR, Baldewijns MM, Rüland AM, Tonk RJW, Vervoort PSAM, Smits KM, van de Beek C, Speel EJM. Modified UroVysion scoring criteria increase the urothelial carcinoma detection rate in cases of equivocal urinary cytology. Histopathology 2011; 58:1048-53. [PMID: 21707706 DOI: 10.1111/j.1365-2559.2011.03859.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AIMS UroVysion(®) is a four-target fluorescence in situ hybridization technique for the detection of urothelial carcinoma (UC) in urinary cytology. The aim of this retrospective study was to investigate the UC detection rate of a modified UroVysion test in patients with equivocal urinary cytology. The modification comprised the addition of a cytological prescreening technique and different evaluation criteria. METHODS AND RESULTS Thin-layer slides were prepared from the residual urine samples of 82 patients with equivocal urinary cytology, prestained and prescreened to confirm the presence of atypical urothelial cells. The same slides were used for the UroVysion test, and scored according to different evaluation criteria. The results were compared with the outcomes of cystoscopic and histological findings. UroVysion detected 68% of the UCs when the manufacturer's evaluation criteria were applied. In cases of altered evaluation criteria, the sensitivity increased to 81% when at least one copy number change of a probe target was considered to be a positive test result. The specificity only decreased from 84% to 82%. CONCLUSIONS Our data suggest that the sensitivity of the UroVysion test can be increased by the addition of a cytological pre-screening technique prior to the UroVysion test and a modification of the UroVysion evaluation criteria.
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Smits KM, Paranjape T, Nallur S, Wouters KAD, Weijenberg MP, Schouten LJ, van den Brandt PA, Bosman FT, Weidhaas JB, van Engeland M. A let-7 microRNA SNP in the KRAS 3'UTR is prognostic in early-stage colorectal cancer. Clin Cancer Res 2011; 17:7723-31. [PMID: 21994416 DOI: 10.1158/1078-0432.ccr-11-0990] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
PURPOSE Colorectal cancer (CRC) is a common cause of death worldwide. Tumor-node-metastasis-system stage is currently used to guide therapy decisions but lacks precision. Prognostic biomarkers are needed to refine stratification of patients for chemotherapy but validated biomarkers are not yet available. Recently, a SNP in a lethal-7 (let-7) miRNA complementary site (LCS6) in the KRAS 3'untranslated region was suggested to affect survival in metastatic CRC. Effects in early-stage CRC are however unknown. We studied KRAS-LCS6 genotype, hypothesizing that it might identify early-stage cases with a poor prognosis, and could potentially be used in therapy decision-making. EXPERIMENTAL DESIGN We studied 409 early stage, 182 stage III, and 69 stage IV cases, and 1,886 subcohort members from the Netherlands Cohort Study. KRAS-LCS6 genotype was assessed with TaqMan PCR. Kaplan-Meier analyses or Cox regression were used to assess associations between genotype and CRC risk or cause-specific survival. RESULTS Early-stage cases with the KRAS-LCS6 variant had a lower CRC risk (incidence-rate ratio 0.68; 95% CI: 0.49-0.94) and a better survival (log-rank P = 0.038; HR 0.46; 95% CI: 0.18-1.14). In patients with KRAS-mutated CRC carrying the KRAS-LCS6 variant, the better outcome was enhanced as no patients died of CRC (log-rank P = 0.017). In advanced patients, no clear association between genotype and CRC risk or survival was observed. CONCLUSIONS Our results indicate that early-stage CRC cases with the KRAS-LCS6 variant have a better outcome. In advanced disease, the better outcome no longer exists. For early-stage patients, KRAS-LCS6 genotype combined with KRAS mutations merits validation as a prognostic biomarker and consideration in therapy decision-making.
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Affiliation(s)
- Kim M Smits
- Departments of Pathology and Epidemiology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
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Bijsmans ITGW, Smits KM, de Graeff P, Wisman GBA, van der Zee AGJ, Slangen BF, de Bruïne AP, van Engeland M, Sieben NL, Van de Vijver KK. Loss of SerpinA5 protein expression is associated with advanced-stage serous ovarian tumors. Mod Pathol 2011; 24:463-70. [PMID: 21102419 DOI: 10.1038/modpathol.2010.214] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Epithelial ovarian cancer, the most lethal neoplasm of the female genital tract, is usually diagnosed at an advanced stage as obvious symptoms are absent at early stages. This disease is believed to originate from malignant transformation of the ovarian surface epithelium or fallopian tube. Histologically, several subtypes are being recognized, with serous histology accounting for the majority of cases. Serous tumors include serous borderline tumors and serous carcinomas. A better understanding of the tumor biology and molecular mechanisms involved in these tumors is needed, as both patient management and prognosis differ substantially. Previous microarray analysis identified SerpinA5, a uPA inhibitor, as key regulator for indolent borderline behavior. As carcinomas are characterized by loss of SerpinA5 mRNA expression, we hypothesized that SerpinA5 protein expression is reduced or lost in carcinomas when compared with borderline tumors. We performed SerpinA5 immunohistochemical staining on 32 serous borderline tumors, 187 primary serous carcinomas and 62 serous omental metastases. Reduced or absent SerpinA5 protein staining was observed in carcinomas when compared with borderline tumors (P<0.001). SerpinA5 protein expression was significantly lowered in the omental metastases (P<0.001) when compared with the matching primary carcinoma. Interestingly, SerpinA5 protein expression was reduced in advanced-stage borderline tumors, often characterized by micropapillary growth and/or microinvasion, when compared with early-stage borderline tumors (P=0.015). In conclusion, SerpinA5 expression is significantly reduced in advanced-stage serous borderline tumors and serous carcinomas when compared with the early-stage counterparts, and reduction of expression is linked to more aggressive features of borderline tumors.
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Affiliation(s)
- Ingrid T G W Bijsmans
- Department of Pathology, GROW, School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
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Yi JM, Dhir M, Van Neste L, Downing SR, Jeschke J, Glöckner SC, de Freitas Calmon M, Hooker CM, Funes JM, Boshoff C, Smits KM, van Engeland M, Weijenberg MP, Iacobuzio-Donahue CA, Herman JG, Schuebel KE, Baylin SB, Ahuja N. Genomic and epigenomic integration identifies a prognostic signature in colon cancer. Clin Cancer Res 2011; 17:1535-45. [PMID: 21278247 DOI: 10.1158/1078-0432.ccr-10-2509] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
PURPOSE The importance of genetic and epigenetic alterations maybe in their aggregate role in altering core pathways in tumorigenesis. EXPERIMENTAL DESIGN Merging genome-wide genomic and epigenomic alterations, we identify key genes and pathways altered in colorectal cancers (CRC). DNA methylation analysis was tested for predicting survival in CRC patients using Cox proportional hazard model. RESULTS We identified 29 low frequency-mutated genes that are also inactivated by epigenetic mechanisms in CRC. Pathway analysis showed the extracellular matrix (ECM) remodeling pathway is silenced in CRC. Six ECM pathway genes were tested for their prognostic potential in large CRC cohorts (n = 777). DNA methylation of IGFBP3 and EVL predicted for poor survival (IGFBP3: HR = 2.58, 95% CI: 1.37-4.87, P = 0.004; EVL: HR = 2.48, 95% CI: 1.07-5.74, P = 0.034) and simultaneous methylation of multiple genes predicted significantly worse survival (HR = 8.61, 95% CI: 2.16-34.36, P < 0.001 for methylation of IGFBP3, EVL, CD109, and FLNC). DNA methylation of IGFBP3 and EVL was validated as a prognostic marker in an independent contemporary-matched cohort (IGFBP3 HR = 2.06, 95% CI: 1.04-4.09, P = 0.038; EVL HR = 2.23, 95% CI: 1.00-5.0, P = 0.05) and EVL DNA methylation remained significant in a secondary historical validation cohort (HR = 1.41, 95% CI: 1.05-1.89, P = 0.022). Moreover, DNA methylation of selected ECM genes helps to stratify the high-risk stage 2 colon cancers patients who would benefit from adjuvant chemotherapy (HR: 5.85, 95% CI: 2.03-16.83, P = 0.001 for simultaneous methylation of IGFBP3, EVL, and CD109). CONCLUSIONS CRC that have silenced genes in ECM pathway components show worse survival suggesting that our finding provides novel prognostic biomarkers for CRC and reflects the high importance of integrative analyses linking genetic and epigenetic abnormalities with pathway disruption in cancer.
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Affiliation(s)
- Joo Mi Yi
- Department of Oncology, Johns Hopkins University, Baltimore, Maryland 20892-8110, USA
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Abstract
Colorectal cancer (CRC) has predominantly been considered a genetic disease, characterized by sequential accumulation of genetic alterations. Growing evidence indicates that epigenetic alterations add an additional layer of complexity to the pathogenesis of CRC, and characterize a subgroup of colorectal cancers with a distinct etiology and prognosis. Epigenetic dysregulation in colorectal cancer is organized at multiple levels, involving DNA methylation, histone modifications, nucleosomal occupancy and remodeling, chromatin looping, and noncoding RNAs. Interactions between these processes and complex associations with genetic alterations have recently been unraveled. It appears that CRC epigenetics will be the paradigm for multistep carcinogenesis, as CRC genetics has been for the past three decades. This review integrates recent data on epigenetic regulation of gene expression in CRC and describes how the understanding of these processes will alter the management of CRC.
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Affiliation(s)
- Manon van Engeland
- GROW-School for Oncology and Developmental Biology, PO Box 616, 6200 Maastricht, The Netherlands.
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Smits KM, Schouten LJ, Hudak E, Verhage B, van Dijk BA, Hulsbergen-van de Kaa CA, Goldbohm RA, Oosterwijk E, van den Brandt PA. Body Mass Index and von Hippel-Lindau Gene Mutations in Clear-cell Renal Cancer: Results of the Netherlands Cohort Study on Diet and Cancer. Ann Epidemiol 2010; 20:401-4. [DOI: 10.1016/j.annepidem.2010.01.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2009] [Revised: 01/28/2010] [Accepted: 01/28/2010] [Indexed: 10/19/2022]
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van Vlodrop IJH, Baldewijns MML, Smits KM, Schouten LJ, van Neste L, van Criekinge W, van Poppel H, Lerut E, Schuebel KE, Ahuja N, Herman JG, de Bruïne AP, van Engeland M. Prognostic significance of Gremlin1 (GREM1) promoter CpG island hypermethylation in clear cell renal cell carcinoma. Am J Pathol 2009; 176:575-84. [PMID: 20042676 DOI: 10.2353/ajpath.2010.090442] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Gremlin1 (GREM1), a bone morphogenetic protein antagonist and putative angiogenesis-modulating gene, is silenced by promoter hypermethylation in human malignancies. Here we study GREM1 methylation in clear cell renal cell carcinoma (ccRCC) and its impact on tumor characteristics and clinical outcome. Three GREM1 promoter CpG island regions (i, ii, iii) were analyzed by methylation-specific PCR and/or bisulfite sequencing in ccRCC cell lines and ccRCCs from two independent patient series. Results were correlated with clinicopathological and angiogenic parameters. Bisulfite sequencing of ccRCC cell lines showed GREM1 methylation, associated with absence of GREM1 mRNA. GREM1 methylation prevalence in ccRCCs varied between regions: 55%, 24%, and 20% for regions i, ii, and iii, respectively. GREM1 region iii methylation was associated with increased tumor size (P = 0.02), stage (P = 0.013), grade (P = 0.04), tumor (P = 0.001), and endothelial cell (P = 0.0001) proliferation and decreased mean vessel density (P = 0.001) in a hospital-based ccRCC series (n = 150). In univariate analysis, GREM1 region iii methylated ccRCCs had a significant worse survival when compared with unmethylated ccRCCs (hazard ratio [HR] = 2.35, 95% confidence interval [CI]:1.29 to 4.28), but not in multivariate analysis (HR = 0.88, 95% CI: 0.45 to 1.74). In a population-based validation series (n = 185), GREM1 region iii methylation was associated with increased Fuhrman grade (P = 0.03) and decreased overall survival (P = 0.001) in univariate and multivariate analysis (HR = 2.32, 95% CI: 1.52 to 3.53 and HR = 2.27, 95% CI: 1.44 to 3.59, respectively). The strong correlation between GREM1 region iii promoter methylation and increased malignancy and its correlation with active angiogenesis indicates a role for GREM1 in ccRCC carcinogenesis and tumor angiogenesis.
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Affiliation(s)
- Iris J H van Vlodrop
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, PO Box 616, 6200 MD Maastricht, The Netherlands
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Baldewijns MM, van Vlodrop IJH, Smits KM, Vermeulen PB, Van den Eynden GG, Schot F, Roskams T, van Poppel H, van Engeland M, de Bruïne AP. Different angiogenic potential in low and high grade sporadic clear cell renal cell carcinoma is not related to alterations in the von Hippel-Lindau gene. Cell Oncol 2009; 31:371-82. [PMID: 19759417 PMCID: PMC4619045 DOI: 10.3233/clo-2009-0482] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND von Hippel-Lindau (VHL) inactivation is common in sporadic clear cell renal cell carcinomas (ccRCC). pVHL is part of the ubiquitin ligase complex that targets the alpha subunits of hypoxia-inducible transcription factor (HIF) for degradation under well-oxygenated conditions. In the absence of wild-type pVHL, as observed in VHL patients and most sporadic ccRCCs, constitutive upregulation of HIF results in transcriptional activation of angiogenesis-related genes, such as VEGF. Differences in angiogenic activity within the group of ccRCCs were reported and strong genotype-phenotype correlations were found in patients with VHL disease, raising a question about the importance of VHL inactivation status in angiogenic behaviour and tumour progression. METHODS To address this question, we investigated the influence of VHL mutation (direct sequencing)/hypermethylation (methylation-specific PCR) on angiogenesis/tumour parameters (immunohistochemistry) in 150 patients with sporadic ccRCC. RESULTS We found no significant association between VHL mutation or methylation and angiogenesis/tumour parameters. CONCLUSION These data indicate that tumour progression and angiogenesis are not directly influenced by VHL alterations and that additional genetic/epigenetic events should be considered to explain the diverse angiogenic and proliferative behaviour during tumour progression.
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Affiliation(s)
- Marcella M Baldewijns
- Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands.
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Melotte V, Lentjes MHFM, van den Bosch SM, Hellebrekers DMEI, de Hoon JPJ, Wouters KAD, Daenen KLJ, Partouns-Hendriks IEJM, Stessels F, Louwagie J, Smits KM, Weijenberg MP, Sanduleanu S, Khalid-de Bakker CAJ, Oort FA, Meijer GA, Jonkers DMAE, Herman JG, de Bruïne AP, van Engeland M. N-Myc downstream-regulated gene 4 (NDRG4): a candidate tumor suppressor gene and potential biomarker for colorectal cancer. J Natl Cancer Inst 2009; 101:916-27. [PMID: 19535783 DOI: 10.1093/jnci/djp131] [Citation(s) in RCA: 161] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Identification of hypermethylated tumor suppressor genes in body fluids is an appealing strategy for the noninvasive detection of colorectal cancer. Here we examined the role of N-Myc downstream-regulated gene 4 (NDRG4) as a novel tumor suppressor and biomarker in colorectal cancer. METHODS NDRG4 promoter methylation was analyzed in human colorectal cancer cell lines, colorectal tissue, and noncancerous colon mucosa by using methylation-specific polymerase chain reaction (PCR) and bisulfite sequencing. NDRG4 mRNA and protein expression were studied using real-time-PCR and immunohistochemistry, respectively. Tumor suppressor functions of NDRG4 were examined by colony formation, cell proliferation, and migration and invasion assays in colorectal cancer cell lines that were stably transfected with an NDRG4 expression construct. Quantitative methylation-specific PCR was used to examine the utility of NDRG4 promoter methylation as a biomarker in fecal DNA from 75 colorectal cancer patients and 75 control subjects. All P values are two-sided. RESULTS The prevalence of NDRG4 promoter methylation in two independent series of colorectal cancers was 86% (71/83) and 70% (128/184) compared with 4% (2/48) in noncancerous colon mucosa (P < .001). NDRG4 mRNA and protein expression were decreased in colorectal cancer tissue compared with noncancerous colon mucosa. NDRG4 overexpression in colorectal cancer cell lines suppressed colony formation (P = .014), cell proliferation (P < .001), and invasion (P < .001). NDRG4 promoter methylation analysis in fecal DNA from a training set of colorectal cancer patients and control subjects yielded a sensitivity of 61% (95% confidence interval [CI] = 43% to 79%) and a specificity of 93% (95% CI = 90% to 97%). An independent test set of colorectal cancer patients and control subjects yielded a sensitivity of 53% (95% CI = 39% to 67%) and a specificity of 100% (95% CI = 86% to 100%). CONCLUSIONS NDRG4 is a candidate tumor suppressor gene in colorectal cancer whose expression is frequently inactivated by promoter methylation. NDRG4 promoter methylation is a potential biomarker for the noninvasive detection of colorectal cancer in stool samples.
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Affiliation(s)
- Veerle Melotte
- Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, The Netherlands
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Hellebrekers DMEI, Lentjes MHFM, van den Bosch SM, Melotte V, Wouters KAD, Daenen KLJ, Smits KM, Akiyama Y, Yuasa Y, Sanduleanu S, Khalid-de Bakker CAJ, Jonkers D, Weijenberg MP, Louwagie J, van Criekinge W, Carvalho B, Meijer GA, Baylin SB, Herman JG, de Bruïne AP, van Engeland M. GATA4 and GATA5 are potential tumor suppressors and biomarkers in colorectal cancer. Clin Cancer Res 2009; 15:3990-7. [PMID: 19509152 DOI: 10.1158/1078-0432.ccr-09-0055] [Citation(s) in RCA: 148] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
PURPOSE The transcription factors GATA4 and GATA5 are involved in gastrointestinal development and are inactivated by promoter hypermethylation in colorectal cancer. Here, we evaluated GATA4/5 promoter methylation as potential biomarkers for noninvasive colorectal cancer detection, and investigated the role of GATA4/5 in colorectal cancer. EXPERIMENTAL DESIGN Promoter methylation of GATA4/5 was analyzed in colorectal tissue and fecal DNA from colorectal cancer patients and healthy controls using methylation-specific PCR. The potential function of GATA4/5 as tumor suppressors was studied by inducing GATA4/5 overexpression in human colorectal cancer cell lines. RESULTS GATA4/5 methylation was observed in 70% (63/90) and 79% (61/77) of colorectal carcinomas, respectively, and was independent of clinicopathologic features. Methylation frequencies in normal colon tissues from noncancerous controls were 6% (5 of 88, GATA4; P < 0.001) and 13% (13 of 100, GATA5; P < 0.001). GATA4/5 overexpression suppressed colony formation (P < 0.005), proliferation (P < 0.001), migration (P < 0.05), invasion (P < 0.05), and anchorage-independent growth (P < 0.0001) of colorectal cancer cells. Examination of GATA4 methylation in fecal DNA from two independent series of colorectal cancer patients and controls yielded a sensitivity of 71% [95% confidence interval (95% CI), 55-88%] and specificity of 84% (95% CI, 74-95%) for colorectal cancer detection in the training set, and a sensitivity of 51% (95% CI, 37-65%) and specificity of 93% (95% CI, 84-100%) in the validation set. CONCLUSIONS Methylation of GATA4/5 is a common and specific event in colorectal carcinomas, and GATA4/5 exhibit tumor suppressive effects in colorectal cancer cells in vitro. GATA4 methylation in fecal DNA may be of interest for colorectal cancer detection.
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Affiliation(s)
- Debby M E I Hellebrekers
- Departments of Pathology and Epidemiology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
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Glöckner SC, Dhir M, Yi JM, McGarvey KE, Van Neste L, Louwagie J, Chan TA, Kleeberger W, de Bruïne AP, Smits KM, Khalid-de Bakker CAJ, Jonkers DMAE, Stockbrügger RW, Meijer GA, Oort FA, Iacobuzio-Donahue C, Bierau K, Herman JG, Baylin SB, Van Engeland M, Schuebel KE, Ahuja N. Methylation of TFPI2 in stool DNA: a potential novel biomarker for the detection of colorectal cancer. Cancer Res 2009; 69:4691-9. [PMID: 19435926 DOI: 10.1158/0008-5472.can-08-0142] [Citation(s) in RCA: 185] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We have used a gene expression array-based strategy to identify the methylation of tissue factor pathway inhibitor 2 (TFPI2), a potential tumor suppressor gene, as a frequent event in human colorectal cancers (CRC). TFPI2 belongs to the recently described group of embryonic cell Polycomb group (PcG)-marked genes that may be predisposed to aberrant DNA methylation in early stages of colorectal carcinogenesis. Aberrant methylation of TFPI2 was detected in almost all CRC adenomas (97%, n = 56) and stages I to IV CRCs (99%, n = 115). We further explored the potential of TFPI2 as a biomarker for the early detection of CRC using stool DNA-based assays in patients with nonmetastatic CRC and average-risk noncancer controls who were candidates for screening. TFPI2 methylation was detected in stool DNA from stage I to III CRC patients with a sensitivity of 76% to 89% and a specificity of 79% to 93%. Detection of TFPI2 methylation in stool DNA may act as a useful adjunct to the noninvasive strategies for screening of CRCs in the future.
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Affiliation(s)
- Sabine C Glöckner
- Departments of Surgery, Oncology, and Pathology, Johns Hopkins University, Baltimore, Maryland 21287, USA
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Smits KM, Cleven AHG, Weijenberg MP, Hughes LAE, Herman JG, de Bruïne AP, van Engeland M. Pharmacoepigenomics in colorectal cancer: a step forward in predicting prognosis and treatment response. Pharmacogenomics 2009; 9:1903-16. [PMID: 19072647 DOI: 10.2217/14622416.9.12.1903] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Despite therapeutic innovations and increasing education on lifestyle to prevent colorectal cancer, it is still one of the most common cancer types, and for men the second cause of cancer-related death. Lately, much attention has been given to identify molecular markers involved in colorectal cancer prognosis and treatment with the aim to develop a more accurate classification system based on (epi)genetic alterations and, in addition, find markers that could potentially enhance management of colorectal cancer by predicting treatment response in advance. Although many genetic markers have been claimed to have prognostic or predictive influence, results are often inconclusive and, with some exception, they are not used in standard practice. Epigenetic alterations have received less attention although they are probably even more interesting as they can potentially be reversed through drug treatment. This review describes the current knowledge on the prognostic and predictive value of epigenetic markers in colorectal cancer.
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Affiliation(s)
- Kim M Smits
- Department of Epidemiology, GROW-School for Oncology and Developmental Biology, Maastricht University, The Netherlands
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Smits KM, Schouten LJ, van Dijk BA, Hulsbergen-van de Kaa CA, Wouters KA, Oosterwijk E, van Engeland M, van den Brandt PA. Genetic and Epigenetic Alterations in the von Hippel-Lindau Gene: the Influence on Renal Cancer Prognosis. Clin Cancer Res 2008; 14:782-7. [DOI: 10.1158/1078-0432.ccr-07-1753] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Smits KM, Schouten LJ, van Dijk BAC, van Houwelingen K, Hulsbergen-van de Kaa CA, Kiemeney LALM, Goldbohm RA, Oosterwijk E, van den Brandt PA. Polymorphisms in genes related to activation or detoxification of carcinogens might interact with smoking to increase renal cancer risk: results from The Netherlands Cohort Study on diet and cancer. World J Urol 2007; 26:103-10. [PMID: 17982751 DOI: 10.1007/s00345-007-0220-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2007] [Accepted: 10/09/2007] [Indexed: 11/29/2022] Open
Abstract
Metabolic gene polymorphisms have previously been suggested as risk factors for renal cell carcinoma (RCC). These polymorphisms are involved in activation or detoxification of carcinogens in cigarette smoke which is another RCC risk factor. We evaluated gene-environment interactions between CYP1A1, GSTmicro1 and smoking in a large population-based RCC case group. The Netherlands Cohort Study on diet and cancer (NLCS) comprises 120,852 persons who completed a questionnaire on smoking and other risk factors at baseline. After 11.3 years of follow-up, 337 incident RCC cases were identified. DNA was collected for 245 cases. In a case-only analysis, interaction-odds ratios (OR) and 95% confidence intervals (95% CI) were calculated using logistic regression. We observed a moderate, not statistically significant, interaction between current smoking and CYP1A1*2C (OR 1.42; 95% CI 0.70-2.89) and GSTmicro1 null (OR 1.35; 95% CI 0.65-2.79). For current smokers with both a variant (heterozygous or homozygous) in CYP1A1 and GSTmicro1 null, risk was also increased (OR 1.63; 95% CI 0.63-4.24). No interaction was observed between ever smokers, smoking duration (increments of 10 smoking years) or amount (increments of 5 cigarettes/day) and CYP1A or GSTmicro1. Our results show a modest trend towards a statistically significant gene-environment interaction between CYP1A1, GSTmicro1 and smoking in RCC. This could indicate that RCC risk among smokers might be more increased with the CYP1A1*2C genotype, GSTmicro1 null, or both a CYP1A1 variant and GSTmicro1 null.
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Affiliation(s)
- Kim M Smits
- Department of Epidemiology, GROW-School for Oncology and Developmental Biology, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands.
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Smits KM, Smits LJM, Schouten JSAG, Peeters FPML, Prins MH. Does pretreatment testing for serotonin transporter polymorphisms lead to earlier effects of drug treatment in patients with major depression? A decision-analytic model. Clin Ther 2007; 29:691-702. [PMID: 17617292 DOI: 10.1016/j.clinthera.2007.04.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/31/2007] [Indexed: 11/20/2022]
Abstract
BACKGROUND An estimated 30% to 40% of patients with depression do not sufficiently respond to treatment with selective serotonin reuptake inhibitors (SSRIs) and the period in which treatment efficacy can be assessed is relatively long. Therefore, a test to identify potential nonresponders could be useful in the treatment of depression. Serotonin transporter gene (SLC6A4) variations have been reported to account for differences in the way individuals respond to SSRI treatment. OBJECTIVE A decision-analytic model was used to assess whether pretreatment genetic testing for 5-HTTLPR, a polymorphism of the SLC6A4 genotype, could be an efficient tool in the treatment of depression. METHODS A theoretical clinical decision-analytic model was constructed to compare the current treatment strategy in The Netherlands with an alternative strategy for the treatment of depression. Under treatment guidelines in The Netherlands, all patients with depression receive SSRI treatment (nontesting strategy). Under the alternative strategy, genetic testing would be performed to identify which class of antidepressant would be the best choice for initiation of treatment (genetic testing strategy). Probabilities (predicted results) for this model were based on data from previous studies and the opinions of experts in the field of psychopharmacology. To test the robustness of the model, 6- and 12-week remission rates for patients treated with SSRIs were varied in a sensitivity analysis using a predetermined range that was established based on expert opinion. Threshold analyses were performed on the parameters of serotonin transporter genotype frequency and response and nonresponse rates for patients receiving SSRIs, serotonin-norepinephrine reuptake inhibitors (SNRIs), and tricyclic antidepressants (TCAs) to determine the value for a variable at which it could be concluded that a change in treatment strategy would be preferred. RESULTS When genetic testing was performed before an antidepressant was prescribed, 64.6% of patients were predicted to be in remission after 6 weeks of treatment compared with 60.0% of patients who did not receive genetic testing. After 12 weeks, 79.5% of patients in the testing group who received an SNRI as initial treatment and 83.2% of those who received a TCA initially were predicted to be in remission compared with 76.7% of patients in the nontesting group. Sensitivity analyses indicated that the model was robust to variation of probability estimates within their plausible ranges. However, these findings were based on a theoretic model and did not include cost assessment. Pretreatment genetic testing must be evaluated further in randomized clinical trials and costs must be assessed before implementing this strategy in routine psychiatric practice can be recommended. CONCLUSIONS The findings of this study suggest that performing genetic testing before prescribing antidepressant treatment may lead to greater numbers of patients experiencing remission early in treatment.
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Affiliation(s)
- Kim M Smits
- Department of Epidemiology, Maastricht University, Maastricht, The Netherlands.
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Abstract
Energy-adjusted magnesium intake was nonsignificantly inversely related to risk of colorectal cancer (n=2328) in the Netherlands Cohort Study on Diet and Cancer that started in 1986 (n=58 279 men and 62 573 women). Statistically significant inverse trends in risk were observed in overweight subjects for colon and proximal colon cancer across increasing quintiles of magnesium uptake (P-trend, 0.05 and 0.02, respectively). Although an overall protective effect was not afforded, our results suggest an effect of magnesium in overweight subjects, possibly through decreasing insulin resistance.
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Affiliation(s)
- P A van den Brandt
- Department of Epidemiology, Maastricht University, PO Box 616, 6200 MD Maastricht, The Netherlands.
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Prins MH, Smits KM, Smits LJ. Methodologic Ramifications of Paying Attention to Sex and Gender Differences in Clinical Research. ACTA ACUST UNITED AC 2007; 4 Suppl B:S106-10. [DOI: 10.1016/s1550-8579(07)80051-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/18/2007] [Indexed: 10/22/2022]
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Smits KM, Schouten JS, Smits LJ, Stelma FF, Nelemans P, Prins MH. A review on the design and reporting of studies on drug–gene interaction. J Clin Epidemiol 2005; 58:651-4. [PMID: 15939214 DOI: 10.1016/j.jclinepi.2005.01.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2004] [Revised: 10/24/2004] [Accepted: 01/12/2005] [Indexed: 11/15/2022]
Abstract
OBJECTIVE Methodological standards for clinical pharmacogenetic studies should be developed to improve reporting of studies and facilitate their inclusion in systematic reviews. The essence of these studies lies within the concept of effect modification. STUDY DESIGN AND SETTING A narrative review discussing methodological issues in the design and reporting of pharmacogenetic studies. RESULTS Studying effect modification within a trial leads to the comparison of subgroups based on genotype. Differences in effect based on genotype should preferably be expressed in absolute terms (risk differences) to facilitate clinical decisions on treatment. Information on the distribution of potential effect modifiers or prognostic factors should be available to prevent a biased comparison of differences in effect between genotypes. The distribution of genotypes should also be presented and compared to Hardy-Weinberg equilibrium to check for selection bias. Additional points of interest include the possibility of selective nonavailability of biomaterial and the choice of a statistical model to study effect modification. CONCLUSION Additional methodological issues should be taken into account when designing and reporting pharmacogenetic studies, to ensure high study quality. We present several important issues for future studies investigating drug-gene interactions that can serve as a basis for further discussion on methodology in pharmacogenetics.
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Affiliation(s)
- Kim M Smits
- Department of Epidemiology, University of Maastricht, P.O. Box 616, 6200 MD Maastricht, The Netherlands.
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Smits KM, Smits LJM, Schouten JSAG, Stelma FF, Nelemans P, Prins MH. Influence of SERTPR and STin2 in the serotonin transporter gene on the effect of selective serotonin reuptake inhibitors in depression: a systematic review. Mol Psychiatry 2004; 9:433-41. [PMID: 15037864 DOI: 10.1038/sj.mp.4001488] [Citation(s) in RCA: 137] [Impact Index Per Article: 6.9] [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: 11/08/2022]
Abstract
Large differences in clinical response to selective serotonin reuptake inhibitors (SSRIs) are observed in depressive patients with different genotypes. Quantification of these differences is needed to decide if genetic testing prior to antidepressant treatment is useful. We conducted a systematic review of the literature on the influence of polymorphisms in the serotonin transporter gene (SERTPR (or 5-HTTLPR) and STin2) on SSRI response. Studies were identified by the use of MEDLINE, EmBase and PsycINFO, references of articles, reviews and information from pharmaceutical companies. Nine studies assessing the influence of SERTPR or STin2 on treatment response were included. Outcome was expressed as the percentage of decrease in depression score (HAM-D or MADRS) or as the percentage of responders (> or =50% reduction on the depression scale). Both study methodologies and study outcomes showed large heterogeneity. Weighted mean decreases in depression score for patients with the s/s, s/l and l/l genotypes were 35.4, 46.3 and 48.0% at week 4, respectively, and 53.9, 54.6 and 48.3% at week 6. Among Caucasian patients, both mean decrease in depression score and response rate were lowest in the s/s group, while among Asian patients, results were inconsistent. Weighted response rates were 36.1% for the 10/12 genotype of the STin2 polymorphism and 80.7% for the 12/12 genotype (chi2=27.8, P<0.001) (only Asians). The available evidence points to a less favourable response to SSRI treatment among Caucasian patients with the SERTPR s/s genotype and among (Asian) patients with the STin2 10/12 genotype. In view of the scarcity and heterogeneity of the studies, however, current information is insufficiently reliable as a basis for implementing genetic testing in the diagnostic work-up of the depressive patient.
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Affiliation(s)
- K M Smits
- Department of Epidemiology, Maastricht University, Maastricht, The Netherlands.
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