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Jevšinek Skok D, Hauptman N. In Silico Gene Prioritization Highlights the Significance of Bone Morphogenetic Protein 4 ( BMP4) Promoter Methylation across All Methylation Clusters in Colorectal Cancer. Int J Mol Sci 2023; 24:12692. [PMID: 37628872 PMCID: PMC10454928 DOI: 10.3390/ijms241612692] [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: 07/15/2023] [Revised: 08/03/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
The cytosine-phosphate-guanine (CpG) island methylator phenotype (CIMP) represents one of the pathways involved in the development of colorectal cancer, characterized by genome-wide hypermethylation. To identify samples exhibiting hypermethylation, we used unsupervised hierarchical clustering on genome-wide methylation data. This clustering analysis revealed the presence of four distinct subtypes within the tumor samples, namely, CIMP-H, CIMP-L, cluster 3, and cluster 4. These subtypes demonstrated varying levels of methylation, categorized as high, intermediate, and very low. To gain further insights, we mapped significant probes from all clusters to Ensembl Regulatory build 89, with a specific focus on those located within promoter regions or bound regions. By intersecting the methylated promoter and bound regions across all methylation subtypes, we identified a total of 253 genes exhibiting aberrant methylation patterns in the promoter regions across all four subtypes of colorectal cancer. Among these genes, our comprehensive genome-wide analysis highlights bone morphogenic protein 4 (BMP4) as the most prominent candidate. This significant finding was derived through the utilization of various bioinformatics tools, emphasizing the potential role of BMP4 in colorectal cancer development and progression.
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Affiliation(s)
- Daša Jevšinek Skok
- Agricultural Institute of Slovenia, Hacquetova ulica 17, SI-1000 Ljubljana, Slovenia;
| | - Nina Hauptman
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Korytkova 2, SI-1000 Ljubljana, Slovenia
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Kerdivel G, Amrouche F, Calmejane MA, Carallis F, Hamroune J, Hantel C, Bertherat J, Assié G, Boeva V. DNA hypermethylation driven by DNMT1 and DNMT3A favors tumor immune escape contributing to the aggressiveness of adrenocortical carcinoma. Clin Epigenetics 2023; 15:121. [PMID: 37528470 PMCID: PMC10394822 DOI: 10.1186/s13148-023-01534-5] [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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 07/16/2023] [Indexed: 08/03/2023] Open
Abstract
BACKGROUND Adrenocortical carcinoma is rare and aggressive endocrine cancer of the adrenal gland. Within adrenocortical carcinoma, a recently described subtype characterized by a CpG island methylator phenotype (CIMP) has been associated with an especially poor prognosis. However, the drivers of CIMP remain unknown. Furthermore, the functional relation between CIMP and poor clinical outcomes of patients with adrenocortical carcinoma stays elusive. RESULTS Here, we show that CIMP in adrenocortical carcinoma is linked to the increased expression of DNA methyltransferases DNMT1 and DNMT3A driven by a gain of gene copy number and cell hyperproliferation. Importantly, we demonstrate that CIMP contributes to tumor aggressiveness by favoring tumor immune escape. This effect could be at least partially reversed by treatment with the demethylating agent 5-azacytidine. CONCLUSIONS In sum, our findings suggest that co-treatment with demethylating agents might enhance the efficacy of immunotherapy and could represent a novel therapeutic approach for patients with high CIMP adrenocortical carcinoma.
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Affiliation(s)
- Gwenneg Kerdivel
- INSERM, U1016, Cochin Institute, CNRS UMR8104, University of Paris, 24 rue du Faubourg Saint-Jacques, Paris, France
| | - Floriane Amrouche
- INSERM, U1016, Cochin Institute, CNRS UMR8104, University of Paris, 24 rue du Faubourg Saint-Jacques, Paris, France
| | - Marie-Ange Calmejane
- INSERM, U1016, Cochin Institute, CNRS UMR8104, University of Paris, 24 rue du Faubourg Saint-Jacques, Paris, France
| | | | - Juliette Hamroune
- INSERM, U1016, Cochin Institute, CNRS UMR8104, University of Paris, 24 rue du Faubourg Saint-Jacques, Paris, France
| | - Constanze Hantel
- Department of Endocrinology, Diabetology and Clinical Nutrition, University Hospital Zurich (USZ) and University of Zurich (UZH), Zurich, Switzerland
- Medizinische Klinik und Poliklinik III, University Hospital Carl Gustav Carus Dresden, Dresden, Germany
| | - Jérôme Bertherat
- INSERM, U1016, Cochin Institute, CNRS UMR8104, University of Paris, 24 rue du Faubourg Saint-Jacques, Paris, France
| | - Guillaume Assié
- INSERM, U1016, Cochin Institute, CNRS UMR8104, University of Paris, 24 rue du Faubourg Saint-Jacques, Paris, France
| | - Valentina Boeva
- INSERM, U1016, Cochin Institute, CNRS UMR8104, University of Paris, 24 rue du Faubourg Saint-Jacques, Paris, France.
- Department of Computer Science, Institute for Machine Learning, ETH Zurich, Universitätstrasse 6, 8092, Zurich, Switzerland.
- Swiss Institute of Bioinformatics (SIB), Zurich, Switzerland.
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Yang G, Yu XR, Weisenberger DJ, Lu T, Liang G. A Multi-Omics Overview of Colorectal Cancer to Address Mechanisms of Disease, Metastasis, Patient Disparities and Outcomes. Cancers (Basel) 2023; 15:cancers15112934. [PMID: 37296894 DOI: 10.3390/cancers15112934] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 05/16/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
Human colorectal cancer (CRC) is one of the most common malignancies in men and women across the globe, albeit CRC incidence and mortality shows a substantial racial and ethnic disparity, with the highest burden in African American patients. Even with effective screening tools such as colonoscopy and diagnostic detection assays, CRC remains a substantial health burden. In addition, primary tumors located in the proximal (right) or distal (left) sides of the colorectum have been shown to be unique tumor types that require unique treatment schema. Distal metastases in the liver and other organ systems are the major causes of mortality in CRC patients. Characterizing genomic, epigenomic, transcriptomic and proteomic (multi-omics) alterations has led to a better understanding of primary tumor biology, resulting in targeted therapeutic advancements. In this regard, molecular-based CRC subgroups have been developed that show correlations with patient outcomes. Molecular characterization of CRC metastases has highlighted similarities and differences between metastases and primary tumors; however, our understanding as to how to improve patient outcomes based on metastasis biology is lagging and remains a major obstacle to improving CRC patient outcomes. In this review, we will summarize the multi-omics features of primary CRC tumors and their metastases across racial and ethnic groups, the differences in proximal and distal tumor biology, molecular-based CRC subgroups, treatment strategies and challenges for improving patient outcomes.
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Affiliation(s)
- Guang Yang
- School of Sciences, China Pharmaceutical University, Nanjing 211121, China
- China Grand Enterprises, Beijing 100101, China
| | - Xi Richard Yu
- China Grand Enterprises, Beijing 100101, China
- Huadong Medicine Co., Ltd., Hangzhou 310011, China
| | - Daniel J Weisenberger
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- USC Institute of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Tao Lu
- School of Sciences, China Pharmaceutical University, Nanjing 211121, China
- State Key Laboratory of Natural Sciences, China Pharmaceutical University, Nanjing 211121, China
| | - Gangning Liang
- USC Institute of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
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Abstract
Epigenetic modifications, such as DNA methylation, is widely studied in cancer. DNA methylation patterns have been shown to distinguish between benign and malignant tumors in various cancers, including prostate cancer. It may also contribute to oncogenesis, as it is frequently associated with downregulation of tumor suppressor genes. Aberrant patterns of DNA methylation, in particular the CpG island hypermethylator phenotype (CIMP), have shown associative evidence with distinct clinical features and outcomes, such as aggressive subtypes, higher Gleason score, prostate-specific antigen (PSA), and overall tumor stage, overall worse prognosis, as well as reduced survival. In prostate cancer, hypermethylation of specific genes is significantly different between tumor and normal tissues. Methylation patterns could distinguish between aggressive subtypes of prostate cancer, including neuroendocrine prostate cancer (NEPC) and castration resistant prostate adenocarcinoma. Further, DNA methylation is detectable in cell-free DNA (cfDNA) and is reflective of clinical outcome, making it a potential biomarker for prostate cancer. This review summarizes recent advances in understanding DNA methylation alterations in cancers with the focus on prostate cancer. We discuss the advanced methodology used for evaluating DNA methylation changes and the molecular regulators behind these changes. We also explore the clinical potential of DNA methylation as prostate cancer biomarkers and its potential for developing targeted treatment of CIMP subtype of prostate cancer.
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Affiliation(s)
- Hyun Jin Shin
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, United States
| | - Junjie T Hua
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, United States
| | - Haolong Li
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, United States
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Jahan Z, Benthani FA, Currey N, Parker HW, Dahlstrom JE, Caldon CE, Kohonen-Corish MRJ. MCC Gene Silencing Is a CpG Island Methylator Phenotype-Associated Factor That Predisposes Colon Cancer Cells to Irinotecan and Olaparib. Cancers (Basel) 2022; 14:cancers14122859. [PMID: 35740525 PMCID: PMC9221012 DOI: 10.3390/cancers14122859] [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: 05/27/2022] [Accepted: 06/06/2022] [Indexed: 12/10/2022] Open
Abstract
Simple Summary DNA hypermethylation of specific regulatory regions causes gene silencing that is an important cancer-promoting mechanism. A subset of colorectal cancers display concordant hypermethylation and silencing of multiple genes, and this appears to change the way in which tumors respond to some cancer therapies. The aim of this study was to evaluate how the presence of the MCC gene silencing relates to the highly methylated subset of colorectal cancers and how it may affect therapy responsiveness. We found that strong MCC silencing is found throughout the hypermethylated subset, but MCC expression is also lost or reduced in some other tumors which show hypomethylated regions of the gene. In cell culture experiments, the deletion of MCC increased the responsiveness of cancer cells to the chemotherapy drug irinotecan (SN38), and this was further augmented by a targeted cancer drug, the PARP-inhibitor Olaparib. Abstract Chemotherapy is a mainstay of colorectal cancer treatment, and often involves a combination drug regime. CpG island methylator phenotype (CIMP)-positive tumors are potentially more responsive to the topoisomerase-inhibitor irinotecan. The mechanistic basis of the increased sensitivity of CIMP cancers to irinotecan is poorly understood. Mutated in Colorectal Cancer (MCC) is emerging as a multifunctional tumor suppressor gene in colorectal and liver cancers, and has been implicated in drug responsiveness. Here, we found that CIMP tumors undergo MCC loss almost exclusively via promoter hypermethylation rather than copy number variation or mutations. A subset of cancers display hypomethylation which is also associated with low MCC expression, particularly in rectal cancer, where CIMP is rare. MCC knockdown or deletion was found to sensitize cells to SN38 (the active metabolite of irinotecan) or the PARP-inhibitor Olaparib. A synergistic effect on cell death was evident when these drugs were used concurrently. The improved SN38/irinotecan efficacy was accompanied by the down-regulation of DNA repair genes. Thus, differential methylation of MCC is potentially a valuable biomarker to identify colorectal cancers suitable for irinotecan therapy, possibly in combination with PARP inhibitors.
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Affiliation(s)
- Zeenat Jahan
- Woolcock Institute of Medical Research, 431 Glebe Point Road, Glebe, Sydney, NSW 2037, Australia; (Z.J.); (H.W.P.)
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; (F.A.B.); (N.C.); (C.E.C.)
| | - Fahad A. Benthani
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; (F.A.B.); (N.C.); (C.E.C.)
- St. Vincent’s Clinical School, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Nicola Currey
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; (F.A.B.); (N.C.); (C.E.C.)
| | - Hannah W. Parker
- Woolcock Institute of Medical Research, 431 Glebe Point Road, Glebe, Sydney, NSW 2037, Australia; (Z.J.); (H.W.P.)
- Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Jane E. Dahlstrom
- ACT Pathology, The Canberra Hospital and Australian National University Medical School, Canberra, ACT 2605, Australia;
| | - C. Elizabeth Caldon
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; (F.A.B.); (N.C.); (C.E.C.)
- St. Vincent’s Clinical School, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Maija R. J. Kohonen-Corish
- Woolcock Institute of Medical Research, 431 Glebe Point Road, Glebe, Sydney, NSW 2037, Australia; (Z.J.); (H.W.P.)
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; (F.A.B.); (N.C.); (C.E.C.)
- Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia
- Microbiome Research Centre, School of Clinical Medicine, UNSW Sydney, Sydney, NSW 2217, Australia
- School of Medicine, Western Sydney University, Sydney, NSW 2560, Australia
- Correspondence: ; Tel.: +61-2-9114-0275
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Yates J, Boeva V. Deciphering the etiology and role in oncogenic transformation of the CpG island methylator phenotype: a pan-cancer analysis. Brief Bioinform 2022; 23:6520307. [PMID: 35134107 PMCID: PMC8921629 DOI: 10.1093/bib/bbab610] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/06/2021] [Accepted: 12/30/2021] [Indexed: 12/25/2022] Open
Abstract
Numerous cancer types have shown to present hypermethylation of CpG islands, also known as a CpG island methylator phenotype (CIMP), often associated with survival variation. Despite extensive research on CIMP, the etiology of this variability remains elusive, possibly due to lack of consistency in defining CIMP. In this work, we utilize a pan-cancer approach to further explore CIMP, focusing on 26 cancer types profiled in the Cancer Genome Atlas (TCGA). We defined CIMP systematically and agnostically, discarding any effects associated with age, gender or tumor purity. We then clustered samples based on their most variable DNA methylation values and analyzed resulting patient groups. Our results confirmed the existence of CIMP in 19 cancers, including gliomas and colorectal cancer. We further showed that CIMP was associated with survival differences in eight cancer types and, in five, represented a prognostic biomarker independent of clinical factors. By analyzing genetic and transcriptomic data, we further uncovered potential drivers of CIMP and classified them in four categories: mutations in genes directly involved in DNA demethylation; mutations in histone methyltransferases; mutations in genes not involved in methylation turnover, such as KRAS and BRAF; and microsatellite instability. Among the 19 CIMP-positive cancers, very few shared potential driver events, and those drivers were only IDH1 and SETD2 mutations. Finally, we found that CIMP was strongly correlated with tumor microenvironment characteristics, such as lymphocyte infiltration. Overall, our results indicate that CIMP does not exhibit a pan-cancer manifestation; rather, general dysregulation of CpG DNA methylation is caused by heterogeneous mechanisms.
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Affiliation(s)
- Josephine Yates
- Institute for Machine Learning, Department of Computer Science, ETH Zürich, Zurich 8092, Switzerland
| | - Valentina Boeva
- Institute for Machine Learning, Department of Computer Science, ETH Zürich, Zurich 8092, Switzerland.,Swiss Institute for Bioinformatics (SIB), Zürich, Switzerland.,Cochin Institute, Inserm U1016, CNRS UMR 8104, Paris Descartes University UMR-S1016, Paris 75014, France
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Paweł K, Maria Małgorzata S. CpG Island Methylator Phenotype-A Hope for the Future or a Road to Nowhere? Int J Mol Sci 2022; 23:ijms23020830. [PMID: 35055016 PMCID: PMC8777692 DOI: 10.3390/ijms23020830] [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] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/01/2021] [Accepted: 12/07/2021] [Indexed: 02/06/2023] Open
Abstract
The CpG island methylator phenotype (CIMP) can be regarded as the most notable emanation of epigenetic instability in cancer. Since its discovery in the late 1990s, CIMP has been extensively studied, mainly in colorectal cancers (CRC) and gliomas. Consequently, knowledge on molecular and pathological characteristics of CIMP in CRC and other tumour types has rapidly expanded. Concordant and widespread hypermethylation of multiple CpG islands observed in CIMP in multiple cancers raised hopes for future epigenetically based diagnostics and treatments of solid tumours. However, studies on CIMP in solid tumours were hampered by a lack of generalisability and reproducibility of epigenetic markers. Moreover, CIMP was not a satisfactory marker in predicting clinical outcomes. The idea of targeting epigenetic abnormalities such as CIMP for cancer therapy has not been implemented for solid tumours, either. Twenty-one years after its discovery, we aim to cover both the fundamental and new aspects of CIMP and its future application as a diagnostic marker and target in anticancer therapies.
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Turpín-Sevilla MDC, Pérez-Sanz F, García-Solano J, Sebastián-León P, Trujillo-Santos J, Carbonell P, Estrada E, Tuomisto A, Herruzo I, Fennell LJ, Mäkinen MJ, Rodríguez-Braun E, Whitehall VLJ, Conesa A, Conesa-Zamora P. Global Methylome Scores Correlate with Histological Subtypes of Colorectal Carcinoma and Show Different Associations with Common Clinical and Molecular Features. Cancers (Basel) 2021; 13:cancers13205165. [PMID: 34680315 PMCID: PMC8533997 DOI: 10.3390/cancers13205165] [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: 08/16/2021] [Revised: 10/03/2021] [Accepted: 10/11/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The typical methylation patterns associated with cancer are hypermethylation at gene promoters and global genome hypomethylation. Aberrant CpG island hypermethylation at promoter regions and global genome hypomethylation have not been associated with histological colorectal carcinomas (CRC) subsets. Using Illumina's 450 k Infinium Human Methylation beadchip, the methylome of 82 CRCs were analyzed, comprising different histological subtypes: 40 serrated adenocarcinomas (SAC), 32 conventional carcinomas (CC) and 10 CRCs showing histological and molecular features of microsatellite instability (hmMSI-H), and, additionally, 35 normal adjacent mucosae. Scores reflecting the overall methylation at 250 bp, 1 kb and 2 kb from the transcription starting site (TSS) were studied. RESULTS SAC has an intermediate methylation pattern between CC and hmMSI-H for the three genome locations. In addition, the shift from promoter hypermethylation to genomic hypomethylation occurs at a small sequence between 250 bp and 1 Kb from the gene TSS, and an asymmetric distribution of methylation was observed between both sides of the CpG islands (N vs. S shores). CONCLUSION These findings show that different histological subtypes of CRC have a particular global methylation pattern depending on sequence distance to TSS and highlight the so far underestimated importance of CpGs aberrantly hypomethylated in the clinical phenotype of CRCs.
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Affiliation(s)
- María del Carmen Turpín-Sevilla
- Facultad de Medicina, Universidad Francisco de Vitoria, Ctra. Pozuelo-Majadahonda, Km 1800, Pozuelo de Alarcón, 28223 Madrid, Spain; (M.d.C.T.-S.); (I.H.)
| | - Fernando Pérez-Sanz
- Biomedical Informatics & Bioinformatics Platform, Institute for Biomedical Research of Murcia (IMIB)/Foundation for Healthcare Training & Research of the Region of Murcia (FFIS), Calle Luis Fontes Pagán 9, 30003 Murcia, Spain;
| | - José García-Solano
- Department of Pathology, Santa Lucía General University Hospital (HGUSL), C/Mezquita s/n, 30202 Cartagena, Spain;
- Facultad de Ciencias de la Salud, Universidad Católica de Murcia (UCAM), Campus Los Jerónimos, 30107 Guadalupe, Spain
- Group of Molecular Pathology and Pharmacogenetics, Institute for Biomedical Research from Murcia (IMIB), HGUSL, 30202 Cartagena, Spain
| | - Patricia Sebastián-León
- IVI Foundation, Instituto de Investigación Sanitaria La Fe (IIS La Fe), 46026 Valencia, Spain;
| | - Javier Trujillo-Santos
- Department of Internal Medicine, Santa Lucía General University Hospital (HGUSL), C/Mezquita s/n, 30202 Cartagena, Spain;
| | - Pablo Carbonell
- Biochemistry and Clinical Genetic Center, Virgen de la Arrixaca University Hospital, 30100 Murcia, Spain;
| | - Eduardo Estrada
- Department of Social Psychology and Methodology, Universidad Autónoma de Madrid, 28049 Madrid, Spain;
| | - Anne Tuomisto
- Cancer and Translational Medicine Research Unit, Department of Pathology, University of Oulu, P.O. Box 5000, 90014 Oulu, Finland; (A.T.); (M.J.M.)
| | - Irene Herruzo
- Facultad de Medicina, Universidad Francisco de Vitoria, Ctra. Pozuelo-Majadahonda, Km 1800, Pozuelo de Alarcón, 28223 Madrid, Spain; (M.d.C.T.-S.); (I.H.)
| | - Lochlan J. Fennell
- QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia; (L.J.F.); (V.L.J.W.)
- Conjoint Internal Medicine Laboratory, Pathology Queensland, Herston, QLD 4006, Australia
- Faculty of Medicine, The University of Queensland, Herston, QLD 4072, Australia
| | - Markus J. Mäkinen
- Cancer and Translational Medicine Research Unit, Department of Pathology, University of Oulu, P.O. Box 5000, 90014 Oulu, Finland; (A.T.); (M.J.M.)
| | - Edith Rodríguez-Braun
- Clinical Oncology Department, Santa Lucía General University Hospital (HGUSL). C/Mezquita s/n, 30202 Cartagena, Spain;
| | - Vicki L. J. Whitehall
- QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia; (L.J.F.); (V.L.J.W.)
- Conjoint Internal Medicine Laboratory, Pathology Queensland, Herston, QLD 4006, Australia
- Faculty of Medicine, The University of Queensland, Herston, QLD 4072, Australia
| | - Ana Conesa
- Microbiology and Cell Sciences Department, Institute for Food and Agricultural Sciences, Genetics Institute, University of Florida, Gainesville, FL 32611, USA;
| | - Pablo Conesa-Zamora
- Facultad de Ciencias de la Salud, Universidad Católica de Murcia (UCAM), Campus Los Jerónimos, 30107 Guadalupe, Spain
- Group of Molecular Pathology and Pharmacogenetics, Institute for Biomedical Research from Murcia (IMIB), HGUSL, 30202 Cartagena, Spain
- Clinical Oncology Department, Santa Lucía General University Hospital (HGUSL). C/Mezquita s/n, 30202 Cartagena, Spain;
- Department of Clinical Analysis, Santa Lucía General University Hospital (HGUSL), C/Mezquita s/n, 30202 Cartagena, Spain
- Correspondence: ; Tel.: +34-968128600 (ext. 951615)
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Jasmine F, Haq Z, Kamal M, Raza M, da Silva G, Gorospe K, Paul R, Strzempek P, Ahsan H, Kibriya MG. Interaction between Microsatellite Instability (MSI) and Tumor DNA Methylation in the Pathogenesis of Colorectal Carcinoma. Cancers (Basel) 2021; 13:4956. [PMID: 34638440 DOI: 10.3390/cancers13194956] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 12/19/2022] Open
Abstract
Simple Summary In colorectal cancer (CRC), mutations may occur in short, repeated DNA sequences, known as microsatellite instability (MSI). Tumor DNA methylation is another molecular change now recognized as an important biomarker in CRC. In a genome-wide scale, for the first time, we explored whether DNA methylation is associated with MSI status in CRC. We analyzed 250 paired samples (tumor and corresponding normal) from 125 CRC patients (m = 72, f = 53) at different stages. We found that many genes were methylated in tumor tissue compared to normal tissue. However, almost four times more genes showed such methylation changes in the tumor if the patient who also had MSI compared to patients without MSI. Our study shows an association of MSI and DNA methylation in CRC. The study also indicates an opportunity for potential use of certain immune checkpoint inhibitors (CTLA4 and HAVCR2 inhibitors) in CRC with MSI. Abstract In colorectal cancer (CRC), the role of microsatellite instability (MSI) is well known. In a genome-wide scale, for the first time, we explored whether differential methylation is associated with MSI. We analyzed 250 paired samples from 125 CRC patients (m = 72, f = 53) at different stages. Of them, 101 had left-sided CRC, 30 had MSI, 34 had somatic mutation in KRAS proto-oncogene (KRAS), and 6 had B-Raf proto-oncogene (BRAF) exon 15p.V600E mutation. MSI was more frequent in right-sided tumors (54% vs. 17%, p = 0.003). Among the microsatellite stable (MSS) CRC, a paired comparison revealed 1641 differentially methylated loci (DML) covering 686 genes at FDR 0.001 with delta beta ≥ 20%. Similar analysis in MSI revealed 6209 DML covering 2316 genes. ANOVA model including interaction (Tumor*MSI) revealed 23,322 loci, where the delta beta was different among MSI and MSS patients. Our study shows an association between MSI and tumor DNA methylation in the pathogenesis of CRC. Given the interaction seen in this study, it may be worth considering the MSI status while looking for methylation markers in CRC. The study also indicates an opportunity for potential use of certain immune checkpoint inhibitors (CTLA4 and HAVCR2 inhibitors) in CRC with MSI.
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Meessen S, Currey N, Jahan Z, Parker HW, Jenkins MA, Buchanan DD, Hopper JL, Segelov E, Dahlstrom JE, Kohonen-Corish MRJ. Tetranucleotide and Low Microsatellite Instability Are Inversely Associated with the CpG Island Methylator Phenotype in Colorectal Cancer. Cancers (Basel) 2021; 13:cancers13143529. [PMID: 34298744 PMCID: PMC8308094 DOI: 10.3390/cancers13143529] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/08/2021] [Accepted: 07/08/2021] [Indexed: 01/19/2023] Open
Abstract
Simple Summary A type of DNA mismatch repair defect known as “elevated microsatellite alterations at selected tetranucleotide repeats” (EMAST) is found across many different cancers. Tetranucleotide microsatellite instability, which is caused by MSH3 mismatch repair gene/protein loss-of-function, shares a molecular basis with “low microsatellite instability” (MSI-L) in colorectal cancer. Tetranucleotide microsatellite instability is also a byproduct of “high microsatellite instability” (MSI-H) that arises from deficiency of mismatch repair due to MSH2, MSH6, MLH1 or PMS2 gene alterations. MSH3-related EMAST is emerging as a biomarker of poor prognosis in colorectal cancer and needs to be clearly differentiated from MSI-H. Here, we show that tumours with non-MSI-H-related EMAST or MSI-L rarely show concordant promoter methylation of multiple marker genes. Colorectal tumours that are positive for a single (1/5) tetranucleotide repeat marker are an important subset of the EMAST spectrum. Abstract MSH3 gene or protein deficiency or loss-of-function in colorectal cancer can cause a DNA mismatch repair defect known as “elevated microsatellite alterations at selected tetranucleotide repeats” (EMAST). A high percentage of MSI-H tumors exhibit EMAST, while MSI-L is also linked with EMAST. However, the distribution of CpG island methylator phenotype (CIMP) within the EMAST spectrum is not known. Five tetranucleotide repeat and five MSI markers were used to classify 100 sporadic colorectal tumours for EMAST, MSI-H and MSI-L according to the number of unstable markers detected. Promoter methylation was determined using methylation-specific PCR for MSH3, MCC, CDKN2A (p16) and five CIMP marker genes. EMAST was found in 55% of sporadic colorectal carcinomas. Carcinomas with only one positive marker (EMAST-1/5, 26%) were associated with advanced tumour stage, increased lymph node metastasis, MSI-L and lack of CIMP-H. EMAST-2/5 (16%) carcinomas displayed some methylation but MSI was rare. Carcinomas with ≥3 positive EMAST markers (13%) were more likely to have a proximal colon location and be MSI-H and CIMP-H. Our study suggests that EMAST/MSI-L is a valuable prognostic and predictive marker for colorectal carcinomas that do not display the high methylation phenotype CIMP-H.
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Affiliation(s)
- Sabine Meessen
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; (S.M.); (N.C.)
| | - Nicola Currey
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; (S.M.); (N.C.)
| | - Zeenat Jahan
- The Woolcock Institute of Medical Research, The University of Sydney, Sydney, NSW 2037, Australia; (Z.J.); (H.W.P.)
| | - Hannah W. Parker
- The Woolcock Institute of Medical Research, The University of Sydney, Sydney, NSW 2037, Australia; (Z.J.); (H.W.P.)
- Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Mark A. Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC 3000, Australia; (M.A.J.); (J.L.H.)
| | - Daniel D. Buchanan
- Department of Clinical Pathology, University of Melbourne, Melbourne, VIC 3010, Australia;
- University of Melbourne Centre for Cancer Research, University of Melbourne, Melbourne, VIC 3010, Australia
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Melbourne, VIC 3010, Australia
| | - John L. Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC 3000, Australia; (M.A.J.); (J.L.H.)
| | - Eva Segelov
- Department of Oncology, Monash University and Monash Health, Melbourne, VIC 3168, Australia;
| | - Jane E. Dahlstrom
- ACT Pathology, The Canberra Hospital and Australian National University Medical School, Canberra, ACT 2605, Australia;
| | - Maija R. J. Kohonen-Corish
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; (S.M.); (N.C.)
- The Woolcock Institute of Medical Research, The University of Sydney, Sydney, NSW 2037, Australia; (Z.J.); (H.W.P.)
- Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia
- Microbiome Research Centre, St George & Sutherland Clinical School, UNSW Sydney, Sydney, NSW 2217, Australia
- School of Medicine, Western Sydney University, Sydney, NSW 2751, Australia
- Correspondence:
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11
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Padmanabhan N, Kyon HK, Boot A, Lim K, Srivastava S, Chen S, Wu Z, Lee HO, Mukundan VT, Chan C, Chan YK, Xuewen O, Pitt JJ, Isa ZFA, Xing M, Lee MH, Tan ALK, Ting SHW, Luftig MA, Kappei D, Kruger WD, Bian J, Ho YS, Teh M, Rozen SG, Tan P. Highly recurrent CBS epimutations in gastric cancer CpG island methylator phenotypes and inflammation. Genome Biol 2021; 22:167. [PMID: 34074348 PMCID: PMC8170989 DOI: 10.1186/s13059-021-02375-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 01/28/2021] [Accepted: 05/06/2021] [Indexed: 02/06/2023] Open
Abstract
Background CIMP (CpG island methylator phenotype) is an epigenetic molecular subtype, observed in multiple malignancies and associated with the epigenetic silencing of tumor suppressors. Currently, for most cancers including gastric cancer (GC), mechanisms underlying CIMP remain poorly understood. We sought to discover molecular contributors to CIMP in GC, by performing global DNA methylation, gene expression, and proteomics profiling across 14 gastric cell lines, followed by similar integrative analysis in 50 GC cell lines and 467 primary GCs. Results We identify the cystathionine beta-synthase enzyme (CBS) as a highly recurrent target of epigenetic silencing in CIMP GC. Likewise, we show that CBS epimutations are significantly associated with CIMP in various other cancers, occurring even in premalignant gastroesophageal conditions and longitudinally linked to clinical persistence. Of note, CRISPR deletion of CBS in normal gastric epithelial cells induces widespread DNA methylation changes that overlap with primary GC CIMP patterns. Reflecting its metabolic role as a gatekeeper interlinking the methionine and homocysteine cycles, CBS loss in vitro also causes reductions in the anti-inflammatory gasotransmitter hydrogen sulfide (H2S), with concomitant increase in NF-κB activity. In a murine genetic model of CBS deficiency, preliminary data indicate upregulated immune-mediated transcriptional signatures in the stomach. Conclusions Our results implicate CBS as a bi-faceted modifier of aberrant DNA methylation and inflammation in GC and highlights H2S donors as a potential new therapy for CBS-silenced lesions. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-021-02375-2.
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Affiliation(s)
- Nisha Padmanabhan
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Huang Kie Kyon
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Arnoud Boot
- Centre for Computational Biology, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Kevin Lim
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Supriya Srivastava
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
| | - Shuwen Chen
- Bioprocessing Technology Institute, A*STAR, 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore
| | - Zhiyuan Wu
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117600, Singapore
| | - Hyung-Ok Lee
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Vineeth T Mukundan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Charlene Chan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Yarn Kit Chan
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Ong Xuewen
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Jason J Pitt
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Zul Fazreen Adam Isa
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Manjie Xing
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Ming Hui Lee
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Angie Lay Keng Tan
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Shamaine Ho Wei Ting
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore
| | - Micah A Luftig
- Department of Molecular Genetics and Microbiology, Duke Centre for Virology, Duke University School of Medicine, Durham, NC, USA
| | - Dennis Kappei
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117596, Singapore
| | - Warren D Kruger
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Jinsong Bian
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117600, Singapore.,National University of Singapore (Suzhou) Research Institute, Suzhou, 215123, China
| | - Ying Swan Ho
- Bioprocessing Technology Institute, A*STAR, 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore
| | - Ming Teh
- Department of Pathology, National University of Singapore, Singapore, 119228, Singapore
| | - Steve George Rozen
- Centre for Computational Biology, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Patrick Tan
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8, College road, Singapore, 169857, Singapore. .,Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore. .,Genome Institute of Singapore, Singapore, 138672, Singapore. .,SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre Singapore, Singapore, 169856, Singapore. .,Singapore Gastric Cancer Consortium, Singapore, 119074, Singapore. .,Department of Physiology, National University of Singapore, Singapore, 117593, Singapore.
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12
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Murcia O, Martínez-Roca A, Juárez M, Giner-Calabuig M, Alustiza M, Mira C, Mangas-Sanjuan C, Serrano E, Ruiz-Gómez FA, Baile-Maxia S, Medina L, Alenda C, Payá A, Rodriguez-Soler M, Zapater P, Jover R. Effects of Somatic Methylation in Colonic Polyps on Risk of Developing Metachronous Advanced Colorectal Lesions. Cancers (Basel) 2021; 13:E246. [PMID: 33440809 DOI: 10.3390/cancers13020246] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/22/2020] [Accepted: 12/27/2020] [Indexed: 12/25/2022] Open
Abstract
The utility of molecular markers for predicting the risk of metachronous advanced colorectal lesions (MACLs) remains poorly investigated. We examined the relationship between somatic hypermethylation in polyps at baseline and the risk of developing MACL. This retrospective cohort study included 281 consecutive patients with colonic polyps who were enrolled between 2007 and 2009 and followed-up until 2014. MACLs were defined as adenomas of ≥10 mm, high-grade dysplasia, or with a villous component; and serrated lesions of ≥10 mm or with dysplasia. In total, 595 polyps were removed at baseline colonoscopy and analyzed for pathological characteristics and CpG island methylator phenotype (CIMP) using the MS-MLPA (Methylation-Specific -- Multiplex Ligation-dependent Probe Amplification) technique. Forty-five patients (16.0%) showed at least one CIMP+ polyp. MACL risk was higher in patients with CIMP+ polyps (odds ratio (OR), 4.50; 95% CI, 1.78-11.4; p = 0.002). Patients with CIMP+ polyps also exhibited shorter time to MACL development (33.8 months vs. 50.1 months; p < 0.001), even with adjustment for polyp size and number (OR, 2.40; 95% CI, 1.33-4.34). Adding CIMP analysis improved the sensitivity (57.0% to 70.9%), negative predictive value (71.1% to 77.3%), and overall accuracy (49.8% to 52.0%) for MACL risk estimation. These results highlight that CIMP may be a useful marker for endoscopic surveillance.
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13
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Advani SM, Swartz MD, Loree J, Davis JS, Sarsashek AM, Lam M, Lee MS, Bressler J, Lopez DS, Daniel CR, Morris V, Shureqi I, Kee B, Dasari A, Vilar E, Overman M, Hamilton S, Maru D, Braithwaite D, Kopetz S. Epidemiology and Molecular-Pathologic Characteristics of CpG Island Methylator Phenotype ( CIMP) in Colorectal Cancer. Clin Colorectal Cancer 2020; 20:137-147.e1. [PMID: 33229221 DOI: 10.1016/j.clcc.2020.09.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 07/06/2020] [Revised: 09/15/2020] [Accepted: 09/18/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND CpG island methylator phenotype (CIMP) forms a distinct epigenetic phenotype in colorectal cancer (CRC). Though associated with distinct clinicopathologic characteristics, limited evidence exists of the association of CIMP with patient's reported lifestyle factors and tumor molecular characteristics. We assessed the associations of these characteristics in a pooled analysis of CRC patients. PATIENTS AND METHODS We pooled data from 3 CRC patient cohorts: Assessment of Targeted Therapies Against Colorectal Cancer (ATTACC), biomarker-based protocol (Integromics), and The Cancer Genome Atlas (TCGA). CIMP was measured using the classical 6-gene methylated-in-tumor (MINT) marker panel (MINT1, MINT2, MINT31, p14, p16, and MLH1) in ATTACC and genome-wide human methylation arrays in Integromics and TCGA, respectively. CIMP-High (CIMP-H) was defined as ≥ 3 of 6 methylated markers in ATTACC. In TCGA and Integromics, CIMP-H group was defined on the basis of clusters of methylation profiles and high levels of methylation in tumor samples. Baseline comparisons of characteristics across CIMP groups (CIMP-H vs. CIMP-0) were performed by Student t test or chi-square test for continuous or categorical variables, respectively. Further logistic regression analyses were performed to compute the odds ratio (OR) of these associations. RESULTS Pooled prevalence of CIMP-H was 22% across 3 data sets. CIMP-H CRC tumors were associated with older age at diagnosis (OR, 1.02; 95% confidence interval [CI], 1.01, 1.03), microsatellite instability-high (MSI-H) status (OR, 9.15; 95% CI, 4.45, 18.81), BRAF mutation (OR, 7.70; 95% CI, 4.98, 11.87), right-sided tumor location (OR, 2.40; 95% CI, 1.78, 3.22), poor differentiation (OR, 2.94; 95% CI, 1.95, 4.45), and mucinous histology (OR, 2.47; 95% CI, 1.77, 3.47), as reported previously in the literature. CIMP-H tumors were also found to be associated with self-reported history of alcohol consumption (OR, ever vs. never, 1.58; 95% CI, 1.07, 2.34). Pathologically, CIMP-H tumors were associated with the presence of intraepithelial lymphocytes (OR, 3.31; 95% CI, 1.41, 7.80) among patients in the Integromics cohort. CONCLUSION CIMP-H tumors were associated with history of alcohol consumption and presence of intraepithelial lymphocytes. In addition, we confirmed the previously known association of CIMP with age, MSI-H status, BRAF mutation, sidedness, and mucinous histology. Molecular pathologic epidemiology associations help us explore the underlying association of lifestyle and clinical factors with molecular subsets like CIMP and help guide cancer prevention and treatment strategies.
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Affiliation(s)
- Shailesh M Advani
- Social Behavioral Research Branch, National Human Genome Research Institute, National Institute of Health, Bethesda, MD; Division of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX; Department of Oncology, Georgetown University School of Medicine, Washington, DC.
| | - Michael D Swartz
- Department of Biostatistics and Data Science, University of Texas Health Science Center at Houston, Houston, TX
| | - Jonathan Loree
- Division of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jennifer S Davis
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Amir Mehvarz Sarsashek
- Division of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Michael Lam
- Division of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Michael Sangmin Lee
- Division of Gastrointestinal Oncology, University of North Carolina Chapel Hill, Chapel Hill, NC
| | - Jan Bressler
- Department of Epidemiology, Human Genetics and Environmental Sciences, University of Texas Health Science Center at Houston, School of Public Health, Houston, TX
| | - David S Lopez
- Department of Preventive Medicine and Population Health, UTMB School of Medicine, Galveston, TX
| | - Carrie R Daniel
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Van Morris
- Division of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Imad Shureqi
- Division of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Bryan Kee
- Division of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Arvind Dasari
- Division of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Eduardo Vilar
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Michael Overman
- Division of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Stanley Hamilton
- Division of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Dipen Maru
- Division of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Dejana Braithwaite
- Department of Oncology, Georgetown University School of Medicine, Washington, DC
| | - Scott Kopetz
- Division of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX.
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14
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Wielandt AM, Hurtado C, Moreno C M, Villarroel C, Castro M, Estay M, Simian D, Martinez M, Vial MT, Kronberg U, López-Köstner F. Characterization of Chilean patients with sporadic colorectal cancer according to the three main carcinogenic pathways: Microsatellite instability, CpG island methylator phenotype and Chromosomal instability. Tumour Biol 2020; 42:1010428320938492. [PMID: 32635826 DOI: 10.1177/1010428320938492] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 12/24/2022] Open
Abstract
Molecular classification of colorectal cancer is difficult to implement in clinical settings where hundreds of genes are involved, and resources are limited. This study aims to characterize the molecular subtypes of patients with sporadic colorectal cancer based on the three main carcinogenic pathways microsatellite instability (MSI), CpG island methylator phenotype (CIMP), and chromosomal instability (CIN) in a Chilean population. Although several reports have characterized colorectal cancer, most do not represent Latin-American populations. Our study includes 103 colorectal cancer patients who underwent surgery, without neoadjuvant treatment, in a private hospital between 2008 and 2017. MSI, CIN, and CIMP status were assessed. Frequent mutations in KRAS, BRAF, and PIK3CA genes were analyzed by Sanger sequencing, and statistical analysis was performed by Fisher's exact and/or chi-square test. Survival curves were estimated with Kaplan-Meier and log-rank test. Based on our observations, we can classify the tumors in four subgroups, Group 1: MSI-high tumors (15%) are located in the right colon, occur at older age, and 60% show a BRAF mutation; Group 2: CIN-high tumors (38%) are in the left colon, and 26% have KRAS mutations. Group 3: [MSI/CIN/CIMP]-low/negative tumors (30%) are left-sided, and 39% have KRAS mutations; Group 4: CIMP-high tumors (15%) were more frequent in men and left side colon, with 27% KRAS and 7% presented BRAF mutations. Three percent of patients could not be classified. We found that CIMP-high was associated with a worse prognosis, both in MSI-high and MSI stable patients (p = 0.0452). Group 3 (Low/negative tumors) tend to have better overall survival compared with MSI-high, CIMP-high, and CIN-high tumors. This study contributes to understanding the heterogeneity of tumors in the Chilean population being one of the few characterizations performed in Latin-America. Given the limited resources of these countries, these results allow to improve molecular characterization in Latin-American colorectal cancer populations and confirm the possibility of using the three main carcinogenic pathways to define therapeutic strategies.
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Affiliation(s)
- Ana María Wielandt
- Oncology and Molecular Genetics Laboratory, Coloproctology Unit, Clínica Las Condes, Santiago, Chile.,Coloproctology Unit, Clínica Las Condes, Santiago, Chile
| | - Claudia Hurtado
- Oncology and Molecular Genetics Laboratory, Coloproctology Unit, Clínica Las Condes, Santiago, Chile.,Coloproctology Unit, Clínica Las Condes, Santiago, Chile
| | - Mauricio Moreno C
- Oncology and Molecular Genetics Laboratory, Coloproctology Unit, Clínica Las Condes, Santiago, Chile.,Coloproctology Unit, Clínica Las Condes, Santiago, Chile
| | - Cynthia Villarroel
- Oncology and Molecular Genetics Laboratory, Coloproctology Unit, Clínica Las Condes, Santiago, Chile
| | - Magdalena Castro
- Academic Department Research Unit, Clínica Las Condes, Santiago, Chile
| | - Marlene Estay
- Coloproctology Unit, Clínica Las Condes, Santiago, Chile
| | - Daniela Simian
- Academic Department Research Unit, Clínica Las Condes, Santiago, Chile
| | - Maripaz Martinez
- Academic Department Research Unit, Clínica Las Condes, Santiago, Chile
| | | | - Udo Kronberg
- Coloproctology Unit, Clínica Las Condes, Santiago, Chile
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15
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Noreen F, Küng T, Tornillo L, Parker H, Silva M, Weis S, Marra G, Rad R, Truninger K, Schär P. DNA methylation instability by BRAF-mediated TET silencing and lifestyle-exposure divides colon cancer pathways. Clin Epigenetics 2019; 11:196. [PMID: 31842975 PMCID: PMC6916434 DOI: 10.1186/s13148-019-0791-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 12/02/2019] [Indexed: 12/22/2022] Open
Abstract
Background Aberrations in DNA methylation are widespread in colon cancer (CC). Understanding origin and progression of DNA methylation aberrations is essential to develop effective preventive and therapeutic strategies. Here, we aimed to dissect CC subtype-specific methylation instability to understand underlying mechanisms and functions. Methods We have assessed genome-wide DNA methylation in the healthy normal colon mucosa (HNM), precursor lesions and CCs in a first comprehensive study to delineate epigenetic change along the process of colon carcinogenesis. Mechanistically, we used stable cell lines, genetically engineered mouse model of mutant BRAFV600E and molecular biology analysis to establish the role of BRAFV600E-mediated-TET inhibition in CpG-island methylator phenotype (CIMP) inititation. Results We identified two distinct patterns of CpG methylation instability, determined either by age–lifestyle (CC-neutral CpGs) or genetically (CIMP-CpGs). CC-neutral-CpGs showed age-dependent hypermethylation in HNM, all precursors, and CCs, while CIMP-CpGs showed hypermethylation specifically in sessile serrated adenomas/polyps (SSA/Ps) and CIMP-CCs. BRAFV600E-mutated CCs and precursors showed a significant downregulation of TET1 and TET2 DNA demethylases. Stable expression of BRAFV600E in nonCIMP CC cells and in a genetic mouse model was sufficient to repress TET1/TET2 and initiate hypermethylation at CIMP-CpGs, reversible by BRAFV600E inhibition. BRAFV600E-driven CIMP-CpG hypermethylation occurred at genes associated with established CC pathways, effecting functional changes otherwise achieved by genetic mutation in carcinogenesis. Conclusions Hence, while age–lifestyle-driven hypermethylation occurs generally in colon carcinogenesis, BRAFV600E-driven hypermethylation is specific for the “serrated” pathway. This knowledge will advance the use of epigenetic biomarkers to assess subgroup-specific CC risk and disease progression.
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Affiliation(s)
- Faiza Noreen
- Department of Biomedicine, University of Basel, Mattenstrasse 28, CH-4058, Basel, Switzerland.,Swiss Institute of Bioinformatics, 4053, Basel, Switzerland
| | - Taya Küng
- Department of Biomedicine, University of Basel, Mattenstrasse 28, CH-4058, Basel, Switzerland
| | - Luigi Tornillo
- Institute of Pathology, University Hospital Basel, 4056, Basel, Switzerland
| | - Hannah Parker
- Institute of Molecular Cancer Research, University of Zurich, 8057, Zurich, Switzerland
| | - Miguel Silva
- Department of Medicine II, Klinikum Rechts der Isar, Technische Universität München, 81675, Munich, Germany
| | - Stefan Weis
- Department of Biomedicine, University of Basel, Mattenstrasse 28, CH-4058, Basel, Switzerland
| | - Giancarlo Marra
- Institute of Molecular Cancer Research, University of Zurich, 8057, Zurich, Switzerland
| | - Roland Rad
- Department of Medicine II, Klinikum Rechts der Isar, Technische Universität München, 81675, Munich, Germany
| | - Kaspar Truninger
- Department of Biomedicine, University of Basel, Mattenstrasse 28, CH-4058, Basel, Switzerland. .,Gastroenterologie Oberaargau, CH-4900, Langenthal, Switzerland.
| | - Primo Schär
- Department of Biomedicine, University of Basel, Mattenstrasse 28, CH-4058, Basel, Switzerland.
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16
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Samadder NJ, Neklason D, Snow A, Samowitz W, Cessna MH, Rowe K, Sandhu I, Boucher K, Pappas L, Smith KR, Wong J, Curtin K, Provenzale D, Burt RW. Clinical and Molecular Features of Post-Colonoscopy Colorectal Cancers. Clin Gastroenterol Hepatol 2019; 17:2731-2739.e2. [PMID: 30930275 DOI: 10.1016/j.cgh.2019.02.040] [Citation(s) in RCA: 20] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 02/15/2019] [Accepted: 02/25/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Post-colonoscopy colorectal cancers (PCCRCs) may arise from missed lesions or due to molecular features of tumors that allow them to grow rapidly. We aimed to compare clinical, pathology, and molecular features of PCCRCs (those detected within 6-60 months of colonoscopy) and detected CRCs (those detected within 6 months of a colonoscopy). METHODS Within a population-based cross-sectional study of incident CRC cases in Utah (from 1995 through 2009), we identified PCCRCs (those cancers that developed within 5 years of a colonoscopy) and matched the patients by age, sex, and hospital site to patients with detected CRC. Archived specimens were retrieved and tested for microsatellite instability (MSI), CpG island methylation, and mutations in KRAS and BRAF. There were 2659 cases of CRC diagnosed within the study window; 6% of these (n = 159) were defined as PCCRCs; 84 of these cases had tissue available and were matched to 84 subjects with detected CRC. RESULTS Higher proportions of PCCRCs than detected CRCs formed in the proximal colon (64% vs 44%; P = .016) and were of an early stage (86% vs 69%; P = .040). MSI was observed in 32% of PCCRCs compared with 13% of detected CRCs (P = .005). The other molecular features were found in similar proportions of PCCRCs and detected CRCs. In a multivariable logistic regression, MSI (odds ratio, 4.20; 95% CI, 1.58-11.14) was associated with PCCRC. There was no difference in 5-year survival between patients with PCCRCs vs detected CRCs. CONCLUSION In this population-based cross-sectional study of incident CRC cases in Utah, we found PCCRCs to be more likely to arise in the proximal colon and demonstrate MSI, so PCCRCs and detected CRC appear to have different features or processes of tumorigenesis. Additional studies are needed to determine if post-colonoscopy cancers arise through a specific genetic pathway.
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Affiliation(s)
- N Jewel Samadder
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah; Department of Medicine (Gastroenterology), University of Utah, Salt Lake City, Utah; Department of Medicine (Gastroenterology), Mayo Clinic, Phoenix, Arizona.
| | - Deb Neklason
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah; Department of Medicine (Genetic Epidemiology), University of Utah, Salt Lake City, Utah
| | - Angela Snow
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Wade Samowitz
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah; Department of Pathology, University of Utah, Salt Lake City, Utah
| | - Melissa H Cessna
- Department of Pathology and Biorepository, Intermountain Healthcare, Salt Lake City, Utah
| | - Kerry Rowe
- Department of Medicine, Intermountain Healthcare, Salt Lake City, Utah
| | - Iqbal Sandhu
- Department of Bioinformatics, Intermountain Healthcare, Salt Lake City, Utah
| | - Kenneth Boucher
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Lisa Pappas
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Ken Robert Smith
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Jathine Wong
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Karen Curtin
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah; Department of Medicine (Genetic Epidemiology), University of Utah, Salt Lake City, Utah
| | - Dawn Provenzale
- Department of Medicine (Gastroenterology), Duke University, Durham, North Carolina; VA Cooperative Studies Program Epidemiology Center, Departments of Medicine (Gastroenterology) and Clinical Genomics, Mayo Clinic, Phoenix, Arizona
| | - Randall W Burt
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah; Department of Medicine (Gastroenterology), University of Utah, Salt Lake City, Utah; Department of Oncological Sciences, University of Utah, Salt Lake City, Utah
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17
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Liu J, Tang L, Yi J, Li G, Lu Y, Xu Y, Zhao S, Mao R, Li X, Ren L, Wang K. Unique characteristics of CpG island methylator phenotype ( CIMP) in a Chinese population with colorectal cancer. BMC Gastroenterol 2019; 19:173. [PMID: 31690257 PMCID: PMC6833289 DOI: 10.1186/s12876-019-1086-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 10/02/2019] [Indexed: 12/21/2022] Open
Abstract
Background Molecular characteristics of CpG island methylator phenotype (CIMP) in colorectal cancer (CRC) have been well documented in Western, but not in Chinese, populations. Methods We investigated the incidence of CIMP, BRAF/KRAS mutation, and microsatellite instability (MSI) in a Chinese population with CRC (n = 401) and analysed associations between CIMP status and clinicopathological and molecular features. Results A total of 41 cases, 310 cases, and 40 cases were classified as CIMP-high, CIMP-low, and CIMP-negative, respectively. We detected a significantly low incidence of BRAF mutation in adenomas (2%) and CRC (0.7%), and a relatively low incidence of KRAS mutation (24.9%) compared with that in other populations. We also detected a relatively low incidence of CIMP-high (10.2%), which was significantly associated with younger age (≤49 years of age), female sex, and proximal tumour location. Conclusions This study revealed unique characteristics of CIMP in a Chinese population with colorectal cancer. Developing specific CIMP markers based on unique populations or ethnic groups will further help to fully elucidate CIMP pathogenesis.
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Affiliation(s)
- Jiang Liu
- Department of Reproduction and Genetics, the First Affiliated Hospital of Kunming Medical University, Kunming, 650032, Yunnan, China.,Yunnan Engineering Technology Center of Digestive Disease, Kunming, 650032, Yunnan, China.,Kunming Engineering Technology Center of Digestive Disease, Kunming, 650032, Yunnan, China
| | - Li Tang
- Department of Reproduction and Genetics, the First Affiliated Hospital of Kunming Medical University, Kunming, 650032, Yunnan, China
| | - Jinhua Yi
- Department of Gastrointestinal Surgery, the First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Disease, Kunming, 650032, Yunnan, China.,Yunnan Engineering Technology Center of Digestive Disease, Kunming, 650032, Yunnan, China.,Kunming Engineering Technology Center of Digestive Disease, Kunming, 650032, Yunnan, China
| | - Guimei Li
- Public Technical Service Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650032, Yunnan, China.,Kunming Biological Diversity Regional Center of Large Apparatus and Equipments, Chinese Academy of Sciences, Kunming, 650032, Yunnan, China
| | - Youwang Lu
- Department of Reproduction and Genetics, the First Affiliated Hospital of Kunming Medical University, Kunming, 650032, Yunnan, China.,Yunnan Engineering Technology Center of Digestive Disease, Kunming, 650032, Yunnan, China.,Kunming Engineering Technology Center of Digestive Disease, Kunming, 650032, Yunnan, China
| | - Yu Xu
- Department of Gastrointestinal Surgery, the First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Disease, Kunming, 650032, Yunnan, China.,Yunnan Engineering Technology Center of Digestive Disease, Kunming, 650032, Yunnan, China.,Kunming Engineering Technology Center of Digestive Disease, Kunming, 650032, Yunnan, China
| | - Shuhua Zhao
- Department of Reproduction and Genetics, the First Affiliated Hospital of Kunming Medical University, Kunming, 650032, Yunnan, China
| | - Rui Mao
- School of Stomatology, Kunming Medical University, Kunming, 650500, Yunnan, China
| | - Xiaolu Li
- Public Technical Service Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650032, Yunnan, China.,Kunming Biological Diversity Regional Center of Large Apparatus and Equipments, Chinese Academy of Sciences, Kunming, 650032, Yunnan, China
| | - Li Ren
- Department of Reproductive Gynecology, the First People's Hospital of Yunnan Province, Kunming, 650031, Yunnan, China
| | - Kunhua Wang
- Department of Gastrointestinal Surgery, the First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Disease, Kunming, 650032, Yunnan, China. .,Yunnan Engineering Technology Center of Digestive Disease, Kunming, 650032, Yunnan, China. .,Kunming Engineering Technology Center of Digestive Disease, Kunming, 650032, Yunnan, China.
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18
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Advani SM, Advani PS, Brown DW, DeSantis SM, Korphaisarn K, VonVille HM, Bressler J, Lopez DS, Davis JS, Daniel CR, Sarshekeh AM, Braithwaite D, Swartz MD, Kopetz S. Global differences in the prevalence of the CpG island methylator phenotype of colorectal cancer. BMC Cancer 2019; 19:964. [PMID: 31623592 PMCID: PMC6796359 DOI: 10.1186/s12885-019-6144-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 09/10/2019] [Indexed: 02/07/2023] Open
Abstract
Background CpG Island Methylator Phenotype (CIMP) is an epigenetic phenotype in CRC characterized by hypermethylation of CpG islands in promoter regions of tumor suppressor genes, leading to their transcriptional silencing and loss of function. While the prevalence of CRC differs across geographical regions, no studies have compared prevalence of CIMP-High phenotype across regions. The purpose of this project was to compare the prevalence of CIMP across geographical regions after adjusting for variations in methodologies to measure CIMP in a meta-analysis. Methods We searched PubMed, Medline, and Embase for articles focusing on CIMP published from 2000 to 2018. Two reviewers independently identified 111 articles to be included in final meta-analysis. We classified methods used to quantify CIMP into 4 categories: a) Classical (MINT marker) Panel group b) Weisenberg-Ogino (W-O) group c) Human Methylation Arrays group and d) Miscellaneous group. We compared the prevalence of CIMP across geographical regions after correcting for methodological variations using meta-regression techniques. Results The pooled prevalence of CIMP-High across all studies was 22% (95% confidence interval:21–24%; I2 = 94.75%). Pooled prevalence of CIMP-H across Asia, Australia, Europe, North America and South America was 22, 21, 21, 27 and 25%, respectively. Meta-regression analysis identified no significant differences in the prevalence of CIMP-H across geographical regions after correction for methodological variations. In exploratory analysis, we observed variations in CIMP-H prevalence across countries. Conclusion Although no differences were found for CIMP-H prevalence across countries, further studies are needed to compare the influence of demographic, lifestyle and environmental factors in relation to the prevalence of CIMP across geographical regions.
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Affiliation(s)
- Shailesh Mahesh Advani
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Unit 0426, Houston, TX, 77030, USA. .,Cancer Prevention and Control Program, Lombardi Comprehensive Cancer Center, Georgetown University, Washington DC, 20007, USA. .,Social Behavioral Research Branch, National Human Genome Research Institute, National Institute of Health, Bethesda, MD, 20892, USA.
| | - Pragati Shailesh Advani
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Institutes of Health, National Cancer Institute, Rockville, MD, 20850, USA
| | - Derek W Brown
- Department of Biostatistics and Data Science, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Stacia M DeSantis
- Department of Biostatistics and Data Science, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Krittiya Korphaisarn
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Unit 0426, Houston, TX, 77030, USA
| | - Helena M VonVille
- Library, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Jan Bressler
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - David S Lopez
- Division of Urology- UTHealth McGovern Medical School, Houston, TX, 77030, USA.,Department of Preventive Medicine and Community Health, UTMB Health-School of Medicine, Galveston, TX, 77555-1153, USA
| | - Jennifer S Davis
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Carrie R Daniel
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Amir Mehrvarz Sarshekeh
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Unit 0426, Houston, TX, 77030, USA
| | - Dejana Braithwaite
- Cancer Prevention and Control Program, Lombardi Comprehensive Cancer Center, Georgetown University, Washington DC, 20007, USA
| | - Michael D Swartz
- Department of Biostatistics and Data Science, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Unit 0426, Houston, TX, 77030, USA.
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De Palma FDE, D'Argenio V, Pol J, Kroemer G, Maiuri MC, Salvatore F. The Molecular Hallmarks of the Serrated Pathway in Colorectal Cancer. Cancers (Basel). 2019;11. [PMID: 31330830 PMCID: PMC6678087 DOI: 10.3390/cancers11071017] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/15/2019] [Accepted: 07/19/2019] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is a leading cause of cancer death worldwide. It includes different subtypes that differ in their clinical and prognostic features. In the past decade, in addition to the conventional adenoma-carcinoma model, an alternative multistep mechanism of carcinogenesis, namely the “serrated pathway”, has been described. Approximately, 15 to 30% of all CRCs arise from neoplastic serrated polyps, a heterogeneous group of lesions that are histologically classified into three morphologic categories: hyperplastic polyps, sessile serrated adenomas/polyps, and the traditional serrated adenomas/polyps. Serrated polyps are characterized by genetic (BRAF or KRAS mutations) and epigenetic (CpG island methylator phenotype (CIMP)) alterations that cooperate to initiate and drive malignant transformation from normal colon mucosa to polyps, and then to CRC. The high heterogeneity of the serrated lesions renders their diagnostic and pathological interpretation difficult. Hence, novel genetic and epigenetic biomarkers are required for better classification and management of CRCs. To date, several molecular alterations have been associated with the serrated polyp-CRC sequence. In addition, the gut microbiota is emerging as a contributor to/modulator of the serrated pathway. This review summarizes the state of the art of the genetic, epigenetic and microbiota signatures associated with serrated CRCs, together with their clinical implications.
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20
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Fedorova MS, Krasnov GS, Lukyanova EN, Zaretsky AR, Dmitriev AA, Melnikova NV, Moskalev AA, Kharitonov SL, Pudova EA, Guvatova ZG, Kobelyatskaya AA, Ishina IA, Slavnova EN, Lipatova AV, Chernichenko MA, Sidorov DV, Popov AY, Kiseleva MV, Kaprin AD, Snezhkina AV, Kudryavtseva AV. The CIMP-high phenotype is associated with energy metabolism alterations in colon adenocarcinoma. BMC Med Genet 2019; 20:52. [PMID: 30967137 PMCID: PMC6454590 DOI: 10.1186/s12881-019-0771-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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] [Indexed: 12/22/2022]
Abstract
Background CpG island methylator phenotype (CIMP) is found in 15–20% of malignant colorectal tumors and is characterized by strong CpG hypermethylation over the genome. The molecular mechanisms of this phenomenon are not still fully understood. The development of CIMP is followed by global gene expression alterations and metabolic changes. In particular, CIMP-low colon adenocarcinoma (COAD), predominantly corresponded to consensus molecular subtype 3 (CMS3, “Metabolic”) subgroup according to COAD molecular classification, is associated with elevated expression of genes participating in metabolic pathways. Methods We performed bioinformatics analysis of RNA-Seq data from The Cancer Genome Atlas (TCGA) project for CIMP-high and non-CIMP COAD samples with DESeq2, clusterProfiler, and topGO R packages. Obtained results were validated on a set of fourteen COAD samples with matched morphologically normal tissues using quantitative PCR (qPCR). Results Upregulation of multiple genes involved in glycolysis and related processes (ENO2, PFKP, HK3, PKM, ENO1, HK2, PGAM1, GAPDH, ALDOA, GPI, TPI1, and HK1) was revealed in CIMP-high tumors compared to non-CIMP ones. Most remarkably, the expression of the PKLR gene, encoding for pyruvate kinase participating in gluconeogenesis, was decreased approximately 20-fold. Up to 8-fold decrease in the expression of OGDHL gene involved in tricarboxylic acid (TCA) cycle was observed in CIMP-high tumors. Using qPCR, we confirmed the increase (4-fold) in the ENO2 expression and decrease (2-fold) in the OGDHL mRNA level on a set of COAD samples. Conclusions We demonstrated the association between CIMP-high status and the energy metabolism changes at the transcriptomic level in colorectal adenocarcinoma against the background of immune pathway activation. Differential methylation of at least nine CpG sites in OGDHL promoter region as well as decreased OGDHL mRNA level can potentially serve as an additional biomarker of the CIMP-high status in COAD. Electronic supplementary material The online version of this article (10.1186/s12881-019-0771-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maria S Fedorova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - George S Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Elena N Lukyanova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Andrew R Zaretsky
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexey A Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Nataliya V Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexey A Moskalev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Sergey L Kharitonov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Elena A Pudova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Zulfiya G Guvatova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - Irina A Ishina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Elena N Slavnova
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Anastasia V Lipatova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Maria A Chernichenko
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Dmitry V Sidorov
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | | | - Marina V Kiseleva
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Andrey D Kaprin
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | | | - Anna V Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
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Keum N, Liu L, Hamada T, Qian ZR, Nowak JA, Cao Y, da Silva A, Kosumi K, Song M, Nevo D, Wang M, Chan AT, Meyerhardt JA, Fuchs CS, Wu K, Ogino S, Nishihara R, Zhang X. Calcium intake and colon cancer risk subtypes by tumor molecular characteristics. Cancer Causes Control 2019; 30:637-649. [PMID: 30963391 DOI: 10.1007/s10552-019-01165-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 11/15/2018] [Accepted: 03/28/2019] [Indexed: 12/22/2022]
Abstract
BACKGROUND A preventive potential of high calcium intake against colorectal cancer has been indicated for distal colon cancer, which is inversely associated with high-level CpG island methylator phenotype (CIMP), high-level microsatellite instability (MSI), and BRAF and PIK3CA mutations. In addition, BRAF mutation is strongly inversely correlated with KRAS mutation. We hypothesized that the association between calcium intake and colon cancer risk might vary by these molecular features. METHODS We prospectively followed 88,506 women from the Nurses' Health Study and 47,733 men from the Health Professionals Follow-up Study for up to 30 years. Duplication-method Cox proportional cause-specific hazards regression was used to estimate multivariable hazard ratios (HRs), and 95% confidence intervals (95% CIs) for the associations between calcium intake and the risk of colon cancer subtypes. By Bonferroni correction, the α-level was adjusted to 0.01. RESULTS Based on 853 colon cancer cases, the inverse association between dietary calcium intake and colon cancer risk differed by CIMP status (pheterogeneity = 0.01). Per each 300 mg/day increase in intake, multivariable HRs were 0.84 (95% CI 0.76-0.94) for CIMP-negative/low and 1.12 (95% CI 0.93-1.34) for CIMP-high. Similar differential associations were suggested for MSI subtypes (pheterogeneity = 0.02), with the corresponding HR being 0.86 (95% CI 0.77-0.95) for non-MSI-high and 1.10 (95% CI 0.92-1.32) for MSI-high. No differential associations were observed by BRAF, KRAS, or PIK3CA mutations. CONCLUSION The inverse association between dietary calcium intake and colon cancer risk may be specific to CIMP-negative/low and possibly non-MSI-high subtypes.
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Affiliation(s)
- NaNa Keum
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Building 2, 3rd Floor, 665 Huntington Avenue, Boston, MA, 02115, USA. .,Department of Food Science and Biotechnology, Dongguk University, Goyang, South Korea.
| | - Li Liu
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Building 2, 3rd Floor, 665 Huntington Avenue, Boston, MA, 02115, USA.,Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.,Department of Epidemiology and Biostatistics, and the Ministry of Education Key Lab of Environment and Health, School of Public Health, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| | - Tsuyoshi Hamada
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Zhi Rong Qian
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Jonathan A Nowak
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Yin Cao
- Division of Public Health Sciences, Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Annacarolina da Silva
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Keisuke Kosumi
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Mingyang Song
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Building 2, 3rd Floor, 665 Huntington Avenue, Boston, MA, 02115, USA.,Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
| | - Daniel Nevo
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Molin Wang
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Andrew T Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jeffrey A Meyerhardt
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Charles S Fuchs
- Yale Cancer Center, New Haven, CT, USA.,Department of Medicine, Yale School of Medicine, New Haven, CT, USA.,Smilow Cancer Hospital, New Haven, CT, USA
| | - Kana Wu
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Building 2, 3rd Floor, 665 Huntington Avenue, Boston, MA, 02115, USA
| | - Shuji Ogino
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Building 2, 3rd Floor, 665 Huntington Avenue, Boston, MA, 02115, USA.,Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.,Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Reiko Nishihara
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Building 2, 3rd Floor, 665 Huntington Avenue, Boston, MA, 02115, USA.,Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.,Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Xuehong Zhang
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
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Fennell L, Dumenil T, Wockner L, Hartel G, Nones K, Bond C, Borowsky J, Liu C, McKeone D, Bowdler L, Montgomery G, Klein K, Hoffmann I, Patch AM, Kazakoff S, Pearson J, Waddell N, Wirapati P, Lochhead P, Imamura Y, Ogino S, Shao R, Tejpar S, Leggett B, Whitehall V. Integrative Genome-Scale DNA Methylation Analysis of a Large and Unselected Cohort Reveals 5 Distinct Subtypes of Colorectal Adenocarcinomas. Cell Mol Gastroenterol Hepatol 2019; 8:269-290. [PMID: 30954552 PMCID: PMC6699251 DOI: 10.1016/j.jcmgh.2019.04.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 03/30/2019] [Accepted: 04/01/2019] [Indexed: 01/05/2023]
Abstract
BACKGROUND & AIMS Colorectal cancer is an epigenetically heterogeneous disease, however, the extent and spectrum of the CpG island methylator phenotype (CIMP) is not clear. METHODS Genome-scale methylation and transcript expression were measured by DNA Methylation and RNA expression microarray in 216 unselected colorectal cancers, and findings were validated using The Cancer Genome Atlas 450K and RNA sequencing data. Mutations in epigenetic regulators were assessed using CIMP-subtyped Cancer Genome Atlas exomes. RESULTS CIMP-high cancers dichotomized into CIMP-H1 and CIMP-H2 based on methylation profile. KRAS mutation was associated significantly with CIMP-H2 cancers, but not CIMP-H1 cancers. Congruent with increasing methylation, there was a stepwise increase in patient age from 62 years in the CIMP-negative subgroup to 75 years in the CIMP-H1 subgroup (P < .0001). CIMP-H1 predominantly comprised consensus molecular subtype 1 cancers (70%) whereas consensus molecular subtype 3 was over-represented in the CIMP-H2 subgroup (55%). Polycomb Repressive Complex-2 (PRC2)-marked loci were subjected to significant gene body methylation in CIMP cancers (P < 1.6 × 10-78). We identified oncogenes susceptible to gene body methylation and Wnt pathway antagonists resistant to gene body methylation. CIMP cluster-specific mutations were observed in chromatin remodeling genes, such as in the SWItch/Sucrose Non-Fermentable and Chromodomain Helicase DNA-Binding gene families. CONCLUSIONS There are 5 clinically and molecularly distinct subgroups of colorectal cancer. We show a striking association between CIMP and age, sex, and tumor location, and identify a role for gene body methylation in the progression of serrated neoplasia. These data support our recent findings that CIMP is uncommon in young patients and that BRAF mutant polyps in young patients may have limited potential for malignant progression.
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Affiliation(s)
- Lochlan Fennell
- Conjoint Gastroenterology Department, QIMR Berghofer Medical Research Institute, Queensland, Australia,School of Sports and Health Science, University of the Sunshine Coast, Queensland, Australia,Correspondence Address correspondence to: Lochlan Fennell, BSc, Level 7 Clive Berghofer Cancer Research Centre, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, 4006 Australia. fax: +617 3362 0101.
| | - Troy Dumenil
- Conjoint Gastroenterology Department, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Leesa Wockner
- Statistics Department, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Gunter Hartel
- Statistics Department, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Katia Nones
- Medical Genomics, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Catherine Bond
- Conjoint Gastroenterology Department, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Jennifer Borowsky
- Conjoint Gastroenterology Department, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Cheng Liu
- Conjoint Gastroenterology Department, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Diane McKeone
- Conjoint Gastroenterology Department, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Lisa Bowdler
- Conjoint Gastroenterology Department, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Grant Montgomery
- Conjoint Gastroenterology Department, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Kerenaftali Klein
- Statistics Department, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Isabell Hoffmann
- Institute of Medical Biostatistics, Epidemiology and Informatics, Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Ann-Marie Patch
- Medical Genomics, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Stephen Kazakoff
- Medical Genomics, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - John Pearson
- Medical Genomics, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Nicola Waddell
- Medical Genomics, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Pratyaksha Wirapati
- Swiss Institute of Bioinformatics, Bioinformatics Core Facility, Lausanne, Switzerland
| | - Paul Lochhead
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, Massachusetts
| | - Yu Imamura
- Department of Gastroenterological Surgery, Cancer Institute Hospital, Tokyo, Japan
| | - Shuji Ogino
- Dana-Farber Cancer Institute, Boston, Massachusetts,Program in Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Renfu Shao
- School of Sports and Health Science, University of the Sunshine Coast, Queensland, Australia
| | - Sabine Tejpar
- Digestive Oncology Unit, Department of Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Barbara Leggett
- Conjoint Gastroenterology Department, QIMR Berghofer Medical Research Institute, Queensland, Australia,School of Medicine, University of Queensland, Queensland, Australia,Department of Gastroenterology and Hepatology, Royal Brisbane and Women’s Hospital, Queensland, Australia
| | - Vicki Whitehall
- Conjoint Gastroenterology Department, QIMR Berghofer Medical Research Institute, Queensland, Australia,School of Medicine, University of Queensland, Queensland, Australia,Chemical Pathology Department, Pathology Queensland, Queensland, Australia
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23
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Overman MJ, Adam L, Raghav K, Wang J, Kee B, Fogelman D, Eng C, Vilar E, Shroff R, Dasari A, Wolff R, Morris J, Karunasena E, Pisanic TR, Azad N, Kopetz S. Phase II study of nab-paclitaxel in refractory small bowel adenocarcinoma and CpG island methylator phenotype ( CIMP)-high colorectal cancer. Ann Oncol 2019; 29:139-144. [PMID: 29069279 DOI: 10.1093/annonc/mdx688] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [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] [Indexed: 02/06/2023] Open
Abstract
Background Hypermethylation of promoter CpG islands [CpG island methylator phenotype (CIMP)] represents a unique pathway for the development of colorectal cancer (CRC), characterized by lack of chromosomal instability and a low rate of adenomatous polyposis coli (APC) mutations, which have both been correlated with taxane resistance. Similarly, small bowel adenocarcinoma (SBA), a rare tumor, also has a low rate of APC mutations. This phase II study evaluated taxane sensitivity in SBA and CIMP-high CRC. Patients and methods The primary objective was Response Evaluation Criteria in Solid Tumors version 1.1 response rate. Eligibility included Eastern Cooperative Oncology Group performance status 0/1, refractory disease, and SBA or CIMP-high metastatic CRC. Nab-paclitaxel was initially administered at a dose of 260 mg/m2 every 3 weeks but was reduced to 220 mg/m2 owing to toxicity. Results A total of 21 patients with CIMP-high CRC and 13 with SBA were enrolled from November 2012 to October 2014. The efficacy-assessable population (patients who received at least three doses of the treatment) comprised 15 CIMP-high CRC patients and 10 SBA patients. Common grade 3 or 4 toxicities were fatigue (12%), neutropenia (9%), febrile neutropenia (9%), dehydration (6%), and thrombocytopenia (6%). No responses were seen in the CIMP-high CRC cohort and two partial responses were seen in the SBA cohort. Median progression-free survival was significantly greater in the SBA cohort than in the CIMP-high CRC cohort (3.2 months compared with 2.1 months, P = 0.03). Neither APC mutation status nor CHFR methylation status correlated with efficacy in the CIMP-high CRC cohort. In vivo testing of paclitaxel in an SBA patient-derived xenograft validated the activity of taxanes in this disease type. Conclusion Although preclinical studies suggested taxane sensitivity was associated with chromosomal stability and wild-type APC, we found that nab-paclitaxel was inactive in CIMP-high metastatic CRC. Nab-paclitaxel may represent a novel therapeutic option for SBA.
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Affiliation(s)
- M J Overman
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - L Adam
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - K Raghav
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - J Wang
- Institute for NanoBioTechnology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, USA
| | - B Kee
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - D Fogelman
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - C Eng
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - E Vilar
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - R Shroff
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - A Dasari
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - R Wolff
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - J Morris
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - E Karunasena
- Department of Gastrointestinal Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, USA
| | - T R Pisanic
- Institute for NanoBioTechnology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, USA
| | - N Azad
- Department of Gastrointestinal Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, USA
| | - S Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
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24
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Tao Y, Kang B, Petkovich DA, Bhandari YR, In J, Stein-O'Brien G, Kong X, Xie W, Zachos N, Maegawa S, Vaidya H, Brown S, Chiu Yen RW, Shao X, Thakor J, Lu Z, Cai Y, Zhang Y, Mallona I, Peinado MA, Zahnow CA, Ahuja N, Fertig E, Issa JP, Baylin SB, Easwaran H. Aging-like Spontaneous Epigenetic Silencing Facilitates Wnt Activation, Stemness, and Braf V600E-Induced Tumorigenesis. Cancer Cell 2019; 35:315-328.e6. [PMID: 30753828 PMCID: PMC6636642 DOI: 10.1016/j.ccell.2019.01.005] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 09/25/2018] [Accepted: 01/07/2019] [Indexed: 11/22/2022]
Abstract
We addressed the precursor role of aging-like spontaneous promoter DNA hypermethylation in initiating tumorigenesis. Using mouse colon-derived organoids, we show that promoter hypermethylation spontaneously arises in cells mimicking the human aging-like phenotype. The silenced genes activate the Wnt pathway, causing a stem-like state and differentiation defects. These changes render aged organoids profoundly more sensitive than young ones to transformation by BrafV600E, producing the typical human proximal BRAFV600E-driven colon adenocarcinomas characterized by extensive, abnormal gene-promoter CpG-island methylation, or the methylator phenotype (CIMP). Conversely, CRISPR-mediated simultaneous inactivation of a panel of the silenced genes markedly sensitizes to BrafV600E-induced transformation. Our studies tightly link aging-like epigenetic abnormalities to intestinal cell fate changes and predisposition to oncogene-driven colon tumorigenesis.
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Affiliation(s)
- Yong Tao
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD 21287, USA
| | - Byunghak Kang
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD 21287, USA
| | - Daniel A Petkovich
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD 21287, USA
| | - Yuba R Bhandari
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD 21287, USA
| | - Julie In
- Hopkins Conte Digestive Disease, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Genevieve Stein-O'Brien
- Division of Biostatistics & Bioinformatics, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Xiangqian Kong
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD 21287, USA
| | - Wenbing Xie
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD 21287, USA
| | - Nicholas Zachos
- Hopkins Conte Digestive Disease, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Shinji Maegawa
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Unit 853, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Himani Vaidya
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19122, USA
| | - Stephen Brown
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD 21287, USA
| | - Ray-Whay Chiu Yen
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD 21287, USA
| | - Xiaojian Shao
- Department of Human Genetics, Canadian Centre for Computational Genomics, McGill University, Montreal, QC, Canada
| | - Jai Thakor
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD 21287, USA
| | - Zhihao Lu
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Yi Cai
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD 21287, USA
| | - Yuezheng Zhang
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Izaskun Mallona
- Germans Trias i Pujol Health Science Research Institute (IGTP), Program for Personalized Medicine of Cancer, Badalona, 08916 Catalonia, Spain
| | - Miguel Angel Peinado
- Germans Trias i Pujol Health Science Research Institute (IGTP), Program for Personalized Medicine of Cancer, Badalona, 08916 Catalonia, Spain
| | - Cynthia A Zahnow
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD 21287, USA
| | - Nita Ahuja
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD 21287, USA
| | - Elana Fertig
- Division of Biostatistics & Bioinformatics, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Jean-Pierre Issa
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19122, USA
| | - Stephen B Baylin
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD 21287, USA.
| | - Hariharan Easwaran
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD 21287, USA.
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25
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Cappellesso R, Lo Mele M, Munari G, Rosa-Rizzotto E, Guido E, De Lazzari F, Pilati P, Tonello M, Farinati F, Realdon S, Fassan M, Rugge M. Molecular characterization of "sessile serrated" adenoma to carcinoma transition in six early colorectal cancers. Pathol Res Pract 2019; 215:957-962. [PMID: 30738693 DOI: 10.1016/j.prp.2019.02.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/21/2019] [Accepted: 02/01/2019] [Indexed: 02/07/2023]
Abstract
Colorectal cancer (CRC) is a heterogeneous group of diseases both from the morphological and molecular point of view. The sessile serrated adenoma/polyp (SSA/P) has been proposed as the precursor lesion of CRCs characterized by CpG island methylator phenotype (CIMP), DNA mismatch repair (MMR) system deficiency, and BRAF gene mutations. However, no study so far investigated the molecular landscape of "sessile serrated" adenoma to carcinoma transition in early CRCs. Six formalin-fixed paraffin-embedded CRCs developed within SSA/P were profiled for the immunohistochemical expression of MMR proteins (MLH1, MSH2, MSH6, PMS2, and Ep-CAM), p16, and β-catenin. DNA was extracted from the two components of each sample, after microdissection, and characterized for CIMP status and by applying a custom hotspot multigene mutational profiling of 164 hotspot regions of eleven CRC-associated genes (AKT1, APC, BRAF, CTNNB1, KIT, KRAS, NRAS, PDGFRA, PIK3CA, PTEN, and TP53). Five out of the six CRCs shared the same molecular profile (i.e. CIMP positive, MSI status, and BRAF mutation) with their SSA/P components. One out of five CRCs was also APC mutated, whereas another one showed an additional TP53 mutation. The remaining case was CIMP negative and MMR proficient in both the components, harbored a BRAF mutation in the SSA/P counterpart, whereas the CRC one was APC and TP53 mutated and showed p16 and β-catenin dysregulation. This study provides the molecular evidence that SSA/P, even without cytological dysplasia, is a precursor lesion of CRC and that conventional CRC might arise from mixed polyp.
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Affiliation(s)
- Rocco Cappellesso
- Department of Medicine (DIMED), Surgical Pathology Unit, University of Padua, Padua, 35121, Italy
| | - Marcello Lo Mele
- Department of Medicine (DIMED), Surgical Pathology Unit, University of Padua, Padua, 35121, Italy
| | - Giada Munari
- Department of Medicine (DIMED), Surgical Pathology Unit, University of Padua, Padua, 35121, Italy; Veneto Institute of Oncology - I.R.C.S.S, Padua, 35128, Italy
| | | | - Ennio Guido
- Gastroenterology Unit, S. Antonio Hospital, Padua, 35128, Italy
| | | | - Pierluigi Pilati
- Unit of Surgical Oncology of the Esophagus and Digestive Tract, Veneto Institute of Oncology - I.R.C.S.S, Padua, 35128, Italy
| | - Marco Tonello
- Unit of Surgical Oncology of the Esophagus and Digestive Tract, Veneto Institute of Oncology - I.R.C.S.S, Padua, 35128, Italy; Department of Surgery, Oncology and Gastroenterology (DISCOG), University of Padua, Padua, 35128, Italy
| | - Fabio Farinati
- Department of Surgery, Oncology and Gastroenterology (DISCOG), University of Padua, Padua, 35128, Italy
| | - Stefano Realdon
- Unit of Digestive Endoscopy, Veneto Institute of Oncology - I.R.C.S.S, Padua, 35128, Italy
| | - Matteo Fassan
- Department of Medicine (DIMED), Surgical Pathology Unit, University of Padua, Padua, 35121, Italy.
| | - Massimo Rugge
- Department of Medicine (DIMED), Surgical Pathology Unit, University of Padua, Padua, 35121, Italy
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26
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Hidaka H, Higashimoto K, Aoki S, Mishima H, Hayashida C, Maeda T, Koga Y, Yatsuki H, Joh K, Noshiro H, Iwakiri R, Kawaguchi A, Yoshiura KI, Fujimoto K, Soejima H. Comprehensive methylation analysis of imprinting-associated differentially methylated regions in colorectal cancer. Clin Epigenetics 2018; 10:150. [PMID: 30509319 PMCID: PMC6278095 DOI: 10.1186/s13148-018-0578-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 11/05/2018] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Imprinted genes are regulated by DNA methylation at imprinting-associated differentially methylated regions (iDMRs). Abnormal expression of imprinted genes is implicated in imprinting disorders and tumors. In colorectal cancer (CRC), methylation and imprinting status of the IGF2/H19 domain have been studied. However, no comprehensive methylation analysis of iDMRs in CRC has been reported. Furthermore, the relationship between iDMR methylation status and other methylation-related issues, such as CpG island methylator phenotype (CIMP) and long interspersed element-1 (LINE-1) methylation, remains unclear. RESULTS We analyzed the methylation status of 38 iDMRs in 106 CRC patients. We also investigated CIMP, LINE-1 methylation, KRAS and BRAF gene mutations, and loss of imprinting (LOI) of IGF2. We further examined the relationship between these factors and clinicopathological factors. The overall trend in iDMR methylation was towards hypermethylation, and iDMRs could be grouped into three categories: susceptible, resistant, and intermediate-to-aberrant methylation. The susceptible and resistant iDMRs consisted of all types of iDMR (gametic and somatic, maternally and paternally methylated). Hypermethylation of multiple iDMRs (HyMiD)-positive status was statistically associated with CIMP-positive status, but not associated with mutations in the BRAF and KRAS genes. HyMiD-positive status was inversely associated with LINE-1 methylation. Among four iDMRs within the IGF2/H19 domain, IGF2-DMR0 hypomethylation occurred most frequently, but was not associated with IGF2 LOI. Finally, we statistically calculated predictive prognostic scores based on aberrant methylation status of three iDMRs. CONCLUSION In CRC tissues, some iDMRs were susceptible to hypermethylation independent of the type of iDMR and genomic sequence. Although HyMiD-positive status was associated with CIMP-positive status, this was independent of the BRAF and KRAS pathways, which are responsible for CIMP. Since IGF2-DMR0 hypomethylation and aberrant methylation of other iDMRs within the IGF2/H19 domain were not associated with IGF2 LOI, dysfunction of any of the molecular components related to imprinting regulation may be involved in IGF2 LOI. The prognostic score calculated based on aberrant methylation of three iDMRs has potential clinical applications as a prognostic predictor in patients. Further study is required to understand the biological significance of, and mechanisms behind, aberrant methylation of iDMRs and IGF2 LOI in CRCs.
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Affiliation(s)
- Hidenori Hidaka
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, Japan.,Department of Internal Medicine and Gastrointestinal Endoscopy, Faculty of Medicine, Saga University, Saga, Japan
| | - Ken Higashimoto
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, Japan.
| | - Saori Aoki
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, Japan.,Department of Obstetrics and Gynecology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Hiroyuki Mishima
- Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Chisa Hayashida
- Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Toshiyuki Maeda
- Department of Pediatrics, Faculty of Medicine, Saga University, Saga, Japan
| | - Yasuo Koga
- Department of Surgery, Faculty of Medicine, Saga University, Saga, Japan
| | - Hitomi Yatsuki
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, Japan
| | - Keiichiro Joh
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, Japan
| | - Hirokazu Noshiro
- Department of Surgery, Faculty of Medicine, Saga University, Saga, Japan
| | - Ryuichi Iwakiri
- Department of Internal Medicine and Gastrointestinal Endoscopy, Faculty of Medicine, Saga University, Saga, Japan
| | - Atsushi Kawaguchi
- Section of Clinical Cooperation System, Center for Comprehensive Community Medicine, Faculty of Medicine, Saga University, Saga, Japan
| | - Koh-Ichiro Yoshiura
- Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Kazuma Fujimoto
- Department of Internal Medicine and Gastrointestinal Endoscopy, Faculty of Medicine, Saga University, Saga, Japan
| | - Hidenobu Soejima
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, Japan.
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27
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Abstract
PURPOSE The pathological and prognostic importance of CpG island methylator phenotype (CIMP) in rectal cancer, as a sub-population of colorectal cancer, is unknown. A meta-analysis was preformed to estimate the prognostic significance of CIMP in rectal cancer. METHODS A systematic search was performed of PubMed, Embase, MEDLINE, PubMed Central, and Cochrane electronic databases for articles pertaining to CIMP and rectal cancer. Articles were analysed and data extracted according to PRISMA standards. RESULTS Six studies including 1529 patients were included in the analysis. Following dichotomisation, the prevalence of CIMP-positive tumours was 10 to 57%, with a median of 12.5%. Meta-analysis demonstrated the pooled odds ratio for all-cause death for CIMP-positive tumours vs CIMP-negative tumours was 1.24 (95% CI 0.88-1.74). Z test for overall effect was 1.21 (p = 0.23). Heterogeneity between the studies was low (X2 5.96, df 5, p = 0.31, I2 = 16%). A total of 15 different loci were used for assessing CIMP across the studies, with a median of 6.5 loci (range 5-8). CONCLUSIONS No significant association between CIMP and poor outcomes in rectal cancer was demonstrated. There was a high degree of heterogeneity in CIMP assessment methodologies and in study populations. Rectal cancer datasets were frequently not extractable from larger colorectal cohorts, limiting analysis.
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Affiliation(s)
- R F Kokelaar
- ABMU Singleton Hospital, Sketty Lane, Swansea, Wales, SA2 8QA, UK.
| | - H Jones
- ABMU Singleton Hospital, Sketty Lane, Swansea, Wales, SA2 8QA, UK
| | - J Beynon
- ABMU Singleton Hospital, Sketty Lane, Swansea, Wales, SA2 8QA, UK
| | - M E Evans
- ABMU Singleton Hospital, Sketty Lane, Swansea, Wales, SA2 8QA, UK
| | - D A Harris
- ABMU Singleton Hospital, Sketty Lane, Swansea, Wales, SA2 8QA, UK
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28
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Yu LB, Tu YT, Huang JW, Zhang YN, Zheng GQ, Xu XW, Wang JW, Xiao JQ, Christiani DC, Xia ZL. Hypermethylation of CpG islands is associated with increasing chromosomal damage in chinese lead-exposed workers. Environ Mol Mutagen 2018; 59:549-556. [PMID: 29761860 DOI: 10.1002/em.22194] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 02/13/2018] [Accepted: 03/14/2018] [Indexed: 06/08/2023]
Abstract
Lead is a widely existing environmental pollutant with potential carcinogenicity. To investigate the association of blood lead level (B-Pb) with potential chromosomal damage and cancer, we analyzed micronucleus (MN) frequency of peripheral blood lymphocytes (PBLs) and the methylation status of six human tumor suppressor genes (TSGs) post lead exposure. In the study, 147 lead-exposed workers were divided into two groups according to their B-Pb P50 value, with other 50 lead-unexposed workers as a control group. The cytokinesis-blocked micronucleus (CBMN) assay was performed to detect chromosomal damage of PBLs of both lead-exposed and -unexposed workers. The methylation-specific polymerase chain reaction (MSP-PCR) was further used to examine the methylation status of six TSGs (GSTP1, hMLH1, MGMT, p14, p15, and p16). Results showed that MN frequencies of high B-Pb workers 8.1 ± 3.1‰ and low B-Pb workers 5.7 ± 2.3‰ were significantly higher than that of control group 2.8 ± 1.9‰ (P < 0.01), while the MN frequency of high B-Pb workers was also higher than that of the low B-Pb workers (P < 0.01). The MN frequency in PBLs of lead-exposed group with the methylated TSGs was significantly higher than that in PBLs with the unmethylated TSGs (P < 0.05). Notably, the CpG island methylator phenotype (CIMP) correlated with chromosome damage (P < 0.05). Additionally, workers with high B-Pb had higher chromosome damage than those with low B-Pb (P < 0.05). Taken altogether, the results suggest that lead-exposed workers with CIMP positive and high B-Pb have a higher risk of being vulnerable to tumorigenesis. Environ. Mol. Mutagen. 59:549-556, 2018. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Li-Bo Yu
- Department of Occupational Health and Toxicology, School of Public Health, Fudan University, and Key laboratory of Public Health and Safety of Ministry of Education of China, 138 Yixueyuan Road, Shanghai, 200032, China
| | - Yu-Ting Tu
- Department of Occupational Health and Toxicology, School of Public Health, Fudan University, and Key laboratory of Public Health and Safety of Ministry of Education of China, 138 Yixueyuan Road, Shanghai, 200032, China
| | - Jing-Wen Huang
- Department of Occupational Health and Toxicology, School of Public Health, Fudan University, and Key laboratory of Public Health and Safety of Ministry of Education of China, 138 Yixueyuan Road, Shanghai, 200032, China
| | - Ya-Nan Zhang
- Department of Occupational Health and Toxicology, School of Public Health, Fudan University, and Key laboratory of Public Health and Safety of Ministry of Education of China, 138 Yixueyuan Road, Shanghai, 200032, China
| | - Guo-Qiao Zheng
- Department of Occupational Health and Toxicology, School of Public Health, Fudan University, and Key laboratory of Public Health and Safety of Ministry of Education of China, 138 Yixueyuan Road, Shanghai, 200032, China
| | - Xiao-Wen Xu
- Department of Occupational Health and Toxicology, School of Public Health, Fudan University, and Key laboratory of Public Health and Safety of Ministry of Education of China, 138 Yixueyuan Road, Shanghai, 200032, China
| | - Jin-Wei Wang
- Department of Occupational Health and Toxicology, School of Public Health, Fudan University, and Key laboratory of Public Health and Safety of Ministry of Education of China, 138 Yixueyuan Road, Shanghai, 200032, China
| | - Jean Qin Xiao
- Waterfront Medical Service/Valley Health System P.O. Box 1378, Ridgewood, NJ 07451
| | - David C Christiani
- Department of Environmental Health and Epidemiology, Harvard TH Chan School of Public Health, 665 Huntington Avenue, Boston, Massachusetts, 02115
| | - Zhao-Lin Xia
- Department of Occupational Health and Toxicology, School of Public Health, Fudan University, and Key laboratory of Public Health and Safety of Ministry of Education of China, 138 Yixueyuan Road, Shanghai, 200032, China
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29
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Wang Z, Yang B, Zhang M, Guo W, Wu Z, Wang Y, Jia L, Li S, Xie W, Yang D. lncRNA Epigenetic Landscape Analysis Identifies EPIC1 as an Oncogenic lncRNA that Interacts with MYC and Promotes Cell-Cycle Progression in Cancer. Cancer Cell 2018; 33:706-720.e9. [PMID: 29622465 PMCID: PMC6143179 DOI: 10.1016/j.ccell.2018.03.006] [Citation(s) in RCA: 336] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Revised: 02/13/2018] [Accepted: 03/05/2018] [Indexed: 02/07/2023]
Abstract
We characterized the epigenetic landscape of genes encoding long noncoding RNAs (lncRNAs) across 6,475 tumors and 455 cancer cell lines. In stark contrast to the CpG island hypermethylation phenotype in cancer, we observed a recurrent hypomethylation of 1,006 lncRNA genes in cancer, including EPIC1 (epigenetically-induced lncRNA1). Overexpression of EPIC1 is associated with poor prognosis in luminal B breast cancer patients and enhances tumor growth in vitro and in vivo. Mechanistically, EPIC1 promotes cell-cycle progression by interacting with MYC through EPIC1's 129-283 nt region. EPIC1 knockdown reduces the occupancy of MYC to its target genes (e.g., CDKN1A, CCNA2, CDC20, and CDC45). MYC depletion abolishes EPIC1's regulation of MYC target and luminal breast cancer tumorigenesis in vitro and in vivo.
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Affiliation(s)
- Zehua Wang
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Bo Yang
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Min Zhang
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Weiwei Guo
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Zhiyuan Wu
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Yue Wang
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Lin Jia
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Song Li
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | | | - Wen Xie
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Da Yang
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261, USA; University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA; Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA.
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30
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Lee CT, Huang YC, Hung LY, Chow NH, Su PF, Ho CL, Tsai HW, Chen YL, Lin SC, Lin BW, Lin PC, Lee JC. Serrated adenocarcinoma morphology in colorectal mucinous adenocarcinoma is associated with improved patient survival. Oncotarget 2018; 8:35165-35175. [PMID: 28422723 PMCID: PMC5471043 DOI: 10.18632/oncotarget.16815] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [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: 12/14/2016] [Accepted: 03/19/2017] [Indexed: 02/06/2023] Open
Abstract
Colorectal mucinous adenocarcinoma (MAC) and serrated adenocarcinoma (SAC) share many characteristics, including right-side colon location, frequent mucin production, and various molecular features. This study examined the frequency of SAC morphology in MACs. We assessed the correlation of SAC morphology with clinicopathological parameters, molecular characteristics, and patient prognosis. Eighty-eight colorectal MACs were collected and reviewed for SAC morphology according to Makinen's criteria. We sequenced KRAS and BRAF, assessed CpG island methylator phenotype (CIMP) frequency, and analyzed DNA mismatch repair enzyme levels using immunohistochemistry in tumor samples. SAC morphology was observed in 38% of MACs, and was associated with proximal location (P=0.001), BRAF mutation (P=0.042), CIMP-positive status (P=0.023), and contiguous traditional serrated adenoma (P=0.019). Multivariate analysis revealed that MACs without both SAC morphology and CIMP-positive status exhibited 3.955 times greater risk of cancer relapse than MACs having both characteristics or either one (P=0.035). Our results show that two MAC groups with distinct features can be identified using Makinen's criteria, and suggest a favorable prognostic role for the serrated neoplastic pathway in colorectal MAC.
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Affiliation(s)
- Chung-Ta Lee
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70403, Taiwan
| | - Yu-Chuan Huang
- Institute of Bioinformatics and Biosignal Transduction, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan
| | - Liang-Yi Hung
- Institute of Bioinformatics and Biosignal Transduction, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan.,Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan
| | - Nan-Haw Chow
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70403, Taiwan
| | - Pei-Fang Su
- Department of Statistics, College of Management, National Cheng Kung University, Tainan 70101, Taiwan
| | - Chung-Liang Ho
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70403, Taiwan
| | - Hung-Wen Tsai
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70403, Taiwan
| | - Yi-Lin Chen
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70403, Taiwan
| | - Shao-Chieh Lin
- Department of Statistics, College of Management, National Cheng Kung University, Tainan 70101, Taiwan
| | - Bo-Wen Lin
- Department of Surgery, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70403, Taiwan
| | - Peng-Chan Lin
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70403, Taiwan
| | - Jenq-Chang Lee
- Department of Surgery, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70403, Taiwan
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31
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Borssén M, Nordlund J, Haider Z, Landfors M, Larsson P, Kanerva J, Schmiegelow K, Flaegstad T, Jónsson ÓG, Frost BM, Palle J, Forestier E, Heyman M, Hultdin M, Lönnerholm G, Degerman S. DNA methylation holds prognostic information in relapsed precursor B-cell acute lymphoblastic leukemia. Clin Epigenetics 2018. [PMID: 29515676 PMCID: PMC5836434 DOI: 10.1186/s13148-018-0466-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [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] [Indexed: 11/22/2022] Open
Abstract
Background Few biological markers are associated with survival after relapse of B-cell precursor acute lymphoblastic leukemia (BCP-ALL). In pediatric T-cell ALL, we have identified promoter-associated methylation alterations that correlate with prognosis. Here, the prognostic relevance of CpG island methylation phenotype (CIMP) classification was investigated in pediatric BCP-ALL patients. Methods Six hundred and one BCP-ALL samples from Nordic pediatric patients (age 1–18) were CIMP classified at initial diagnosis and analyzed in relation to clinical data. Results Among the 137 patients that later relapsed, patients with a CIMP− profile (n = 42) at initial diagnosis had an inferior overall survival (pOS5years 33%) compared to CIMP+ patients (n = 95, pOS5years 65%) (p = 0.001), which remained significant in a Cox proportional hazards model including previously defined risk factors. Conclusion CIMP classification is a strong candidate for improved risk stratification of relapsed BCP-ALL. Electronic supplementary material The online version of this article (10.1186/s13148-018-0466-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Magnus Borssén
- 1Department of Medical Biosciences, Umeå University, Blg 6M, 2nd floor, SE-90185 Umeå, Sweden
| | - Jessica Nordlund
- 2Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Zahra Haider
- 1Department of Medical Biosciences, Umeå University, Blg 6M, 2nd floor, SE-90185 Umeå, Sweden
| | - Mattias Landfors
- 1Department of Medical Biosciences, Umeå University, Blg 6M, 2nd floor, SE-90185 Umeå, Sweden
| | - Pär Larsson
- 1Department of Medical Biosciences, Umeå University, Blg 6M, 2nd floor, SE-90185 Umeå, Sweden
| | - Jukka Kanerva
- 3Children's Hospital, Helsinki University Central Hospital, University of Helsinki, Helsinki, Finland
| | - Kjeld Schmiegelow
- 4Department of Paediatrics and Adolescent Medicine, Rigshospitalet, and Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Trond Flaegstad
- 5Department of Pediatrics, University of Tromsø and University Hospital of North Norway, Tromsø, Norway
| | - Ólafur Gísli Jónsson
- 6Pediatric Hematology-Oncology, Children's Hospital, Landspitali University Hospital, Reykjavik, Iceland
| | - Britt-Marie Frost
- 7Department of Women's and Children's Health, Pediatrics, University of Uppsala, Uppsala, Sweden
| | - Josefine Palle
- 7Department of Women's and Children's Health, Pediatrics, University of Uppsala, Uppsala, Sweden
| | - Erik Forestier
- 1Department of Medical Biosciences, Umeå University, Blg 6M, 2nd floor, SE-90185 Umeå, Sweden
| | - Mats Heyman
- 8Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Magnus Hultdin
- 1Department of Medical Biosciences, Umeå University, Blg 6M, 2nd floor, SE-90185 Umeå, Sweden
| | - Gudmar Lönnerholm
- 7Department of Women's and Children's Health, Pediatrics, University of Uppsala, Uppsala, Sweden
| | - Sofie Degerman
- 1Department of Medical Biosciences, Umeå University, Blg 6M, 2nd floor, SE-90185 Umeå, Sweden
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32
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Takane K, Matsusaka K, Ota S, Fukuyo M, Yue Y, Nishimura M, Sakai E, Matsushita K, Miyauchi H, Aburatani H, Nakatani Y, Takayama T, Matsubara H, Akagi K, Kaneda A. Two subtypes of colorectal tumor with distinct molecular features in familial adenomatous polyposis. Oncotarget 2018; 7:84003-84016. [PMID: 27563825 PMCID: PMC5356641 DOI: 10.18632/oncotarget.11510] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [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: 07/02/2016] [Accepted: 08/17/2016] [Indexed: 12/30/2022] Open
Abstract
While sporadic colorectal cancer (CRC) is classified into several molecular subtypes, stratification of familial colorectal tumors is yet to be well investigated. We previously established two groups of methylation markers through genome-wide DNA methylation analysis, which classified sporadic CRC and adenoma into three distinct subgroups: high-, intermediate-, and low-methylation epigenotypes. Here, we investigated familial adenomatous polyposis (FAP), through quantitative methylation analysis of 127 samples (16 cancers, 96 adenomas, and 15 benign mucosa from 14 patients with FAP) using six Group-1 and 14 Group-2 methylation markers, APC, BRAF, and KRAS mutation analysis, and CTNNB1 and TP53 immunohistochemical analysis. All the 14 patients presented with APC germline mutation. Three were from the same family and presented the same APC mutation. FAP tumors lacked BRAF-mutation(+) high-methylation epigenotype and were classified into two methylation epigenotypes. While 24 of 112 tumor samples showed intermediate-methylation epigenotype significantly correlating with KRAS-mutation(+) (P=3×10-4), 88 tumor samples showed low-methylation epigenotype correlating with the absence of KRAS- and BRAF-mutations. Similar to sporadic CRC, CTNNB1 was frequently activated at the adenoma stage, and TP53 mutation occurred during cancer development from adenoma. Whereas some patients showed a single epigenotype in all tumors throughout the colon, tumors with two distinct epigenotypes developed within a family with the same APC mutation or even within one patient. Methylation accumulation significantly correlated with proximal location and older age. These results indicate that there are at least two distinct molecular subtypes of FAP tumors, resembling sporadic CRC and independent from the APC germline mutation status.
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Affiliation(s)
- Kiyoko Takane
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan.,Department of Digestive Surgery, Nihon University School of Medicine, Tokyo, Japan
| | - Keisuke Matsusaka
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Satoshi Ota
- Department of Pathology, Chiba University Hospital, Chiba, Japan
| | - Masaki Fukuyo
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yao Yue
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Motoi Nishimura
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Eiji Sakai
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan.,Department of Gastroenterology, Yokohama City University School of Medicine, Yokohama, Japan
| | - Kazuyuki Matsushita
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hideaki Miyauchi
- Department of Frontier Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hiroyuki Aburatani
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Yukio Nakatani
- Department of Pathology, Chiba University Hospital, Chiba, Japan.,Department of Diagnostic Pathology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Tadatoshi Takayama
- Department of Digestive Surgery, Nihon University School of Medicine, Tokyo, Japan
| | - Hisahiro Matsubara
- Department of Frontier Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Kiwamu Akagi
- Division of Molecular Diagnosis, Saitama Cancer Center, Saitama, Japan
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan.,Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
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33
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Overman MJ, Morris V, Moinova H, Manyam G, Ensor J, Lee MS, Eng C, Kee B, Fogelman D, Shroff RT, LaFramboise T, Mazard T, Feng T, Hamilton S, Broom B, Lutterbaugh J, Issa JP, Markowitz SD, Kopetz S. Phase I/II study of azacitidine and capecitabine/oxaliplatin (CAPOX) in refractory CIMP-high metastatic colorectal cancer: evaluation of circulating methylated vimentin. Oncotarget 2018; 7:67495-67506. [PMID: 27542211 PMCID: PMC5341892 DOI: 10.18632/oncotarget.11317] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [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: 04/14/2016] [Accepted: 08/10/2016] [Indexed: 12/13/2022] Open
Abstract
Purpose Hypermethylation of promoter CpG islands (CIMP) has been strongly implicated in chemotherapy resistance and is implicated in the pathogenesis of a subset of colorectal cancers (CRCs) termed CIMP-high. Experimental Design This phase I/II study in CRC (phase II portion restricted to CIMP-high CRC), treated fluoropyrimidine/oxaliplatin refractory patients with azacitidine (75 mg/m2/day subcutaneously D1-5) and CAPOX (capecitibine and oxaliplatin) every three weeks. Results Twenty-six patients (pts) were enrolled in this study: 15 pts (12 treated at MTD) in phase I and 11 pts in phase II. No dose limiting toxicities were observed. A total of 14 pts were CIMP-high. No responses were seen. CIMP-high status did not correlate with efficacy endpoints [stable disease (SD) or progression-free survival (PFS)] or baseline vimentin methylation level. Changes in vimentin methylation over time did not correlate with efficacy outcomes. Baseline methylated vimentin correlated with tumor volume (P<0.001) and higher levels of baseline methylation correlated with the obtainment of stable disease (P=0.04). Conclusions Azacitidine and CAPOX were well tolerated with high rates of stable disease in CIMP-high pts, but no objective responses. Serum methylated vimentin may be associated with benefit from a regimen including a hypomethylation agent, although this study is not able to separate a potential prognostic or predictive role for the biomarker.
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Affiliation(s)
- Michael J Overman
- Department of Gastrointestinal Medical Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Van Morris
- Department of Gastrointestinal Medical Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Helen Moinova
- Department of Medicine and Case Comprehensive Cancer Center, Case Western Reserve University and Case Medical Center, Cleveland, OH, USA
| | - Ganiraju Manyam
- Department of Bioinformatics and Computational Biology, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Joe Ensor
- Houston Methodist Cancer Center, Houston Methodist Research Institute, Houston, TX, USA
| | - Michael S Lee
- Division of Hematology/Oncology, Department of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Cathy Eng
- Department of Gastrointestinal Medical Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Bryan Kee
- Department of Gastrointestinal Medical Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - David Fogelman
- Department of Gastrointestinal Medical Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Rachna T Shroff
- Department of Gastrointestinal Medical Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Thomas LaFramboise
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Thibault Mazard
- Department of Gastrointestinal Medical Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Tian Feng
- Department of Gastrointestinal Medical Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Stanley Hamilton
- Division of Pathology and Laboratory Medicine, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Bradley Broom
- Department of Bioinformatics and Computational Biology, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - James Lutterbaugh
- Department of Medicine and Case Comprehensive Cancer Center, Case Western Reserve University and Case Medical Center, Cleveland, OH, USA
| | - Jean-Pierre Issa
- Fels Institute for Cancer and Molecular Biology, Temple University, Philadelphia, PA, USA
| | - Sanford D Markowitz
- Department of Medicine and Case Comprehensive Cancer Center, Case Western Reserve University and Case Medical Center, Cleveland, OH, USA
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
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34
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Kokelaar RF, Jones HG, Williamson J, Williams N, Griffiths AP, Beynon J, Jenkins GJ, Harris DA. DNA hypermethylation as a predictor of extramural vascular invasion (EMVI) in rectal cancer. Cancer Biol Ther 2018; 19:214-221. [PMID: 29260978 DOI: 10.1080/15384047.2017.1416933] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [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: 12/15/2022] Open
Abstract
PURPOSE DNA hypermethylation in gene promoter regions (CpG islands) is emerging as an important pathway in colorectal cancer tumourigenesis. Whilst genetic mutations have been associated with extramural vascular invasion (EMVI) in rectal cancer, no such association has yet been made with epigenetic factors. METHODS 100 consecutive neoadjuvant-naïve patients undergoing curative surgery for rectal were classified according to the presence or absence of EMVI on histopathological examination. DNA was extracted from tumours and subjected to bisulfite conversion and methylation-specific PCR to determine CIMP status (high, intermediate, or low; according to a validated panel of 8 genes). CIMP status was correlated with EMVI status, histopathological, clinical, and demographic variables, in addition to overall (OS) and disease free (DFS) survival. RESULTS 51 patients were characterised as CIMP-low, 48 CIMP-intermediate, and one patient CIMP-high. EMVI-positivity was associated with CIMP-intermediate epigenotype (p < 0.001). Patients with EMVI-positive tumours were found to have significantly more advanced disease by pT, pN, and pAJCC categorisation (p = 0.002, p < 0.001, and = p < 0.001, respectively). EMVI-positivity was significantly associated with the requirement for adjuvant chemotherapy (p < 0.001), and worse DFS but not OS (p = 0.012 and p = 0.052). CONCLUSIONS Given the association between CIMP-intermediate epigenotype and EMVI-positivity, and the subsequent disadvantage in pathological stage, requirement for adjuvant therapy and worse survival, tumour epigenotyping could potentially play an important role in personalising patients' cancer care. Further work is required to understand the mechanisms that underlie the observed effect, with the hope that they may provide novel opportunities for intervention and inform treatment decisions in rectal cancer.
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Affiliation(s)
- Rory F Kokelaar
- a Departments of Colorectal Surgery and Pathology , Abertawe Bro Morgannwg University Health Board , Swansea , Wales , United Kingdom.,c Cancer Biomarker Group, Institute of Life Science, School of Medicine, Swansea University , Swansea , Wales , United Kingdom
| | - Huw G Jones
- a Departments of Colorectal Surgery and Pathology , Abertawe Bro Morgannwg University Health Board , Swansea , Wales , United Kingdom
| | - Jeremy Williamson
- a Departments of Colorectal Surgery and Pathology , Abertawe Bro Morgannwg University Health Board , Swansea , Wales , United Kingdom
| | - Namor Williams
- b Pathology, Abertawe Bro Morgannwg University Health Board , Swansea , Wales , United Kingdom
| | - A Paul Griffiths
- b Pathology, Abertawe Bro Morgannwg University Health Board , Swansea , Wales , United Kingdom
| | - John Beynon
- a Departments of Colorectal Surgery and Pathology , Abertawe Bro Morgannwg University Health Board , Swansea , Wales , United Kingdom
| | - Gareth J Jenkins
- c Cancer Biomarker Group, Institute of Life Science, School of Medicine, Swansea University , Swansea , Wales , United Kingdom
| | - Dean A Harris
- a Departments of Colorectal Surgery and Pathology , Abertawe Bro Morgannwg University Health Board , Swansea , Wales , United Kingdom
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35
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Aoki H, Yamamoto E, Takasawa A, Niinuma T, Yamano HO, Harada T, Matsushita HO, Yoshikawa K, Takagi R, Harada E, Tanaka Y, Yoshida Y, Aoyama T, Eizuka M, Yorozu A, Kitajima H, Kai M, Sawada N, Sugai T, Nakase H, Suzuki H. Epigenetic silencing of SMOC1 in traditional serrated adenoma and colorectal cancer. Oncotarget 2017; 9:4707-4721. [PMID: 29435136 PMCID: PMC5797007 DOI: 10.18632/oncotarget.23523] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [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: 06/26/2017] [Accepted: 11/30/2017] [Indexed: 02/07/2023] Open
Abstract
Colorectal sessile serrated adenoma/polyps (SSA/Ps) are well-known precursors of colorectal cancer (CRC) characterized by BRAF mutation and microsatellite instability. By contrast, the molecular characteristics of traditional serrated adenoma (TSAs) are not fully understood. We analyzed genome-wide DNA methylation in TSAs having both protruding and flat components. We identified 11 genes, including SMOC1, methylation of which progressively increased during the development of TSAs. SMOC1 was prevalently methylated in TSAs, but was rarely methylated in SSA/Ps (p < 0.001). RT-PCR and immunohistochemistry revealed that SMOC1 was expressed in normal colon and SSA/Ps, but its expression was decreased in TSAs. Ectopic expression of SMOC1 suppressed proliferation, colony formation and in vivo tumor formation by CRC cells. Analysis of colorectal lesions (n = 847) revealed that SMOC1 is frequently methylated in TSAs, high-grade adenomas and CRCs. Among these, SMOC1 methylation was strongly associated with KRAS mutation and CpG island methylator phenotype (CIMP)-low. These results demonstrate that epigenetic silencing of SMOC1 is associated with TSA development but is rarely observed in SSA/Ps. SMOC1 expression could thus be a diagnostic marker of serrated lesions, and SMOC1 methylation could play a role in neoplastic pathways in TSAs and conventional adenomas.
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Affiliation(s)
- Hironori Aoki
- Department of Molecular Biology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Eiichiro Yamamoto
- Department of Molecular Biology, Sapporo Medical University School of Medicine, Sapporo, Japan.,Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Akira Takasawa
- Department of Pathology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Takeshi Niinuma
- Department of Molecular Biology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Hiro-O Yamano
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Taku Harada
- Department of Molecular Biology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Hiro-O Matsushita
- Department of Digestive Disease Center, Akita Red Cross Hospital, Akita, Japan
| | - Kenjiro Yoshikawa
- Department of Digestive Disease Center, Akita Red Cross Hospital, Akita, Japan
| | - Ryo Takagi
- Department of Digestive Disease Center, Akita Red Cross Hospital, Akita, Japan
| | - Eiji Harada
- Department of Digestive Disease Center, Akita Red Cross Hospital, Akita, Japan
| | - Yoshihito Tanaka
- Department of Digestive Disease Center, Akita Red Cross Hospital, Akita, Japan
| | - Yuko Yoshida
- Department of Digestive Disease Center, Akita Red Cross Hospital, Akita, Japan
| | - Tomoyuki Aoyama
- Department of Pathology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Makoto Eizuka
- Department of Molecular Diagnostic Pathology, School of Medicine, Iwate Medical University, Morioka, Japan
| | - Akira Yorozu
- Department of Molecular Biology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Hiroshi Kitajima
- Department of Molecular Biology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Masahiro Kai
- Department of Molecular Biology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Norimasa Sawada
- Department of Pathology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Tamotsu Sugai
- Department of Molecular Diagnostic Pathology, School of Medicine, Iwate Medical University, Morioka, Japan
| | - Hiroshi Nakase
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Hiromu Suzuki
- Department of Molecular Biology, Sapporo Medical University School of Medicine, Sapporo, Japan
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36
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Kurihara H, Maruyama R, Ishiguro K, Kanno S, Yamamoto I, Ishigami K, Mitsuhashi K, Igarashi H, Ito M, Tanuma T, Sukawa Y, Okita K, Hasegawa T, Imai K, Yamamoto H, Shinomura Y, Nosho K. The relationship between EZH2 expression and microRNA-31 in colorectal cancer and the role in evolution of the serrated pathway. Oncotarget 2017; 7:12704-17. [PMID: 26871294 PMCID: PMC4914316 DOI: 10.18632/oncotarget.7260] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [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: 10/28/2015] [Accepted: 01/27/2016] [Indexed: 02/07/2023] Open
Abstract
Polycomb group protein enhancer of zeste homolog 2 (EZH2) is a methyltransferase that correlates with the regulation of invasion and metastasis and is overexpressed in human cancers such as colorectal cancer. MicroRNA-31 (miR-31) plays an oncogenic role and is associated with BRAF mutation and poor prognosis in colorectal cancer. EZH2 is functionally considered to suppress miR-31 expression in human cancers; however, no study has reported its relationship with colon cancer. We therefore evaluated EZH2 expression using immunohistochemistry and assessed miR-31 and epigenetic alterations using 301 colorectal carcinomas and 207 premalignant lesions. Functional analysis was performed to identify the association between EZH2 and miR-31 using cancer cell lines. In the current study, negative, weak, moderate, and strong EZH2 expressions were observed in 15%, 19%, 25%, and 41% of colorectal cancers, respectively. EZH2 was inversely associated with miR-31 (P < 0.0001), independent of clinicopathological and molecular features. In a multivariate stage-stratified analysis, high EZH2 expression was related to favorable prognosis (P = 0.0022). Regarding premalignant lesions, negative EZH2 expression was frequently detected in sessile serrated adenomas/polyps (SSA/Ps) (76%; P < 0.0001) compared with hyperplastic polyps, traditional serrated adenomas, and non-serrated adenomas (25–36%). Functional analysis demonstrated that the knockdown of EZH2 increased miR-31 expression. In conclusion, an inverse association was identified between EZH2 and miR-31 in colorectal cancers. Our data also showed that upregulation of EZH2 expression may be rare in SSA/Ps. These results suggest that EZH2 suppresses miR-31 in colorectal cancer and may correlate with differentiation and evolution of serrated pathway.
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Affiliation(s)
- Hiroyoshi Kurihara
- Department of Gastroenterology, Rheumatology and Clinical Immunology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Reo Maruyama
- Department of Molecular Biology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Kazuya Ishiguro
- Department of Gastroenterology, Rheumatology and Clinical Immunology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Shinichi Kanno
- Department of Gastroenterology, Rheumatology and Clinical Immunology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Itaru Yamamoto
- Department of Gastroenterology, Rheumatology and Clinical Immunology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Keisuke Ishigami
- Department of Gastroenterology, Rheumatology and Clinical Immunology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Kei Mitsuhashi
- Department of Gastroenterology, Rheumatology and Clinical Immunology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Hisayoshi Igarashi
- Department of Gastroenterology, Rheumatology and Clinical Immunology, Sapporo Medical University School of Medicine, Sapporo, Japan.,The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Miki Ito
- Department of Gastroenterology, Rheumatology and Clinical Immunology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Tokuma Tanuma
- Department of Gastroenterology, Rheumatology and Clinical Immunology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Yasutaka Sukawa
- Department of Gastroenterology, Rheumatology and Clinical Immunology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Kenji Okita
- Department of Surgery, Surgical Oncology and Science, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Tadashi Hasegawa
- Department of Surgical Pathology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Kohzoh Imai
- The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Yamamoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Japan
| | | | - Katsuhiko Nosho
- Department of Gastroenterology, Rheumatology and Clinical Immunology, Sapporo Medical University School of Medicine, Sapporo, Japan
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37
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Puccini A, Berger MD, Naseem M, Tokunaga R, Battaglin F, Cao S, Hanna DL, McSkane M, Soni S, Zhang W, Lenz HJ. Colorectal cancer: epigenetic alterations and their clinical implications. Biochim Biophys Acta Rev Cancer 2017; 1868:439-448. [PMID: 28939182 DOI: 10.1016/j.bbcan.2017.09.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [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: 07/26/2017] [Revised: 09/16/2017] [Accepted: 09/17/2017] [Indexed: 12/20/2022]
Abstract
Colorectal cancer (CRC) is a heterogeneous disease with distinct molecular and clinical features, which reflects the wide range of prognostic outcomes and treatment responses observed among CRC patients worldwide. Our understanding of the CRC epigenome has been largely developed over the last decade and it is now believed that among thousands of epigenetic alterations present in each tumor, a small subgroup of these may be considered as a CRC driver event. DNA methylation profiles have been the most widely studied in CRC, which includes a subset of patients with distinct molecular and clinical features now categorized as CpG island methylator phenotype (CIMP). Major advances have been made in our capacity to detect epigenetic alterations, providing us with new potential biomarkers for diagnostic, prognostic and therapeutic purposes. This review aims to summarize our current knowledge about epigenetic alterations occurring in CRC, underlying their potential future clinical implications in terms of diagnosis, prognosis and therapeutic strategies for CRC patients.
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Affiliation(s)
- Alberto Puccini
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Martin D Berger
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Madiha Naseem
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Ryuma Tokunaga
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Francesca Battaglin
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Shu Cao
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Diana L Hanna
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Michelle McSkane
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Shivani Soni
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Wu Zhang
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Heinz-Josef Lenz
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, USA.
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38
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Yamamoto I, Nosho K, Kanno S, Igarashi H, Kurihara H, Ishigami K, Ishiguro K, Mitsuhashi K, Maruyama R, Koide H, Okuda H, Hasegawa T, Sukawa Y, Okita K, Takemasa I, Yamamoto H, Shinomura Y, Nakase H. EZH2 expression is a prognostic biomarker in patients with colorectal cancer treated with anti-EGFR therapeutics. Oncotarget 2017; 8:17810-17818. [PMID: 28147317 PMCID: PMC5392288 DOI: 10.18632/oncotarget.14863] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 01/16/2017] [Indexed: 01/09/2023] Open
Abstract
The polycomb group protein enhancer of zeste homolog 2 (EZH2) is a methyltransferase that suppresses microRNA-31 (miR-31) in various human malignancies including colorectal cancer. We recently suggested that miR-31 regulates the signaling pathway downstream of epidermal growth factor receptor (EGFR) in colorectal cancer. Therefore, we conducted this study for assessing the relationship between EZH2 expression and clinical outcomes in patients with colorectal cancer treated with anti-EGFR therapeutics. We immunohistochemically evaluated EZH2 expression and assessed miR-31 and gene mutations [KRAS (codon 61/146), NRAS (codon 12/13/61), and BRAF (codon 600)] in 109 patients with colorectal cancer harboring KRAS (codon 12/13) wild-type. We also evaluated the progression-free survival (PFS) and overall survival (OS). In the result, low EZH2 expression was significantly associated with shorter PFS (log-rank test: P = 0.023) and OS (P = 0.036) in patients with colorectal cancer. In the low-miR-31-expression group and the KRAS (codon 61/146), NRAS, and BRAF wild-type groups, a significantly shorter PFS (P = 0.022, P = 0.039, P = 0.021, and P = 0.036, respectively) was observed in the EZH2 low-expression groups than in the high-expression groups. In the multivariate analysis, low EZH2 expression was associated with a shorter PFS (P = 0.046), independent of the mutational status and miR-31. In conclusion, EZH2 expression was associated with survival in patients with colorectal cancer who were treated with anti-EGFR therapeutics. Moreover, low EZH2 expression was independently associated with shorter PFS in patients with cancer, suggesting that EZH2 expression is a useful additional prognostic biomarker for anti-EGFR therapy.
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Affiliation(s)
- Itaru Yamamoto
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Katsuhiko Nosho
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Shinichi Kanno
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Hisayoshi Igarashi
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Hiroyoshi Kurihara
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Keisuke Ishigami
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Kazuya Ishiguro
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Kei Mitsuhashi
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Reo Maruyama
- Department of Molecular Biology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Hideyuki Koide
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Hiroyuki Okuda
- Department of Oncology, Keiyukai Sapporo Hospital, Sapporo, Japan
| | - Tadashi Hasegawa
- Department of Surgical Pathology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Yasutaka Sukawa
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Kenji Okita
- Department of Surgery, Surgical Oncology and Science, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Ichiro Takemasa
- Department of Surgery, Surgical Oncology and Science, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Hiroyuki Yamamoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Japan
| | | | - Hiroshi Nakase
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, Sapporo, Japan
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Vedeld HM, Merok M, Jeanmougin M, Danielsen SA, Honne H, Presthus GK, Svindland A, Sjo OH, Hektoen M, Eknaes M, Nesbakken A, Lothe RA, Lind GE. CpG island methylator phenotype identifies high risk patients among microsatellite stable BRAF mutated colorectal cancers. Int J Cancer 2017; 141:967-976. [PMID: 28542846 PMCID: PMC5518206 DOI: 10.1002/ijc.30796] [Citation(s) in RCA: 36] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 05/08/2017] [Indexed: 12/26/2022]
Abstract
The prognostic value of CpG island methylator phenotype (CIMP) in colorectal cancer remains unsettled. We aimed to assess the prognostic value of this phenotype analyzing a total of 1126 tumor samples obtained from two Norwegian consecutive colorectal cancer series. CIMP status was determined by analyzing the 5‐markers CAGNA1G, IGF2, NEUROG1, RUNX3 and SOCS1 by quantitative methylation specific PCR (qMSP). The effect of CIMP on time to recurrence (TTR) and overall survival (OS) were determined by uni‐ and multivariate analyses. Subgroup analyses were conducted according to MSI and BRAF mutation status, disease stage, and also age at time of diagnosis (<60, 60‐74, ≥75 years). Patients with CIMP positive tumors demonstrated significantly shorter TTR and worse OS compared to those with CIMP negative tumors (multivariate hazard ratio [95% CI] 1.86 [1.31‐2.63] and 1.89 [1.34‐2.65], respectively). In stratified analyses, CIMP tumors showed significantly worse outcome among patients with microsatellite stable (MSS, P < 0.001), and MSS BRAF mutated tumors (P < 0.001), a finding that persisted in patients with stage II, III or IV disease, and that remained significant in multivariate analysis (P < 0.01). Consistent results were found for all three age groups. To conclude, CIMP is significantly associated with inferior outcome for colorectal cancer patients, and can stratify the poor prognostic patients with MSS BRAF mutated tumors. What's new? As many as one‐fifth of colorectal cancers have a CpG island methylator phenotype (CIMP) involving widespread promoter DNA methylation. CIMP is associated with key factors related to disease outcome, including microsatellite instability and BRAF mutations. In this study, CIMP was found to be significantly associated with worse prognosis in colorectal cancer patients, particularly those with microsatellite stable (MSS) BRAF‐mutated tumors. In stratified analyses, trends toward worse survival were identified for CIMP‐positive stage III and stage IV patients in the MSS BRAF‐mutated group. The findings suggest that CIMP status should be included in prognostic analyses at time of diagnosis.
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Affiliation(s)
- Hege Marie Vedeld
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital - Norwegian Radium Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Marianne Merok
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital - Norwegian Radium Hospital, Oslo, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,Department of Gastrointestinal Surgery, Oslo University Hospital - Aker, Oslo, Norway
| | - Marine Jeanmougin
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital - Norwegian Radium Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Stine A Danielsen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital - Norwegian Radium Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Hilde Honne
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital - Norwegian Radium Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Gro Kummeneje Presthus
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital - Norwegian Radium Hospital, Oslo, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Aud Svindland
- Department of Pathology, Oslo University Hospital, Oslo, Norway.,Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Ole H Sjo
- K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.,Department of Gastrointestinal Surgery, Oslo University Hospital - Aker, Oslo, Norway
| | - Merete Hektoen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital - Norwegian Radium Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Mette Eknaes
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital - Norwegian Radium Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Arild Nesbakken
- K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,Department of Gastrointestinal Surgery, Oslo University Hospital - Aker, Oslo, Norway
| | - Ragnhild A Lothe
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital - Norwegian Radium Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Guro E Lind
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital - Norwegian Radium Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
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40
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Cohen SA, Yu M, Baker K, Redman M, Wu C, Heinzerling TJ, Wirtz RM, Charalambous E, Pentheroudakis G, Kotoula V, Kalogeras KT, Fountzilas G, Grady WM. The CpG island methylator phenotype is concordant between primary colorectal carcinoma and matched distant metastases. Clin Epigenetics 2017; 9:46. [PMID: 28469732 PMCID: PMC5414304 DOI: 10.1186/s13148-017-0347-1] [Citation(s) in RCA: 14] [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: 10/14/2016] [Accepted: 04/21/2017] [Indexed: 12/13/2022] Open
Abstract
Background The CpG island methylator phenotype (CIMP) in stage III colon cancer (CRC) has been associated with improved survival after treatment with adjuvant irinotecan-based chemotherapy. In this analysis, we determine whether CIMP status in the primary CRC is concordant with the CIMP status of matched metastases in order to determine if assessment of CIMP status in the primary tumor can be used to predict CIMP status of metastatic disease, which is relevant for patient management as well as for understanding the biology of CIMP CRCs. Methods We assessed the CIMP status of 70 pairs of primary CRC and matched metastases using a CRC-specific panel of five markers (CACNA1G, IGF2, NEUROG1, RUNX3, and SOCS1) where CIMP positive was defined as 3/5 positive markers at a percent methylated reference threshold of ≥10%. Concordance was compared using the Fisher’s exact test and P < 0.05 was considered significant. Results Sixty-nine of the pairs (98.6%) showed concordant CIMP status in the primary tumor and matched metastasis; five (7.0%) of the pairs were concordantly CIMP positive. Only one pair (1.4%) had divergent CIMP status, demonstrating CIMP positivity (4/5 markers positive) in the primary tumor, while the matched metastasis was CIMP negative (0 markers positive). Conclusions CIMP status is generally concordant between primary CRCs and matched metastases. Thus, CIMP status in the primary tumor is maintained in matched metastases and can be used to inform CIMP-based therapy options for the metastases. Electronic supplementary material The online version of this article (doi:10.1186/s13148-017-0347-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stacey A Cohen
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA.,Division of Oncology, University of Washington, Seattle, WA USA.,825 Eastlake Ave E, G4-830, Seattle, WA 98109 USA
| | - Ming Yu
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA.,1100 Fairview Ave N, D4-100, Seattle, WA 98109 USA
| | - Kelsey Baker
- Clinical Statistics, Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA USA.,1100 Fairview Ave N, M2-B230, Seattle, WA 98109 USA
| | - Mary Redman
- Clinical Statistics, Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA USA.,1100 Fairview Ave N, M2-B230, Seattle, WA 98109 USA
| | - Chen Wu
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA.,College of Life Sciences, Hebei University, Baoding, Hebei People's Republic of China.,1100 Fairview Ave N, D4-100, Seattle, WA 98109 USA
| | - Tai J Heinzerling
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA.,1100 Fairview Ave N, D4-100, Seattle, WA 98109 USA
| | - Ralph M Wirtz
- STRATIFYER Molecular Pathology GmbH, Cologne, Germany.,Werthmann Str. Str. 1c, D-50935 Cologne, Germany
| | - Elpida Charalambous
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece.,University Campus, Building 17B, 540 06 Thessaloniki, Greece
| | - George Pentheroudakis
- Department of Medical Oncology, Ioannina University Hospital, Ioannina, Greece.,Niarchos Av, Ioannina, 455 00 Greece
| | - Vassiliki Kotoula
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece.,Department of Pathology, Faculty of Medicine, School of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece.,University Campus, Building 17B, 540 06 Thessaloniki, Greece
| | - Konstantine T Kalogeras
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece.,Translational Research Section, Hellenic Cooperative Oncology Group, Data Office, Athens, Greece.,18 Hatzikonstanti Str, 115 24 Athens, Greece
| | - George Fountzilas
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece.,Aristotle University of Thessaloniki, Thessaloniki, Greece.,30 Kapetan Kotta Str, 552 36 Panorama, Thessaloniki Greece
| | - William M Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA.,Division of Gastroenterology, University of Washington School of Medicine, Seattle, WA USA.,1100 Fairview Ave N, D4-100, Seattle, WA 98109 USA
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41
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McInnes T, Zou D, Rao DS, Munro FM, Phillips VL, McCall JL, Black MA, Reeve AE, Guilford PJ. Genome-wide methylation analysis identifies a core set of hypermethylated genes in CIMP-H colorectal cancer. BMC Cancer 2017; 17:228. [PMID: 28351398 PMCID: PMC5371203 DOI: 10.1186/s12885-017-3226-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 03/23/2017] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Aberrant DNA methylation profiles are a characteristic of all known cancer types, epitomized by the CpG island methylator phenotype (CIMP) in colorectal cancer (CRC). Hypermethylation has been observed at CpG islands throughout the genome, but it is unclear which factors determine whether an individual island becomes methylated in cancer. METHODS DNA methylation in CRC was analysed using the Illumina HumanMethylation450K array. Differentially methylated loci were identified using Significance Analysis of Microarrays (SAM) and the Wilcoxon Signed Rank (WSR) test. Unsupervised hierarchical clustering was used to identify methylation subtypes in CRC. RESULTS In this study we characterized the DNA methylation profiles of 94 CRC tissues and their matched normal counterparts. Consistent with previous studies, unsupervized hierarchical clustering of genome-wide methylation data identified three subtypes within the tumour samples, designated CIMP-H, CIMP-L and CIMP-N, that showed high, low and very low methylation levels, respectively. Differential methylation between normal and tumour samples was analysed at the individual CpG level, and at the gene level. The distribution of hypermethylation in CIMP-N tumours showed high inter-tumour variability and appeared to be highly stochastic in nature, whereas CIMP-H tumours exhibited consistent hypermethylation at a subset of genes, in addition to a highly variable background of hypermethylated genes. EYA4, TFPI2 and TLX1 were hypermethylated in more than 90% of all tumours examined. One-hundred thirty-two genes were hypermethylated in 100% of CIMP-H tumours studied and these were highly enriched for functions relating to skeletal system development (Bonferroni adjusted p value =2.88E-15), segment specification (adjusted p value =9.62E-11), embryonic development (adjusted p value =1.52E-04), mesoderm development (adjusted p value =1.14E-20), and ectoderm development (adjusted p value =7.94E-16). CONCLUSIONS Our genome-wide characterization of DNA methylation in colorectal cancer has identified 132 genes hypermethylated in 100% of CIMP-H samples. Three genes, EYA4, TLX1 and TFPI2 are hypermethylated in >90% of all tumour samples, regardless of CIMP subtype.
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Affiliation(s)
- Tyler McInnes
- Cancer Genetics Laboratory, Centre for Translational Cancer Research (Te Aho Matatū), Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
| | - Donghui Zou
- Cancer Genetics Laboratory, Centre for Translational Cancer Research (Te Aho Matatū), Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
| | - Dasari S Rao
- Cancer Genetics Laboratory, Centre for Translational Cancer Research (Te Aho Matatū), Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand.,Department of Surgical Sciences, Dunedin School of Medicine, University of Otago, Dunedin, 9054, New Zealand
| | - Francesca M Munro
- Department of Surgical Sciences, Dunedin School of Medicine, University of Otago, Dunedin, 9054, New Zealand
| | - Vicky L Phillips
- Department of Surgical Sciences, Dunedin School of Medicine, University of Otago, Dunedin, 9054, New Zealand
| | - John L McCall
- Department of Surgical Sciences, Dunedin School of Medicine, University of Otago, Dunedin, 9054, New Zealand
| | - Michael A Black
- Cancer Genetics Laboratory, Centre for Translational Cancer Research (Te Aho Matatū), Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
| | - Anthony E Reeve
- Cancer Genetics Laboratory, Centre for Translational Cancer Research (Te Aho Matatū), Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
| | - Parry J Guilford
- Cancer Genetics Laboratory, Centre for Translational Cancer Research (Te Aho Matatū), Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand.
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42
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Arribas AJ, Bertoni F. Methylation patterns in marginal zone lymphoma. Best Pract Res Clin Haematol 2016; 30:24-31. [PMID: 28288713 DOI: 10.1016/j.beha.2016.09.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [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: 09/01/2016] [Revised: 09/16/2016] [Accepted: 09/19/2016] [Indexed: 02/07/2023]
Abstract
Promoter DNA methylation is a major regulator of gene expression and transcription. The identification of methylation changes is important for understanding disease pathogenesis, for identifying prognostic markers and can drive novel therapeutic approaches. In this review we summarize the current knowledge regarding DNA methylation in MALT lymphoma, splenic marginal zone lymphoma, nodal marginal zone lymphoma. Despite important differences in the study design for different publications and the existence of a sole large and genome-wide methylation study for splenic marginal zone lymphoma, it is clear that DNA methylation plays an important role in marginal zone lymphomas, in which it contributes to the inactivation of tumor suppressors but also to the expression of genes sustaining tumor cell survival and proliferation. Existing preclinical data provide the rationale to target the methylation machinery in these disorders.
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Affiliation(s)
- Alberto J Arribas
- Lymphoma & Genomics Research Program, Institute of Oncology Research (IOR), Bellinzona, Switzerland.
| | - Francesco Bertoni
- Lymphoma & Genomics Research Program, Institute of Oncology Research (IOR), Bellinzona, Switzerland; Oncology Institute of Southern Switzerland (IOSI), Bellinzona, Switzerland.
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43
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Wick W, Roth P, Hartmann C, Hau P, Nakamura M, Stockhammer F, Sabel MC, Wick A, Koeppen S, Ketter R, Vajkoczy P, Eyupoglu I, Kalff R, Pietsch T, Happold C, Galldiks N, Schmidt-Graf F, Bamberg M, Reifenberger G, Platten M, von Deimling A, Meisner C, Wiestler B, Weller M. Long-term analysis of the NOA-04 randomized phase III trial of sequential radiochemotherapy of anaplastic glioma with PCV or temozolomide. Neuro Oncol 2016; 18:1529-1537. [PMID: 27370396 PMCID: PMC5063521 DOI: 10.1093/neuonc/now133] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [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: 03/28/2016] [Accepted: 05/18/2016] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Optimal treatment and precise classification for anaplastic glioma are needed. METHODS The objective for long-term follow-up of NOA-04 is to optimize the treatment sequence for patients with anaplastic gliomas. Patients were randomized 2:1:1 to receive the standard radiotherapy (RT) (arm A), procarbazine, lomustine and vincristine (PCV) (arm B1), or temozolomide (TMZ) (arm B2). RESULTS Primary endpoint was time-to-treatment-failure (TTF), defined as progression after 2 lines of therapy or any time before if no further therapy was administered. Exploratory analyses examined associations of molecular marker status with TTF, progression-free survival (PFS), and overall survival (OS). At 9.5 (95% CI: 8.6-10.2) years, no difference between arms (A vs B1/B2) was observed: median TTF (4.6 [3.4-5.1] y vs 4.4 [3.3-5.3) y), PFS (2.5 [1.3-3.5] y vs 2.7 [1.9-3.2] y), and OS (8 [5.5-10.3] y vs 6.5 [5.4-8.3] y). Oligodendroglial versus astrocytic histology-but more so the subgroups according to CpG island methylator phenotype (CIMP) and 1p/19q co-deletion status-revealed a strong prognostic value of CIMPpos with (CIMPcodel) versus without 1p/19 co-deletion (CIMPnon-codel) versus CIMPneg. but no differential efficacy of RT versus chemotherapy for any of the endpoints. PFS was better for PCV- than for TMZ-treated patients with CIMPcodel tumors (HR B1 vs B2 0.39 [0.17-0.92], P = .031). In CIMPneg. tumors, hypermethylation of the O6-methyl-guanyl-DNA methyltransferase promoter (MGMT) provided a risk reduction for PFS with chemotherapy. CONCLUSIONS There is no differential activity of primary chemotherapy versus RT in any subgroup of anaplastic glioma. Molecular diagnosis is superior to histology. TRIAL REGISTRATION clinicaltrials.gov Identifier: NCT00717210.
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Affiliation(s)
- Wolfgang Wick
- Department of Neurology Clinic, University of Heidelberg, Heidelberg, Germany (W.W., A.W., M.P., B.W.); Clinical Cooperation Unit (CCU Neurooncology), German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany (W.W., B.W.); Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland (P.R., C.H., M.W.); Department of Neuropathology, Hannover Medical School, Hannover, Germany (C.H.); Department of Neurology, Regensburg University, Regensburg, Germany (P.H.); Department of Neurosurgery Clinic, Hannover Medical School, Hannover, Germany (M.N.); Department of Neurosurgery Clinic, Charité, Berlin, Germany (F.S., P.V.); Department of Neurosurgery, Heinrich Heine University, Düsseldorf, Germany (M.C.S.); Department of Neurology Clinic, Essen Medical Center, Essen, Germany (S.K.); Department of Neurosurgery Clinic, Saarland University, Homburg, Germany (R.K.); Department of Neurosurgery Clinic, University of Göttingen, Göttingen, Germany (F.S.); Department of Neurosurgery Clinic, University of Erlangen, Erlangen, Germany (I.E.); Department of Neurosurgery Clinic, University of Jena, Jena, Germany (R.K.); Department of Neurology Clinic, Cologne University, Cologne, Germany (N.G.); Department of Neurology Clinic, TU Munich, Munich, Germany (F.S.-G.); Department of Neuropathology, University of Heidelberg, Heidelberg, Germany (A.v.D.); CCU Neuropathology, (C.H., A.v.D.); CCU Brain Tumor Immunology, DKFZ, all Heidelberg, Germany (M.P.); Department of Neuropathology, Heinrich Heine University, Düsseldorf, Germany (G.R.); DKTK partner site Essen/Düsseldorf, Düsseldorf, Germany (G.R.), Department of General Neurology, Tübingen, Germany (W.W., A.W., F.S.-G., M.P., M.W.), Department of Radiation Oncology, Tübingen, Germany (M.B.), Department of Medical Biometry, University Hospital Tübingen, Tübingen, Germany (C.M.)
| | - Patrick Roth
- Department of Neurology Clinic, University of Heidelberg, Heidelberg, Germany (W.W., A.W., M.P., B.W.); Clinical Cooperation Unit (CCU Neurooncology), German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany (W.W., B.W.); Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland (P.R., C.H., M.W.); Department of Neuropathology, Hannover Medical School, Hannover, Germany (C.H.); Department of Neurology, Regensburg University, Regensburg, Germany (P.H.); Department of Neurosurgery Clinic, Hannover Medical School, Hannover, Germany (M.N.); Department of Neurosurgery Clinic, Charité, Berlin, Germany (F.S., P.V.); Department of Neurosurgery, Heinrich Heine University, Düsseldorf, Germany (M.C.S.); Department of Neurology Clinic, Essen Medical Center, Essen, Germany (S.K.); Department of Neurosurgery Clinic, Saarland University, Homburg, Germany (R.K.); Department of Neurosurgery Clinic, University of Göttingen, Göttingen, Germany (F.S.); Department of Neurosurgery Clinic, University of Erlangen, Erlangen, Germany (I.E.); Department of Neurosurgery Clinic, University of Jena, Jena, Germany (R.K.); Department of Neurology Clinic, Cologne University, Cologne, Germany (N.G.); Department of Neurology Clinic, TU Munich, Munich, Germany (F.S.-G.); Department of Neuropathology, University of Heidelberg, Heidelberg, Germany (A.v.D.); CCU Neuropathology, (C.H., A.v.D.); CCU Brain Tumor Immunology, DKFZ, all Heidelberg, Germany (M.P.); Department of Neuropathology, Heinrich Heine University, Düsseldorf, Germany (G.R.); DKTK partner site Essen/Düsseldorf, Düsseldorf, Germany (G.R.), Department of General Neurology, Tübingen, Germany (W.W., A.W., F.S.-G., M.P., M.W.), Department of Radiation Oncology, Tübingen, Germany (M.B.), Department of Medical Biometry, University Hospital Tübingen, Tübingen, Germany (C.M.)
| | - Christian Hartmann
- Department of Neurology Clinic, University of Heidelberg, Heidelberg, Germany (W.W., A.W., M.P., B.W.); Clinical Cooperation Unit (CCU Neurooncology), German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany (W.W., B.W.); Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland (P.R., C.H., M.W.); Department of Neuropathology, Hannover Medical School, Hannover, Germany (C.H.); Department of Neurology, Regensburg University, Regensburg, Germany (P.H.); Department of Neurosurgery Clinic, Hannover Medical School, Hannover, Germany (M.N.); Department of Neurosurgery Clinic, Charité, Berlin, Germany (F.S., P.V.); Department of Neurosurgery, Heinrich Heine University, Düsseldorf, Germany (M.C.S.); Department of Neurology Clinic, Essen Medical Center, Essen, Germany (S.K.); Department of Neurosurgery Clinic, Saarland University, Homburg, Germany (R.K.); Department of Neurosurgery Clinic, University of Göttingen, Göttingen, Germany (F.S.); Department of Neurosurgery Clinic, University of Erlangen, Erlangen, Germany (I.E.); Department of Neurosurgery Clinic, University of Jena, Jena, Germany (R.K.); Department of Neurology Clinic, Cologne University, Cologne, Germany (N.G.); Department of Neurology Clinic, TU Munich, Munich, Germany (F.S.-G.); Department of Neuropathology, University of Heidelberg, Heidelberg, Germany (A.v.D.); CCU Neuropathology, (C.H., A.v.D.); CCU Brain Tumor Immunology, DKFZ, all Heidelberg, Germany (M.P.); Department of Neuropathology, Heinrich Heine University, Düsseldorf, Germany (G.R.); DKTK partner site Essen/Düsseldorf, Düsseldorf, Germany (G.R.), Department of General Neurology, Tübingen, Germany (W.W., A.W., F.S.-G., M.P., M.W.), Department of Radiation Oncology, Tübingen, Germany (M.B.), Department of Medical Biometry, University Hospital Tübingen, Tübingen, Germany (C.M.)
| | - Peter Hau
- Department of Neurology Clinic, University of Heidelberg, Heidelberg, Germany (W.W., A.W., M.P., B.W.); Clinical Cooperation Unit (CCU Neurooncology), German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany (W.W., B.W.); Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland (P.R., C.H., M.W.); Department of Neuropathology, Hannover Medical School, Hannover, Germany (C.H.); Department of Neurology, Regensburg University, Regensburg, Germany (P.H.); Department of Neurosurgery Clinic, Hannover Medical School, Hannover, Germany (M.N.); Department of Neurosurgery Clinic, Charité, Berlin, Germany (F.S., P.V.); Department of Neurosurgery, Heinrich Heine University, Düsseldorf, Germany (M.C.S.); Department of Neurology Clinic, Essen Medical Center, Essen, Germany (S.K.); Department of Neurosurgery Clinic, Saarland University, Homburg, Germany (R.K.); Department of Neurosurgery Clinic, University of Göttingen, Göttingen, Germany (F.S.); Department of Neurosurgery Clinic, University of Erlangen, Erlangen, Germany (I.E.); Department of Neurosurgery Clinic, University of Jena, Jena, Germany (R.K.); Department of Neurology Clinic, Cologne University, Cologne, Germany (N.G.); Department of Neurology Clinic, TU Munich, Munich, Germany (F.S.-G.); Department of Neuropathology, University of Heidelberg, Heidelberg, Germany (A.v.D.); CCU Neuropathology, (C.H., A.v.D.); CCU Brain Tumor Immunology, DKFZ, all Heidelberg, Germany (M.P.); Department of Neuropathology, Heinrich Heine University, Düsseldorf, Germany (G.R.); DKTK partner site Essen/Düsseldorf, Düsseldorf, Germany (G.R.), Department of General Neurology, Tübingen, Germany (W.W., A.W., F.S.-G., M.P., M.W.), Department of Radiation Oncology, Tübingen, Germany (M.B.), Department of Medical Biometry, University Hospital Tübingen, Tübingen, Germany (C.M.)
| | - Makoto Nakamura
- Department of Neurology Clinic, University of Heidelberg, Heidelberg, Germany (W.W., A.W., M.P., B.W.); Clinical Cooperation Unit (CCU Neurooncology), German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany (W.W., B.W.); Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland (P.R., C.H., M.W.); Department of Neuropathology, Hannover Medical School, Hannover, Germany (C.H.); Department of Neurology, Regensburg University, Regensburg, Germany (P.H.); Department of Neurosurgery Clinic, Hannover Medical School, Hannover, Germany (M.N.); Department of Neurosurgery Clinic, Charité, Berlin, Germany (F.S., P.V.); Department of Neurosurgery, Heinrich Heine University, Düsseldorf, Germany (M.C.S.); Department of Neurology Clinic, Essen Medical Center, Essen, Germany (S.K.); Department of Neurosurgery Clinic, Saarland University, Homburg, Germany (R.K.); Department of Neurosurgery Clinic, University of Göttingen, Göttingen, Germany (F.S.); Department of Neurosurgery Clinic, University of Erlangen, Erlangen, Germany (I.E.); Department of Neurosurgery Clinic, University of Jena, Jena, Germany (R.K.); Department of Neurology Clinic, Cologne University, Cologne, Germany (N.G.); Department of Neurology Clinic, TU Munich, Munich, Germany (F.S.-G.); Department of Neuropathology, University of Heidelberg, Heidelberg, Germany (A.v.D.); CCU Neuropathology, (C.H., A.v.D.); CCU Brain Tumor Immunology, DKFZ, all Heidelberg, Germany (M.P.); Department of Neuropathology, Heinrich Heine University, Düsseldorf, Germany (G.R.); DKTK partner site Essen/Düsseldorf, Düsseldorf, Germany (G.R.), Department of General Neurology, Tübingen, Germany (W.W., A.W., F.S.-G., M.P., M.W.), Department of Radiation Oncology, Tübingen, Germany (M.B.), Department of Medical Biometry, University Hospital Tübingen, Tübingen, Germany (C.M.)
| | - Florian Stockhammer
- Department of Neurology Clinic, University of Heidelberg, Heidelberg, Germany (W.W., A.W., M.P., B.W.); Clinical Cooperation Unit (CCU Neurooncology), German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany (W.W., B.W.); Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland (P.R., C.H., M.W.); Department of Neuropathology, Hannover Medical School, Hannover, Germany (C.H.); Department of Neurology, Regensburg University, Regensburg, Germany (P.H.); Department of Neurosurgery Clinic, Hannover Medical School, Hannover, Germany (M.N.); Department of Neurosurgery Clinic, Charité, Berlin, Germany (F.S., P.V.); Department of Neurosurgery, Heinrich Heine University, Düsseldorf, Germany (M.C.S.); Department of Neurology Clinic, Essen Medical Center, Essen, Germany (S.K.); Department of Neurosurgery Clinic, Saarland University, Homburg, Germany (R.K.); Department of Neurosurgery Clinic, University of Göttingen, Göttingen, Germany (F.S.); Department of Neurosurgery Clinic, University of Erlangen, Erlangen, Germany (I.E.); Department of Neurosurgery Clinic, University of Jena, Jena, Germany (R.K.); Department of Neurology Clinic, Cologne University, Cologne, Germany (N.G.); Department of Neurology Clinic, TU Munich, Munich, Germany (F.S.-G.); Department of Neuropathology, University of Heidelberg, Heidelberg, Germany (A.v.D.); CCU Neuropathology, (C.H., A.v.D.); CCU Brain Tumor Immunology, DKFZ, all Heidelberg, Germany (M.P.); Department of Neuropathology, Heinrich Heine University, Düsseldorf, Germany (G.R.); DKTK partner site Essen/Düsseldorf, Düsseldorf, Germany (G.R.), Department of General Neurology, Tübingen, Germany (W.W., A.W., F.S.-G., M.P., M.W.), Department of Radiation Oncology, Tübingen, Germany (M.B.), Department of Medical Biometry, University Hospital Tübingen, Tübingen, Germany (C.M.)
| | - Michael C Sabel
- Department of Neurology Clinic, University of Heidelberg, Heidelberg, Germany (W.W., A.W., M.P., B.W.); Clinical Cooperation Unit (CCU Neurooncology), German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany (W.W., B.W.); Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland (P.R., C.H., M.W.); Department of Neuropathology, Hannover Medical School, Hannover, Germany (C.H.); Department of Neurology, Regensburg University, Regensburg, Germany (P.H.); Department of Neurosurgery Clinic, Hannover Medical School, Hannover, Germany (M.N.); Department of Neurosurgery Clinic, Charité, Berlin, Germany (F.S., P.V.); Department of Neurosurgery, Heinrich Heine University, Düsseldorf, Germany (M.C.S.); Department of Neurology Clinic, Essen Medical Center, Essen, Germany (S.K.); Department of Neurosurgery Clinic, Saarland University, Homburg, Germany (R.K.); Department of Neurosurgery Clinic, University of Göttingen, Göttingen, Germany (F.S.); Department of Neurosurgery Clinic, University of Erlangen, Erlangen, Germany (I.E.); Department of Neurosurgery Clinic, University of Jena, Jena, Germany (R.K.); Department of Neurology Clinic, Cologne University, Cologne, Germany (N.G.); Department of Neurology Clinic, TU Munich, Munich, Germany (F.S.-G.); Department of Neuropathology, University of Heidelberg, Heidelberg, Germany (A.v.D.); CCU Neuropathology, (C.H., A.v.D.); CCU Brain Tumor Immunology, DKFZ, all Heidelberg, Germany (M.P.); Department of Neuropathology, Heinrich Heine University, Düsseldorf, Germany (G.R.); DKTK partner site Essen/Düsseldorf, Düsseldorf, Germany (G.R.), Department of General Neurology, Tübingen, Germany (W.W., A.W., F.S.-G., M.P., M.W.), Department of Radiation Oncology, Tübingen, Germany (M.B.), Department of Medical Biometry, University Hospital Tübingen, Tübingen, Germany (C.M.)
| | - Antje Wick
- Department of Neurology Clinic, University of Heidelberg, Heidelberg, Germany (W.W., A.W., M.P., B.W.); Clinical Cooperation Unit (CCU Neurooncology), German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany (W.W., B.W.); Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland (P.R., C.H., M.W.); Department of Neuropathology, Hannover Medical School, Hannover, Germany (C.H.); Department of Neurology, Regensburg University, Regensburg, Germany (P.H.); Department of Neurosurgery Clinic, Hannover Medical School, Hannover, Germany (M.N.); Department of Neurosurgery Clinic, Charité, Berlin, Germany (F.S., P.V.); Department of Neurosurgery, Heinrich Heine University, Düsseldorf, Germany (M.C.S.); Department of Neurology Clinic, Essen Medical Center, Essen, Germany (S.K.); Department of Neurosurgery Clinic, Saarland University, Homburg, Germany (R.K.); Department of Neurosurgery Clinic, University of Göttingen, Göttingen, Germany (F.S.); Department of Neurosurgery Clinic, University of Erlangen, Erlangen, Germany (I.E.); Department of Neurosurgery Clinic, University of Jena, Jena, Germany (R.K.); Department of Neurology Clinic, Cologne University, Cologne, Germany (N.G.); Department of Neurology Clinic, TU Munich, Munich, Germany (F.S.-G.); Department of Neuropathology, University of Heidelberg, Heidelberg, Germany (A.v.D.); CCU Neuropathology, (C.H., A.v.D.); CCU Brain Tumor Immunology, DKFZ, all Heidelberg, Germany (M.P.); Department of Neuropathology, Heinrich Heine University, Düsseldorf, Germany (G.R.); DKTK partner site Essen/Düsseldorf, Düsseldorf, Germany (G.R.), Department of General Neurology, Tübingen, Germany (W.W., A.W., F.S.-G., M.P., M.W.), Department of Radiation Oncology, Tübingen, Germany (M.B.), Department of Medical Biometry, University Hospital Tübingen, Tübingen, Germany (C.M.)
| | - Susanne Koeppen
- Department of Neurology Clinic, University of Heidelberg, Heidelberg, Germany (W.W., A.W., M.P., B.W.); Clinical Cooperation Unit (CCU Neurooncology), German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany (W.W., B.W.); Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland (P.R., C.H., M.W.); Department of Neuropathology, Hannover Medical School, Hannover, Germany (C.H.); Department of Neurology, Regensburg University, Regensburg, Germany (P.H.); Department of Neurosurgery Clinic, Hannover Medical School, Hannover, Germany (M.N.); Department of Neurosurgery Clinic, Charité, Berlin, Germany (F.S., P.V.); Department of Neurosurgery, Heinrich Heine University, Düsseldorf, Germany (M.C.S.); Department of Neurology Clinic, Essen Medical Center, Essen, Germany (S.K.); Department of Neurosurgery Clinic, Saarland University, Homburg, Germany (R.K.); Department of Neurosurgery Clinic, University of Göttingen, Göttingen, Germany (F.S.); Department of Neurosurgery Clinic, University of Erlangen, Erlangen, Germany (I.E.); Department of Neurosurgery Clinic, University of Jena, Jena, Germany (R.K.); Department of Neurology Clinic, Cologne University, Cologne, Germany (N.G.); Department of Neurology Clinic, TU Munich, Munich, Germany (F.S.-G.); Department of Neuropathology, University of Heidelberg, Heidelberg, Germany (A.v.D.); CCU Neuropathology, (C.H., A.v.D.); CCU Brain Tumor Immunology, DKFZ, all Heidelberg, Germany (M.P.); Department of Neuropathology, Heinrich Heine University, Düsseldorf, Germany (G.R.); DKTK partner site Essen/Düsseldorf, Düsseldorf, Germany (G.R.), Department of General Neurology, Tübingen, Germany (W.W., A.W., F.S.-G., M.P., M.W.), Department of Radiation Oncology, Tübingen, Germany (M.B.), Department of Medical Biometry, University Hospital Tübingen, Tübingen, Germany (C.M.)
| | - Ralf Ketter
- Department of Neurology Clinic, University of Heidelberg, Heidelberg, Germany (W.W., A.W., M.P., B.W.); Clinical Cooperation Unit (CCU Neurooncology), German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany (W.W., B.W.); Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland (P.R., C.H., M.W.); Department of Neuropathology, Hannover Medical School, Hannover, Germany (C.H.); Department of Neurology, Regensburg University, Regensburg, Germany (P.H.); Department of Neurosurgery Clinic, Hannover Medical School, Hannover, Germany (M.N.); Department of Neurosurgery Clinic, Charité, Berlin, Germany (F.S., P.V.); Department of Neurosurgery, Heinrich Heine University, Düsseldorf, Germany (M.C.S.); Department of Neurology Clinic, Essen Medical Center, Essen, Germany (S.K.); Department of Neurosurgery Clinic, Saarland University, Homburg, Germany (R.K.); Department of Neurosurgery Clinic, University of Göttingen, Göttingen, Germany (F.S.); Department of Neurosurgery Clinic, University of Erlangen, Erlangen, Germany (I.E.); Department of Neurosurgery Clinic, University of Jena, Jena, Germany (R.K.); Department of Neurology Clinic, Cologne University, Cologne, Germany (N.G.); Department of Neurology Clinic, TU Munich, Munich, Germany (F.S.-G.); Department of Neuropathology, University of Heidelberg, Heidelberg, Germany (A.v.D.); CCU Neuropathology, (C.H., A.v.D.); CCU Brain Tumor Immunology, DKFZ, all Heidelberg, Germany (M.P.); Department of Neuropathology, Heinrich Heine University, Düsseldorf, Germany (G.R.); DKTK partner site Essen/Düsseldorf, Düsseldorf, Germany (G.R.), Department of General Neurology, Tübingen, Germany (W.W., A.W., F.S.-G., M.P., M.W.), Department of Radiation Oncology, Tübingen, Germany (M.B.), Department of Medical Biometry, University Hospital Tübingen, Tübingen, Germany (C.M.)
| | - Peter Vajkoczy
- Department of Neurology Clinic, University of Heidelberg, Heidelberg, Germany (W.W., A.W., M.P., B.W.); Clinical Cooperation Unit (CCU Neurooncology), German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany (W.W., B.W.); Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland (P.R., C.H., M.W.); Department of Neuropathology, Hannover Medical School, Hannover, Germany (C.H.); Department of Neurology, Regensburg University, Regensburg, Germany (P.H.); Department of Neurosurgery Clinic, Hannover Medical School, Hannover, Germany (M.N.); Department of Neurosurgery Clinic, Charité, Berlin, Germany (F.S., P.V.); Department of Neurosurgery, Heinrich Heine University, Düsseldorf, Germany (M.C.S.); Department of Neurology Clinic, Essen Medical Center, Essen, Germany (S.K.); Department of Neurosurgery Clinic, Saarland University, Homburg, Germany (R.K.); Department of Neurosurgery Clinic, University of Göttingen, Göttingen, Germany (F.S.); Department of Neurosurgery Clinic, University of Erlangen, Erlangen, Germany (I.E.); Department of Neurosurgery Clinic, University of Jena, Jena, Germany (R.K.); Department of Neurology Clinic, Cologne University, Cologne, Germany (N.G.); Department of Neurology Clinic, TU Munich, Munich, Germany (F.S.-G.); Department of Neuropathology, University of Heidelberg, Heidelberg, Germany (A.v.D.); CCU Neuropathology, (C.H., A.v.D.); CCU Brain Tumor Immunology, DKFZ, all Heidelberg, Germany (M.P.); Department of Neuropathology, Heinrich Heine University, Düsseldorf, Germany (G.R.); DKTK partner site Essen/Düsseldorf, Düsseldorf, Germany (G.R.), Department of General Neurology, Tübingen, Germany (W.W., A.W., F.S.-G., M.P., M.W.), Department of Radiation Oncology, Tübingen, Germany (M.B.), Department of Medical Biometry, University Hospital Tübingen, Tübingen, Germany (C.M.)
| | - Ilker Eyupoglu
- Department of Neurology Clinic, University of Heidelberg, Heidelberg, Germany (W.W., A.W., M.P., B.W.); Clinical Cooperation Unit (CCU Neurooncology), German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany (W.W., B.W.); Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland (P.R., C.H., M.W.); Department of Neuropathology, Hannover Medical School, Hannover, Germany (C.H.); Department of Neurology, Regensburg University, Regensburg, Germany (P.H.); Department of Neurosurgery Clinic, Hannover Medical School, Hannover, Germany (M.N.); Department of Neurosurgery Clinic, Charité, Berlin, Germany (F.S., P.V.); Department of Neurosurgery, Heinrich Heine University, Düsseldorf, Germany (M.C.S.); Department of Neurology Clinic, Essen Medical Center, Essen, Germany (S.K.); Department of Neurosurgery Clinic, Saarland University, Homburg, Germany (R.K.); Department of Neurosurgery Clinic, University of Göttingen, Göttingen, Germany (F.S.); Department of Neurosurgery Clinic, University of Erlangen, Erlangen, Germany (I.E.); Department of Neurosurgery Clinic, University of Jena, Jena, Germany (R.K.); Department of Neurology Clinic, Cologne University, Cologne, Germany (N.G.); Department of Neurology Clinic, TU Munich, Munich, Germany (F.S.-G.); Department of Neuropathology, University of Heidelberg, Heidelberg, Germany (A.v.D.); CCU Neuropathology, (C.H., A.v.D.); CCU Brain Tumor Immunology, DKFZ, all Heidelberg, Germany (M.P.); Department of Neuropathology, Heinrich Heine University, Düsseldorf, Germany (G.R.); DKTK partner site Essen/Düsseldorf, Düsseldorf, Germany (G.R.), Department of General Neurology, Tübingen, Germany (W.W., A.W., F.S.-G., M.P., M.W.), Department of Radiation Oncology, Tübingen, Germany (M.B.), Department of Medical Biometry, University Hospital Tübingen, Tübingen, Germany (C.M.)
| | - Rolf Kalff
- Department of Neurology Clinic, University of Heidelberg, Heidelberg, Germany (W.W., A.W., M.P., B.W.); Clinical Cooperation Unit (CCU Neurooncology), German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany (W.W., B.W.); Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland (P.R., C.H., M.W.); Department of Neuropathology, Hannover Medical School, Hannover, Germany (C.H.); Department of Neurology, Regensburg University, Regensburg, Germany (P.H.); Department of Neurosurgery Clinic, Hannover Medical School, Hannover, Germany (M.N.); Department of Neurosurgery Clinic, Charité, Berlin, Germany (F.S., P.V.); Department of Neurosurgery, Heinrich Heine University, Düsseldorf, Germany (M.C.S.); Department of Neurology Clinic, Essen Medical Center, Essen, Germany (S.K.); Department of Neurosurgery Clinic, Saarland University, Homburg, Germany (R.K.); Department of Neurosurgery Clinic, University of Göttingen, Göttingen, Germany (F.S.); Department of Neurosurgery Clinic, University of Erlangen, Erlangen, Germany (I.E.); Department of Neurosurgery Clinic, University of Jena, Jena, Germany (R.K.); Department of Neurology Clinic, Cologne University, Cologne, Germany (N.G.); Department of Neurology Clinic, TU Munich, Munich, Germany (F.S.-G.); Department of Neuropathology, University of Heidelberg, Heidelberg, Germany (A.v.D.); CCU Neuropathology, (C.H., A.v.D.); CCU Brain Tumor Immunology, DKFZ, all Heidelberg, Germany (M.P.); Department of Neuropathology, Heinrich Heine University, Düsseldorf, Germany (G.R.); DKTK partner site Essen/Düsseldorf, Düsseldorf, Germany (G.R.), Department of General Neurology, Tübingen, Germany (W.W., A.W., F.S.-G., M.P., M.W.), Department of Radiation Oncology, Tübingen, Germany (M.B.), Department of Medical Biometry, University Hospital Tübingen, Tübingen, Germany (C.M.)
| | - Torsten Pietsch
- Department of Neurology Clinic, University of Heidelberg, Heidelberg, Germany (W.W., A.W., M.P., B.W.); Clinical Cooperation Unit (CCU Neurooncology), German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany (W.W., B.W.); Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland (P.R., C.H., M.W.); Department of Neuropathology, Hannover Medical School, Hannover, Germany (C.H.); Department of Neurology, Regensburg University, Regensburg, Germany (P.H.); Department of Neurosurgery Clinic, Hannover Medical School, Hannover, Germany (M.N.); Department of Neurosurgery Clinic, Charité, Berlin, Germany (F.S., P.V.); Department of Neurosurgery, Heinrich Heine University, Düsseldorf, Germany (M.C.S.); Department of Neurology Clinic, Essen Medical Center, Essen, Germany (S.K.); Department of Neurosurgery Clinic, Saarland University, Homburg, Germany (R.K.); Department of Neurosurgery Clinic, University of Göttingen, Göttingen, Germany (F.S.); Department of Neurosurgery Clinic, University of Erlangen, Erlangen, Germany (I.E.); Department of Neurosurgery Clinic, University of Jena, Jena, Germany (R.K.); Department of Neurology Clinic, Cologne University, Cologne, Germany (N.G.); Department of Neurology Clinic, TU Munich, Munich, Germany (F.S.-G.); Department of Neuropathology, University of Heidelberg, Heidelberg, Germany (A.v.D.); CCU Neuropathology, (C.H., A.v.D.); CCU Brain Tumor Immunology, DKFZ, all Heidelberg, Germany (M.P.); Department of Neuropathology, Heinrich Heine University, Düsseldorf, Germany (G.R.); DKTK partner site Essen/Düsseldorf, Düsseldorf, Germany (G.R.), Department of General Neurology, Tübingen, Germany (W.W., A.W., F.S.-G., M.P., M.W.), Department of Radiation Oncology, Tübingen, Germany (M.B.), Department of Medical Biometry, University Hospital Tübingen, Tübingen, Germany (C.M.)
| | - Caroline Happold
- Department of Neurology Clinic, University of Heidelberg, Heidelberg, Germany (W.W., A.W., M.P., B.W.); Clinical Cooperation Unit (CCU Neurooncology), German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany (W.W., B.W.); Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland (P.R., C.H., M.W.); Department of Neuropathology, Hannover Medical School, Hannover, Germany (C.H.); Department of Neurology, Regensburg University, Regensburg, Germany (P.H.); Department of Neurosurgery Clinic, Hannover Medical School, Hannover, Germany (M.N.); Department of Neurosurgery Clinic, Charité, Berlin, Germany (F.S., P.V.); Department of Neurosurgery, Heinrich Heine University, Düsseldorf, Germany (M.C.S.); Department of Neurology Clinic, Essen Medical Center, Essen, Germany (S.K.); Department of Neurosurgery Clinic, Saarland University, Homburg, Germany (R.K.); Department of Neurosurgery Clinic, University of Göttingen, Göttingen, Germany (F.S.); Department of Neurosurgery Clinic, University of Erlangen, Erlangen, Germany (I.E.); Department of Neurosurgery Clinic, University of Jena, Jena, Germany (R.K.); Department of Neurology Clinic, Cologne University, Cologne, Germany (N.G.); Department of Neurology Clinic, TU Munich, Munich, Germany (F.S.-G.); Department of Neuropathology, University of Heidelberg, Heidelberg, Germany (A.v.D.); CCU Neuropathology, (C.H., A.v.D.); CCU Brain Tumor Immunology, DKFZ, all Heidelberg, Germany (M.P.); Department of Neuropathology, Heinrich Heine University, Düsseldorf, Germany (G.R.); DKTK partner site Essen/Düsseldorf, Düsseldorf, Germany (G.R.), Department of General Neurology, Tübingen, Germany (W.W., A.W., F.S.-G., M.P., M.W.), Department of Radiation Oncology, Tübingen, Germany (M.B.), Department of Medical Biometry, University Hospital Tübingen, Tübingen, Germany (C.M.)
| | - Norbert Galldiks
- Department of Neurology Clinic, University of Heidelberg, Heidelberg, Germany (W.W., A.W., M.P., B.W.); Clinical Cooperation Unit (CCU Neurooncology), German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany (W.W., B.W.); Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland (P.R., C.H., M.W.); Department of Neuropathology, Hannover Medical School, Hannover, Germany (C.H.); Department of Neurology, Regensburg University, Regensburg, Germany (P.H.); Department of Neurosurgery Clinic, Hannover Medical School, Hannover, Germany (M.N.); Department of Neurosurgery Clinic, Charité, Berlin, Germany (F.S., P.V.); Department of Neurosurgery, Heinrich Heine University, Düsseldorf, Germany (M.C.S.); Department of Neurology Clinic, Essen Medical Center, Essen, Germany (S.K.); Department of Neurosurgery Clinic, Saarland University, Homburg, Germany (R.K.); Department of Neurosurgery Clinic, University of Göttingen, Göttingen, Germany (F.S.); Department of Neurosurgery Clinic, University of Erlangen, Erlangen, Germany (I.E.); Department of Neurosurgery Clinic, University of Jena, Jena, Germany (R.K.); Department of Neurology Clinic, Cologne University, Cologne, Germany (N.G.); Department of Neurology Clinic, TU Munich, Munich, Germany (F.S.-G.); Department of Neuropathology, University of Heidelberg, Heidelberg, Germany (A.v.D.); CCU Neuropathology, (C.H., A.v.D.); CCU Brain Tumor Immunology, DKFZ, all Heidelberg, Germany (M.P.); Department of Neuropathology, Heinrich Heine University, Düsseldorf, Germany (G.R.); DKTK partner site Essen/Düsseldorf, Düsseldorf, Germany (G.R.), Department of General Neurology, Tübingen, Germany (W.W., A.W., F.S.-G., M.P., M.W.), Department of Radiation Oncology, Tübingen, Germany (M.B.), Department of Medical Biometry, University Hospital Tübingen, Tübingen, Germany (C.M.)
| | - Friederike Schmidt-Graf
- Department of Neurology Clinic, University of Heidelberg, Heidelberg, Germany (W.W., A.W., M.P., B.W.); Clinical Cooperation Unit (CCU Neurooncology), German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany (W.W., B.W.); Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland (P.R., C.H., M.W.); Department of Neuropathology, Hannover Medical School, Hannover, Germany (C.H.); Department of Neurology, Regensburg University, Regensburg, Germany (P.H.); Department of Neurosurgery Clinic, Hannover Medical School, Hannover, Germany (M.N.); Department of Neurosurgery Clinic, Charité, Berlin, Germany (F.S., P.V.); Department of Neurosurgery, Heinrich Heine University, Düsseldorf, Germany (M.C.S.); Department of Neurology Clinic, Essen Medical Center, Essen, Germany (S.K.); Department of Neurosurgery Clinic, Saarland University, Homburg, Germany (R.K.); Department of Neurosurgery Clinic, University of Göttingen, Göttingen, Germany (F.S.); Department of Neurosurgery Clinic, University of Erlangen, Erlangen, Germany (I.E.); Department of Neurosurgery Clinic, University of Jena, Jena, Germany (R.K.); Department of Neurology Clinic, Cologne University, Cologne, Germany (N.G.); Department of Neurology Clinic, TU Munich, Munich, Germany (F.S.-G.); Department of Neuropathology, University of Heidelberg, Heidelberg, Germany (A.v.D.); CCU Neuropathology, (C.H., A.v.D.); CCU Brain Tumor Immunology, DKFZ, all Heidelberg, Germany (M.P.); Department of Neuropathology, Heinrich Heine University, Düsseldorf, Germany (G.R.); DKTK partner site Essen/Düsseldorf, Düsseldorf, Germany (G.R.), Department of General Neurology, Tübingen, Germany (W.W., A.W., F.S.-G., M.P., M.W.), Department of Radiation Oncology, Tübingen, Germany (M.B.), Department of Medical Biometry, University Hospital Tübingen, Tübingen, Germany (C.M.)
| | - Michael Bamberg
- Department of Neurology Clinic, University of Heidelberg, Heidelberg, Germany (W.W., A.W., M.P., B.W.); Clinical Cooperation Unit (CCU Neurooncology), German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany (W.W., B.W.); Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland (P.R., C.H., M.W.); Department of Neuropathology, Hannover Medical School, Hannover, Germany (C.H.); Department of Neurology, Regensburg University, Regensburg, Germany (P.H.); Department of Neurosurgery Clinic, Hannover Medical School, Hannover, Germany (M.N.); Department of Neurosurgery Clinic, Charité, Berlin, Germany (F.S., P.V.); Department of Neurosurgery, Heinrich Heine University, Düsseldorf, Germany (M.C.S.); Department of Neurology Clinic, Essen Medical Center, Essen, Germany (S.K.); Department of Neurosurgery Clinic, Saarland University, Homburg, Germany (R.K.); Department of Neurosurgery Clinic, University of Göttingen, Göttingen, Germany (F.S.); Department of Neurosurgery Clinic, University of Erlangen, Erlangen, Germany (I.E.); Department of Neurosurgery Clinic, University of Jena, Jena, Germany (R.K.); Department of Neurology Clinic, Cologne University, Cologne, Germany (N.G.); Department of Neurology Clinic, TU Munich, Munich, Germany (F.S.-G.); Department of Neuropathology, University of Heidelberg, Heidelberg, Germany (A.v.D.); CCU Neuropathology, (C.H., A.v.D.); CCU Brain Tumor Immunology, DKFZ, all Heidelberg, Germany (M.P.); Department of Neuropathology, Heinrich Heine University, Düsseldorf, Germany (G.R.); DKTK partner site Essen/Düsseldorf, Düsseldorf, Germany (G.R.), Department of General Neurology, Tübingen, Germany (W.W., A.W., F.S.-G., M.P., M.W.), Department of Radiation Oncology, Tübingen, Germany (M.B.), Department of Medical Biometry, University Hospital Tübingen, Tübingen, Germany (C.M.)
| | - Guido Reifenberger
- Department of Neurology Clinic, University of Heidelberg, Heidelberg, Germany (W.W., A.W., M.P., B.W.); Clinical Cooperation Unit (CCU Neurooncology), German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany (W.W., B.W.); Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland (P.R., C.H., M.W.); Department of Neuropathology, Hannover Medical School, Hannover, Germany (C.H.); Department of Neurology, Regensburg University, Regensburg, Germany (P.H.); Department of Neurosurgery Clinic, Hannover Medical School, Hannover, Germany (M.N.); Department of Neurosurgery Clinic, Charité, Berlin, Germany (F.S., P.V.); Department of Neurosurgery, Heinrich Heine University, Düsseldorf, Germany (M.C.S.); Department of Neurology Clinic, Essen Medical Center, Essen, Germany (S.K.); Department of Neurosurgery Clinic, Saarland University, Homburg, Germany (R.K.); Department of Neurosurgery Clinic, University of Göttingen, Göttingen, Germany (F.S.); Department of Neurosurgery Clinic, University of Erlangen, Erlangen, Germany (I.E.); Department of Neurosurgery Clinic, University of Jena, Jena, Germany (R.K.); Department of Neurology Clinic, Cologne University, Cologne, Germany (N.G.); Department of Neurology Clinic, TU Munich, Munich, Germany (F.S.-G.); Department of Neuropathology, University of Heidelberg, Heidelberg, Germany (A.v.D.); CCU Neuropathology, (C.H., A.v.D.); CCU Brain Tumor Immunology, DKFZ, all Heidelberg, Germany (M.P.); Department of Neuropathology, Heinrich Heine University, Düsseldorf, Germany (G.R.); DKTK partner site Essen/Düsseldorf, Düsseldorf, Germany (G.R.), Department of General Neurology, Tübingen, Germany (W.W., A.W., F.S.-G., M.P., M.W.), Department of Radiation Oncology, Tübingen, Germany (M.B.), Department of Medical Biometry, University Hospital Tübingen, Tübingen, Germany (C.M.)
| | - Michael Platten
- Department of Neurology Clinic, University of Heidelberg, Heidelberg, Germany (W.W., A.W., M.P., B.W.); Clinical Cooperation Unit (CCU Neurooncology), German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany (W.W., B.W.); Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland (P.R., C.H., M.W.); Department of Neuropathology, Hannover Medical School, Hannover, Germany (C.H.); Department of Neurology, Regensburg University, Regensburg, Germany (P.H.); Department of Neurosurgery Clinic, Hannover Medical School, Hannover, Germany (M.N.); Department of Neurosurgery Clinic, Charité, Berlin, Germany (F.S., P.V.); Department of Neurosurgery, Heinrich Heine University, Düsseldorf, Germany (M.C.S.); Department of Neurology Clinic, Essen Medical Center, Essen, Germany (S.K.); Department of Neurosurgery Clinic, Saarland University, Homburg, Germany (R.K.); Department of Neurosurgery Clinic, University of Göttingen, Göttingen, Germany (F.S.); Department of Neurosurgery Clinic, University of Erlangen, Erlangen, Germany (I.E.); Department of Neurosurgery Clinic, University of Jena, Jena, Germany (R.K.); Department of Neurology Clinic, Cologne University, Cologne, Germany (N.G.); Department of Neurology Clinic, TU Munich, Munich, Germany (F.S.-G.); Department of Neuropathology, University of Heidelberg, Heidelberg, Germany (A.v.D.); CCU Neuropathology, (C.H., A.v.D.); CCU Brain Tumor Immunology, DKFZ, all Heidelberg, Germany (M.P.); Department of Neuropathology, Heinrich Heine University, Düsseldorf, Germany (G.R.); DKTK partner site Essen/Düsseldorf, Düsseldorf, Germany (G.R.), Department of General Neurology, Tübingen, Germany (W.W., A.W., F.S.-G., M.P., M.W.), Department of Radiation Oncology, Tübingen, Germany (M.B.), Department of Medical Biometry, University Hospital Tübingen, Tübingen, Germany (C.M.)
| | - Andreas von Deimling
- Department of Neurology Clinic, University of Heidelberg, Heidelberg, Germany (W.W., A.W., M.P., B.W.); Clinical Cooperation Unit (CCU Neurooncology), German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany (W.W., B.W.); Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland (P.R., C.H., M.W.); Department of Neuropathology, Hannover Medical School, Hannover, Germany (C.H.); Department of Neurology, Regensburg University, Regensburg, Germany (P.H.); Department of Neurosurgery Clinic, Hannover Medical School, Hannover, Germany (M.N.); Department of Neurosurgery Clinic, Charité, Berlin, Germany (F.S., P.V.); Department of Neurosurgery, Heinrich Heine University, Düsseldorf, Germany (M.C.S.); Department of Neurology Clinic, Essen Medical Center, Essen, Germany (S.K.); Department of Neurosurgery Clinic, Saarland University, Homburg, Germany (R.K.); Department of Neurosurgery Clinic, University of Göttingen, Göttingen, Germany (F.S.); Department of Neurosurgery Clinic, University of Erlangen, Erlangen, Germany (I.E.); Department of Neurosurgery Clinic, University of Jena, Jena, Germany (R.K.); Department of Neurology Clinic, Cologne University, Cologne, Germany (N.G.); Department of Neurology Clinic, TU Munich, Munich, Germany (F.S.-G.); Department of Neuropathology, University of Heidelberg, Heidelberg, Germany (A.v.D.); CCU Neuropathology, (C.H., A.v.D.); CCU Brain Tumor Immunology, DKFZ, all Heidelberg, Germany (M.P.); Department of Neuropathology, Heinrich Heine University, Düsseldorf, Germany (G.R.); DKTK partner site Essen/Düsseldorf, Düsseldorf, Germany (G.R.), Department of General Neurology, Tübingen, Germany (W.W., A.W., F.S.-G., M.P., M.W.), Department of Radiation Oncology, Tübingen, Germany (M.B.), Department of Medical Biometry, University Hospital Tübingen, Tübingen, Germany (C.M.)
| | - Christoph Meisner
- Department of Neurology Clinic, University of Heidelberg, Heidelberg, Germany (W.W., A.W., M.P., B.W.); Clinical Cooperation Unit (CCU Neurooncology), German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany (W.W., B.W.); Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland (P.R., C.H., M.W.); Department of Neuropathology, Hannover Medical School, Hannover, Germany (C.H.); Department of Neurology, Regensburg University, Regensburg, Germany (P.H.); Department of Neurosurgery Clinic, Hannover Medical School, Hannover, Germany (M.N.); Department of Neurosurgery Clinic, Charité, Berlin, Germany (F.S., P.V.); Department of Neurosurgery, Heinrich Heine University, Düsseldorf, Germany (M.C.S.); Department of Neurology Clinic, Essen Medical Center, Essen, Germany (S.K.); Department of Neurosurgery Clinic, Saarland University, Homburg, Germany (R.K.); Department of Neurosurgery Clinic, University of Göttingen, Göttingen, Germany (F.S.); Department of Neurosurgery Clinic, University of Erlangen, Erlangen, Germany (I.E.); Department of Neurosurgery Clinic, University of Jena, Jena, Germany (R.K.); Department of Neurology Clinic, Cologne University, Cologne, Germany (N.G.); Department of Neurology Clinic, TU Munich, Munich, Germany (F.S.-G.); Department of Neuropathology, University of Heidelberg, Heidelberg, Germany (A.v.D.); CCU Neuropathology, (C.H., A.v.D.); CCU Brain Tumor Immunology, DKFZ, all Heidelberg, Germany (M.P.); Department of Neuropathology, Heinrich Heine University, Düsseldorf, Germany (G.R.); DKTK partner site Essen/Düsseldorf, Düsseldorf, Germany (G.R.), Department of General Neurology, Tübingen, Germany (W.W., A.W., F.S.-G., M.P., M.W.), Department of Radiation Oncology, Tübingen, Germany (M.B.), Department of Medical Biometry, University Hospital Tübingen, Tübingen, Germany (C.M.)
| | - Benedikt Wiestler
- Department of Neurology Clinic, University of Heidelberg, Heidelberg, Germany (W.W., A.W., M.P., B.W.); Clinical Cooperation Unit (CCU Neurooncology), German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany (W.W., B.W.); Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland (P.R., C.H., M.W.); Department of Neuropathology, Hannover Medical School, Hannover, Germany (C.H.); Department of Neurology, Regensburg University, Regensburg, Germany (P.H.); Department of Neurosurgery Clinic, Hannover Medical School, Hannover, Germany (M.N.); Department of Neurosurgery Clinic, Charité, Berlin, Germany (F.S., P.V.); Department of Neurosurgery, Heinrich Heine University, Düsseldorf, Germany (M.C.S.); Department of Neurology Clinic, Essen Medical Center, Essen, Germany (S.K.); Department of Neurosurgery Clinic, Saarland University, Homburg, Germany (R.K.); Department of Neurosurgery Clinic, University of Göttingen, Göttingen, Germany (F.S.); Department of Neurosurgery Clinic, University of Erlangen, Erlangen, Germany (I.E.); Department of Neurosurgery Clinic, University of Jena, Jena, Germany (R.K.); Department of Neurology Clinic, Cologne University, Cologne, Germany (N.G.); Department of Neurology Clinic, TU Munich, Munich, Germany (F.S.-G.); Department of Neuropathology, University of Heidelberg, Heidelberg, Germany (A.v.D.); CCU Neuropathology, (C.H., A.v.D.); CCU Brain Tumor Immunology, DKFZ, all Heidelberg, Germany (M.P.); Department of Neuropathology, Heinrich Heine University, Düsseldorf, Germany (G.R.); DKTK partner site Essen/Düsseldorf, Düsseldorf, Germany (G.R.), Department of General Neurology, Tübingen, Germany (W.W., A.W., F.S.-G., M.P., M.W.), Department of Radiation Oncology, Tübingen, Germany (M.B.), Department of Medical Biometry, University Hospital Tübingen, Tübingen, Germany (C.M.)
| | - Michael Weller
- Department of Neurology Clinic, University of Heidelberg, Heidelberg, Germany (W.W., A.W., M.P., B.W.); Clinical Cooperation Unit (CCU Neurooncology), German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany (W.W., B.W.); Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland (P.R., C.H., M.W.); Department of Neuropathology, Hannover Medical School, Hannover, Germany (C.H.); Department of Neurology, Regensburg University, Regensburg, Germany (P.H.); Department of Neurosurgery Clinic, Hannover Medical School, Hannover, Germany (M.N.); Department of Neurosurgery Clinic, Charité, Berlin, Germany (F.S., P.V.); Department of Neurosurgery, Heinrich Heine University, Düsseldorf, Germany (M.C.S.); Department of Neurology Clinic, Essen Medical Center, Essen, Germany (S.K.); Department of Neurosurgery Clinic, Saarland University, Homburg, Germany (R.K.); Department of Neurosurgery Clinic, University of Göttingen, Göttingen, Germany (F.S.); Department of Neurosurgery Clinic, University of Erlangen, Erlangen, Germany (I.E.); Department of Neurosurgery Clinic, University of Jena, Jena, Germany (R.K.); Department of Neurology Clinic, Cologne University, Cologne, Germany (N.G.); Department of Neurology Clinic, TU Munich, Munich, Germany (F.S.-G.); Department of Neuropathology, University of Heidelberg, Heidelberg, Germany (A.v.D.); CCU Neuropathology, (C.H., A.v.D.); CCU Brain Tumor Immunology, DKFZ, all Heidelberg, Germany (M.P.); Department of Neuropathology, Heinrich Heine University, Düsseldorf, Germany (G.R.); DKTK partner site Essen/Düsseldorf, Düsseldorf, Germany (G.R.), Department of General Neurology, Tübingen, Germany (W.W., A.W., F.S.-G., M.P., M.W.), Department of Radiation Oncology, Tübingen, Germany (M.B.), Department of Medical Biometry, University Hospital Tübingen, Tübingen, Germany (C.M.)
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Mullany LE, Herrick JS, Wolff RK, Stevens JR, Slattery ML. Association of cigarette smoking and microRNA expression in rectal cancer: Insight into tumor phenotype. Cancer Epidemiol 2016; 45:98-107. [PMID: 27780077 DOI: 10.1016/j.canep.2016.10.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [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: 06/20/2016] [Revised: 09/27/2016] [Accepted: 10/17/2016] [Indexed: 02/08/2023]
Abstract
Smoking is known to influence messenger RNA (mRNA) expression in colorectal cancer (CRC) cases. As microRNAs (miRNAs) are known repressors of mRNAs, we hypothesize that smoking may influence miRNA expression, thus altering mRNA expression. Our sample consisted of 1447 CRC cases that had normal colorectal mucosa and carcinoma miRNA data and lifestyle data. We examined current smoking, current versus never and former versus never (C/F/N) smoking1, and pack-years smoked with miRNA expression in normal mucosa as well as differential miRNA expression between paired normal and carcinoma tissue for colon and rectal tissue to determine associations between smoking and miRNA expression. We adjusted for multiple comparisons using the Benjamini Hochberg false discovery rate (FDR). Significant associations were seen for rectal differential miRNA expression only. We analyzed miRNAs significantly associated with smoking with CIMP and MSI status, using a polytomous logistic regression. Two hundred and thirty-one miRNAs were differentially expressed with current smoking, 172 with C/F/N, and 206 with pack-years smoked; 111 were associated with all three. Forty-three miRNAs were unique to current smoking, 14 were unique to C/F/N and 57 were unique to pack years smoked. Of the 306 unique miRNAs associated with cigarette smoking, 41 were inversely associated and 200 were directly associated with CIMP high or MSI tumor molecular phenotype for either colon or rectal cancer. Our results suggest that cigarette smoking can alter miRNA expression and, given associations with CIMP high and MSI tumor molecular phenotype, it is possible that smoking influences tumor phenotype through altered miRNA expression.
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Affiliation(s)
- Lila E Mullany
- Department of Internal Medicine, University of Utah, 383 Colorow Bldg., Salt Lake City, UT 84108, USA.
| | - Jennifer S Herrick
- Department of Internal Medicine, University of Utah, 383 Colorow Bldg., Salt Lake City, UT 84108, USA.
| | - Roger K Wolff
- Department of Internal Medicine, University of Utah, 383 Colorow Bldg., Salt Lake City, UT 84108, USA.
| | - John R Stevens
- Department of Mathematics and Statistics, Utah State University, 3900 Old Main Hill, Logan, UT 84322, USA.
| | - Martha L Slattery
- Department of Internal Medicine, University of Utah, 383 Colorow Bldg., Salt Lake City, UT 84108, USA.
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Abstract
Epigenetics is a relatively recent field of molecular biology that has arisen over the past 25 years. Cancer is now understood to be a disease of widespread epigenetic dysregulation that interacts extensively with underlying genetic mutations. The development of drugs targeting these processes has rapidly progressed; with several drugs already FDA approved as first-line therapy in hematological malignancies. Gastrointestinal (GI) cancers possess high degrees of epigenetic dysregulation, exemplified by subtypes such as CpG island methylator phenotype (CIMP), and the potential benefit of epigenetic therapy in these cancers is evident. The application of epigenetic drugs in solid tumors, including GI cancers, is just emerging, with increased understanding of the cancer epigenome. In this review, we provide a brief overview of cancer epigenetics and the epigenetic targets of therapy including deoxyribonucleic acid (DNA) methylation, histone modifications, and chromatin remodeling. We discuss the epigenetic drugs currently in use, with a focus on DNA methyltransferase (DNMT) and histone deacetylase (HDAC) inhibitors, and explain the pharmacokinetic and mechanistic challenges in their application. We present the strategies employed in incorporating these drugs into the treatment of GI cancers, and explain the concept of the cancer stem cell in epigenetic reprogramming and reversal of chemo resistance. We discuss the most promising combination strategies in GI cancers including: (1) epigenetic sensitization to radiotherapy, (2) epigenetic sensitization to cytotoxic chemotherapy, and (3) epigenetic immune modulation and priming for immune therapy. Finally, we present preclinical and clinical trial data employing these strategies thus far in various GI cancers including colorectal, esophageal, gastric, and pancreatic cancer.
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Affiliation(s)
- Eihab Abdelfatah
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Zachary Kerner
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nainika Nanda
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA,West Virginia University School of Medicine, Morgantown, WV, USA
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McCarthy D, Pulverer W, Weinhaeusel A, Diago OR, Hogan DJ, Ostertag D, Hanna MM. MethylMeter(®): bisulfite-free quantitative and sensitive DNA methylation profiling and mutation detection in FFPE samples. Epigenomics 2016; 8:747-65. [PMID: 27337298 DOI: 10.2217/epi-2016-0004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM Development of a sensitive method for DNA methylation profiling and associated mutation detection in clinical samples. MATERIALS & METHODS Formalin-fixed and paraffin-embedded tumors received by clinical laboratories often contain insufficient DNA for analysis with bisulfite or methylation sensitive restriction enzymes-based methods. To increase sensitivity, methyl-CpG DNA capture and Coupled Abscription PCR Signaling detection were combined in a new assay, MethylMeter(®). Gliomas were analyzed for MGMT methylation, glioma CpG island methylator phenotype and IDH1 R132H. RESULTS MethylMeter had 100% assay success rate measuring all five biomarkers in formalin-fixed and paraffin-embedded tissue. MGMT methylation results were supported by survival and mRNA expression data. CONCLUSION MethylMeter is a sensitive and quantitative method for multitarget DNA methylation profiling and associated mutation detection. The MethylMeter-based GliomaSTRAT assay measures methylation of four targets and one mutation to simultaneously grade gliomas and predict their response to temozolomide. This information is clinically valuable in management of gliomas.
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Affiliation(s)
- David McCarthy
- Ribomed Biotechnologies Inc., 3469 Kurtz St., San Diego, CA 92110, USA
| | - Walter Pulverer
- Molecular Diagnostics, Health & Environment Department, Austrian Institute of Technology, Muthgasse 11, 1190 Vienna, Austria
| | - Andreas Weinhaeusel
- Molecular Diagnostics, Health & Environment Department, Austrian Institute of Technology, Muthgasse 11, 1190 Vienna, Austria
| | - Oscar R Diago
- Tocagen Inc., 3030 Bunker Hill Street, Suite 230; San Diego, CA 92109, USA
| | - Daniel J Hogan
- Tocagen Inc., 3030 Bunker Hill Street, Suite 230; San Diego, CA 92109, USA
| | - Derek Ostertag
- Tocagen Inc., 3030 Bunker Hill Street, Suite 230; San Diego, CA 92109, USA
| | - Michelle M Hanna
- Ribomed Biotechnologies Inc., 3469 Kurtz St., San Diego, CA 92110, USA
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Abstract
Adult diffuse gliomas account for the majority of primary malignant brain tumours, and are in most cases lethal. Current therapies are often only marginally effective, and improved options will almost certainly benefit from further insight into the various processes contributing to gliomagenesis and pathology. While molecular characterization of these tumours classifies them on the basis of genetic alterations and chromosomal abnormalities, DNA methylation patterns are increasingly understood to play a role in glioma pathogenesis. Indeed, a subset of gliomas associated with improved survival is characterized by the glioma CpG island methylator phenotype (G-CIMP), which can be induced by the expression of mutant isocitrate dehydrogenase (IDH1/2). Aberrant methylation of particular genes or regulatory elements, within the context of G-CIMP-positive and/or negative tumours, has also been shown to be associated with differential survival. In this review, we provide an overview of the current knowledge regarding the role of DNA methylation in adult diffuse gliomas. In particular, we discuss IDH mutations and G-CIMP, MGMT promoter methylation, DNA methylation-mediated microRNA regulation and aberrant methylation of specific genes or groups of genes.
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48
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Gao F, Wang J, Ji G, Liu S, Yao Y, Wang T, Wu H, Xia Y, Gong D, Jiang H, Yang H, Zhang X. Clustering of Cancer Cell Lines Using A Promoter- Targeted Liquid Hybridization Capture-Based Bisulfite Sequencing Approach. Technol Cancer Res Treat 2016; 14:383-94. [PMID: 26269607 DOI: 10.1177/1533034614500416] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [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: 11/16/2022] Open
Abstract
DNA methylation plays a significant role in assuring cell identity, thus potentiating its application in molecular classification of cancers in respect to tissue-origins or clinically and etiologically distinct subtypes. In this study, we optimized our liquid hybridization capture-based bisulfite sequencing (LHC-BS) approach on the gene promoter regions of 11 cell lines. Our results indicated that promoter methylomes could not only cluster cancer cell lines with respect to tissue origins but also differentiate cancer subtypes based on CpG island methylator phenotype (CIMP). Promoter-targeted LHC-BS as means for comprehensive screening and classifying cancer cells with promoter methylomes provided a powerful strategy for further complex clinical studies.
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Affiliation(s)
- Fei Gao
- Science & Technology Department, BGI-Shenzhen, Shenzhen 518083, China These authors contributed equally to this work.
| | - Junwen Wang
- Science & Technology Department, BGI-Shenzhen, Shenzhen 518083, China These authors contributed equally to this work
| | - Guanyu Ji
- Science & Technology Department, BGI-Shenzhen, Shenzhen 518083, China These authors contributed equally to this work
| | - Siyang Liu
- Science & Technology Department, BGI-Shenzhen, Shenzhen 518083, China
| | - Yu Yao
- Science & Technology Department, BGI-Shenzhen, Shenzhen 518083, China
| | - Tong Wang
- Science & Technology Department, BGI-Shenzhen, Shenzhen 518083, China
| | - Honglong Wu
- Science & Technology Department, BGI-Shenzhen, Shenzhen 518083, China
| | - Yudong Xia
- Science & Technology Department, BGI-Shenzhen, Shenzhen 518083, China
| | - Desheng Gong
- Science & Technology Department, BGI-Shenzhen, Shenzhen 518083, China
| | - Hui Jiang
- Science & Technology Department, BGI-Shenzhen, Shenzhen 518083, China
| | - Huanming Yang
- Science & Technology Department, BGI-Shenzhen, Shenzhen 518083, China King Abdulaziz University, Jeddah, Saudi Arabia James D. Watson Institute of Genome Science, Hangzhou, China
| | - Xiuqing Zhang
- The Guangdong Enterprise Key Laboratory of Human Disease Genomics, BGI-Shenzhen, Shenzhen, China
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Murcia O, Juárez M, Hernández-Illán E, Egoavil C, Giner-Calabuig M, Rodríguez-Soler M, Jover R. Serrated colorectal cancer: Molecular classification, prognosis, and response to chemotherapy. World J Gastroenterol 2016; 22:3516-3530. [PMID: 27053844 PMCID: PMC4814638 DOI: 10.3748/wjg.v22.i13.3516] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 12/04/2015] [Accepted: 01/30/2016] [Indexed: 02/06/2023] Open
Abstract
Molecular advances support the existence of an alternative pathway of colorectal carcinogenesis that is based on the hypermethylation of specific DNA regions that silences tumor suppressor genes. This alternative pathway has been called the serrated pathway due to the serrated appearance of tumors in histological analysis. New classifications for colorectal cancer (CRC) were proposed recently based on genetic profiles that show four types of molecular alterations: BRAF gene mutations, KRAS gene mutations, microsatellite instability, and hypermethylation of CpG islands. This review summarizes what is known about the serrated pathway of CRC, including CRC molecular and clinical features, prognosis, and response to chemotherapy.
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50
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Abstract
Neuroblastoma is a very heterogeneous tumor of childhood. The clinical spectra range from very aggressive metastatic disease to spontaneous regression, even without therapy. Aberrant DNA methylation pattern is a common feature of most cancers. For neuroblastoma, it has been demonstrated both for single genes as well as genome-wide, where a so-called methylator phenotype has been described. Here, we present a study using Illumina 450K methylation arrays on 60 neuroblastoma tumors. We show that aggressive tumors, characterized by International Neuroblastoma Risk Group (INRG) as stage M, are hypermethylated compared to low-grade tumors. On the contrary, INRG stage L tumors display more non-CpG methylation. The genes with the highest number of hypermethylated CpG sites in INRG M tumors are TERT, PCDHGA4, DLX5, and DLX6-AS1. Gene ontology analysis showed a representation of neuronal tumor relevant gene functions among the differentially methylated genes. For validation, we used a set of independent tumors previously analyzed with the Illumina 27K methylation arrays, which confirmed the differentially methylated sites. Top candidate genes with aberrant methylation were analyzed for altered gene expression through the R2 platform (http://r2.amc.nl), and for correlations between methylation and gene expression in a public dataset. Altered expression in nonsurvivors was found for the genes B3GALT4 and KIAA1949, CLIC5, DLX6-AS, TERT, and PIRT, and strongest correlations were found for TRIM36, KIAA0513, and PIRT. Our data indicate that methylation profiling can be used for patient stratification and informs on epigenetically deregulated genes with the potential of increasing our knowledge about the underlying mechanisms of tumor development.
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Affiliation(s)
- Maja Olsson
- a Sahlgrenska Cancer Center , Department of Pathology , Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg , Sweden
| | - Stephan Beck
- b Department of Cancer Biology , UCL Cancer Institute, University College London , UK
| | - Per Kogner
- c Childhood Cancer Research Unit , Department of Woman and Child Health , Karolinska Institute, Karolinska Hospital , Sweden
| | - Tommy Martinsson
- d Department of Clinical Genetics , Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg , Sweden
| | - Helena Carén
- a Sahlgrenska Cancer Center , Department of Pathology , Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg , Sweden
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