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Chung FFL, Maldonado SG, Nemc A, Bouaoun L, Cahais V, Cuenin C, Salle A, Johnson T, Ergüner B, Laplana M, Datlinger P, Jeschke J, Weiderpass E, Kristensen V, Delaloge S, Fuks F, Risch A, Ghantous A, Plass C, Bock C, Kaaks R, Herceg Z. Buffy coat signatures of breast cancer risk in a prospective cohort study. Clin Epigenetics 2023; 15:102. [PMID: 37309009 PMCID: PMC10262593 DOI: 10.1186/s13148-023-01509-6] [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: 01/30/2023] [Accepted: 05/20/2023] [Indexed: 06/14/2023] Open
Abstract
BACKGROUND Epigenetic alterations are a near-universal feature of human malignancy and have been detected in malignant cells as well as in easily accessible specimens such as blood and urine. These findings offer promising applications in cancer detection, subtyping, and treatment monitoring. However, much of the current evidence is based on findings in retrospective studies and may reflect epigenetic patterns that have already been influenced by the onset of the disease. METHODS Studying breast cancer, we established genome-scale DNA methylation profiles of prospectively collected buffy coat samples (n = 702) from a case-control study nested within the EPIC-Heidelberg cohort using reduced representation bisulphite sequencing (RRBS). RESULTS We observed cancer-specific DNA methylation events in buffy coat samples. Increased DNA methylation in genomic regions associated with SURF6 and REXO1/CTB31O20.3 was linked to the length of time to diagnosis in the prospectively collected buffy coat DNA from individuals who subsequently developed breast cancer. Using machine learning methods, we piloted a DNA methylation-based classifier that predicted case-control status in a held-out validation set with 76.5% accuracy, in some cases up to 15 years before clinical diagnosis of the disease. CONCLUSIONS Taken together, our findings suggest a model of gradual accumulation of cancer-associated DNA methylation patterns in peripheral blood, which may be detected long before clinical manifestation of cancer. Such changes may provide useful markers for risk stratification and, ultimately, personalized cancer prevention.
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Affiliation(s)
- Felicia Fei-Lei Chung
- International Agency for Research On Cancer (IARC), 25 avenue Tony Garnier, CS 90627, 69366, Lyon, France.
- Department of Medical Sciences, School of Medical and Life Sciences, Sunway University, 5, Jalan Universiti, Bandar Sunway, 47500, Subang Jaya, Selangor, Malaysia.
| | | | - Amelie Nemc
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Liacine Bouaoun
- International Agency for Research On Cancer (IARC), 25 avenue Tony Garnier, CS 90627, 69366, Lyon, France
| | - Vincent Cahais
- International Agency for Research On Cancer (IARC), 25 avenue Tony Garnier, CS 90627, 69366, Lyon, France
| | - Cyrille Cuenin
- International Agency for Research On Cancer (IARC), 25 avenue Tony Garnier, CS 90627, 69366, Lyon, France
| | - Aurelie Salle
- International Agency for Research On Cancer (IARC), 25 avenue Tony Garnier, CS 90627, 69366, Lyon, France
| | - Theron Johnson
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bekir Ergüner
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Marina Laplana
- Division of Cancer Epigenomics, German Cancer Research Center, Heidelberg, Germany
- Department of Basic Medical Sciences, University of Lleida, IRBLleida, 25198, Lleida, Spain
| | - Paul Datlinger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Jana Jeschke
- Laboratory of Cancer Epigenetics, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Elisabete Weiderpass
- International Agency for Research On Cancer (IARC), 25 avenue Tony Garnier, CS 90627, 69366, Lyon, France
| | - Vessela Kristensen
- Faculty of Medicine, Institute for Clinical Epidemiology and Molecular Biology, University of Oslo, Oslo, Norway
| | - Suzette Delaloge
- Department of Cancer Medicine, Institut Gustave Roussy, Villejuif, France
| | - François Fuks
- Laboratory of Cancer Epigenetics, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Angela Risch
- Division of Cancer Epigenomics, German Cancer Research Center, Heidelberg, Germany
- Department of Biosciences and Medical Biology, Allergy-Cancer-BioNano Research Centre, University of Salzburg, 5020, Salzburg, Austria
- Cancer Cluster Salzburg, Salzburg, Austria
| | - Akram Ghantous
- International Agency for Research On Cancer (IARC), 25 avenue Tony Garnier, CS 90627, 69366, Lyon, France
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center, Heidelberg, Germany
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Medical University of Vienna, Institute of Artificial Intelligence, Center for Medical Data Science, Vienna, Austria
| | - Rudolf Kaaks
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Zdenko Herceg
- International Agency for Research On Cancer (IARC), 25 avenue Tony Garnier, CS 90627, 69366, Lyon, France.
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Bizet M, Defrance M, Calonne E, Bontempi G, Sotiriou C, Fuks F, Jeschke J. Improving Infinium MethylationEPIC data processing: re-annotation of enhancers and long noncoding RNA genes and benchmarking of normalization methods. Epigenetics 2022; 17:2434-2454. [DOI: 10.1080/15592294.2022.2135201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Martin Bizet
- Laboratory of Cancer Epigenetics, Faculty of Medicine, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Matthieu Defrance
- Interuniversity Institute of Bioinformatics in Brussels (IB2), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Emilie Calonne
- Laboratory of Cancer Epigenetics, Faculty of Medicine, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Gianluca Bontempi
- Interuniversity Institute of Bioinformatics in Brussels (IB2), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | | | - François Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Institut Jules Bordet, ULB, Brussels, Belgium
| | - Jana Jeschke
- Laboratory of Cancer Epigenetics, Faculty of Medicine, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Institut Jules Bordet, ULB, Brussels, Belgium
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3
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Bizet M, Defrance M, Calonne E, Bontempi G, Fuks F, Jeschke J. Abstract 6283: Reannotation and normalisation of Infinium 850k data for improved analysis of methylation at enhancers and non-coding RNAs. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-6283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
In this study, we evaluated the MethylationEPIC BeadChip (850k) technology for enhancer methylation analysis with respect to RRBS, both high-throughput technologies commonly used to screen large patient cohorts. We developed and applied a new approach to re-annotate the 850k data, which greatly improved the association of probes to enhancers and show that 850k targets more enhancers than RRBS. We further investigated the reproducibility of the two technologies and applied various existing normalization methods to 850k data that reduce variability between replicates and variability with other technologies. We thereby showed that normalization methods developed for 450k greatly reduced variability in 850k data to a level below that of highly variable RRBS data. We finally performed differential methylation analysis with 850k data from breast cancer samples applying our new re-annotation method and highlight that the majority of differentially methylated cytosines were detected with probes specific to the 850k mapping to enhancers, confirming the deregulation of enhancer methylation in breast cancer. In summary, our study provides a new annotation for the 850k array, which greatly increases the number of cytosines mapping to enhancers and therefore allows for the improved analysis of enhancer methylation. Overall, we conclude that the 850k array allows for detection of methylation changes in regions not covered by previous Infinium arrays and is the best choice, as compared to RRBS, for high-throughput analysis of enhancer methylation in large clinical cohorts.
Citation Format: Martin Bizet, Matthieu Defrance, Emilie Calonne, Gianluca Bontempi, François Fuks, Jana Jeschke. Reannotation and normalisation of Infinium 850k data for improved analysis of methylation at enhancers and non-coding RNAs [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6283.
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Affiliation(s)
- Martin Bizet
- 1Université libre de Bruxelles (ULB), Brussels, Belgium
| | | | | | | | - François Fuks
- 1Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Jana Jeschke
- 1Université libre de Bruxelles (ULB), Brussels, Belgium
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4
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Jeschke J, Collignon E, Al Wardi C, Krayem M, Bizet M, Jia Y, Garaud S, Wimana Z, Calonne E, Hassabi B, Morandini R, Deplus R, Putmans P, Dube G, Singh NK, Koch A, Shostak K, Rizzotto L, Ross RL, Desmedt C, Bareche Y, Rothé F, Lehmann-Che J, Duterque-Coquillaud M, Leroy X, Menschaert G, Teixeira L, Guo M, Limbach PA, Close P, Chariot A, Leucci E, Ghanem G, Yuan BF, Willard-Gallo K, Sotiriou C, Marine JC, Fuks F. Downregulation of the FTO m 6A RNA demethylase promotes EMT-mediated progression of epithelial tumors and sensitivity to Wnt inhibitors. Nat Cancer 2021; 2:611-628. [PMID: 35121941 PMCID: PMC10734094 DOI: 10.1038/s43018-021-00223-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 05/17/2021] [Indexed: 02/05/2023]
Abstract
Post-transcriptional modifications of RNA constitute an emerging regulatory layer of gene expression. The demethylase fat mass- and obesity-associated protein (FTO), an eraser of N6-methyladenosine (m6A), has been shown to play a role in cancer, but its contribution to tumor progression and the underlying mechanisms remain unclear. Here, we report widespread FTO downregulation in epithelial cancers associated with increased invasion, metastasis and worse clinical outcome. Both in vitro and in vivo, FTO silencing promotes cancer growth, cell motility and invasion. In human-derived tumor xenografts (PDXs), FTO pharmacological inhibition favors tumorigenesis. Mechanistically, we demonstrate that FTO depletion elicits an epithelial-to-mesenchymal transition (EMT) program through increased m6A and altered 3'-end processing of key mRNAs along the Wnt signaling cascade. Accordingly, FTO knockdown acts via EMT to sensitize mouse xenografts to Wnt inhibition. We thus identify FTO as a key regulator, across epithelial cancers, of Wnt-triggered EMT and tumor progression and reveal a therapeutically exploitable vulnerability of FTO-low tumors.
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Affiliation(s)
- Jana Jeschke
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Evelyne Collignon
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Clémence Al Wardi
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Mohammad Krayem
- Laboratory of Oncology and Experimental Surgery, Institut Jules Bordet, ULB, Brussels, Belgium
| | - Martin Bizet
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Yan Jia
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
- Department of Breast Oncology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Soizic Garaud
- Molecular Immunology Laboratory, Institut Jules Bordet, ULB, Brussels, Belgium
| | - Zéna Wimana
- Laboratory of Oncology and Experimental Surgery, Institut Jules Bordet, ULB, Brussels, Belgium
- Department of Nuclear Medicine, Institut Jules Bordet, ULB, Brussels, Belgium
| | - Emilie Calonne
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Bouchra Hassabi
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Renato Morandini
- Laboratory of Oncology and Experimental Surgery, Institut Jules Bordet, ULB, Brussels, Belgium
| | - Rachel Deplus
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Pascale Putmans
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Gaurav Dube
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Nitesh Kumar Singh
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Alexander Koch
- Department of Pathology, Maastricht UMC, Maastricht, the Netherlands
| | - Kateryna Shostak
- Laboratory of Medical Chemistry, GIGA Stem Cells, University of Liège, Liège, Belgium
| | - Lara Rizzotto
- Trace, LKI Leuven Cancer Institute, KU Leuven, Leuven, Belgium
| | - Robert L Ross
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | - Christine Desmedt
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet, U-CRC, ULB, Brussels, Belgium
| | - Yacine Bareche
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet, U-CRC, ULB, Brussels, Belgium
| | - Françoise Rothé
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet, U-CRC, ULB, Brussels, Belgium
| | - Jacqueline Lehmann-Che
- Pathophysiology of Breast Cancer Team, Université de Paris, INSERM U976, HIPI, Paris, France
- Breast Disease Unit and Molecular Oncology Unit, AP-HP, Hôpital Saint-Louis, Paris, France
| | - Martine Duterque-Coquillaud
- Université Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR9020-UMR-S 1277, CANTHER, Lille, France
| | - Xavier Leroy
- Université Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR9020-UMR-S 1277, CANTHER, Lille, France
- Department of Pathology, CHU Lille, Université Lille, Lille, France
| | - Gerben Menschaert
- Biobix, Laboratory of Bioinformatics and Computational Genomics, Ghent University, Ghent, Belgium
| | - Luis Teixeira
- Pathophysiology of Breast Cancer Team, Université de Paris, INSERM U976, HIPI, Paris, France
- Breast Disease Unit and Molecular Oncology Unit, AP-HP, Hôpital Saint-Louis, Paris, France
| | - Mingzhou Guo
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, Beijing, China
| | - Patrick A Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | - Pierre Close
- Laboratory of Cancer Signaling, GIGA Stem Cells, University of Liège, Liège, Belgium
- WELBIO, University of Liège, Liège, Belgium
| | - Alain Chariot
- Laboratory of Medical Chemistry, GIGA Stem Cells, University of Liège, Liège, Belgium
- WELBIO, University of Liège, Liège, Belgium
| | - Eleonora Leucci
- Trace, LKI Leuven Cancer Institute, KU Leuven, Leuven, Belgium
- Laboratory of RNA Cancer Biology, Department of Oncology, LKI, KU Leuven, Leuven, Belgium
| | - Ghanem Ghanem
- Laboratory of Oncology and Experimental Surgery, Institut Jules Bordet, ULB, Brussels, Belgium
| | - Bi-Feng Yuan
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, China
| | - Karen Willard-Gallo
- Molecular Immunology Laboratory, Institut Jules Bordet, ULB, Brussels, Belgium
| | - Christos Sotiriou
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet, U-CRC, ULB, Brussels, Belgium
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, VIB, KU Leuven, Leuven, Belgium
- Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - François Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium.
- WELBIO, Université Libre de Bruxelles (ULB), Brussels, Belgium.
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Siebenkäs C, Chiappinelli KB, Guzzetta AA, Sharma A, Jeschke J, Vatapalli R, Baylin SB, Ahuja N. Correction: Inhibiting DNA methylation activates cancer testis antigens and expression of the antigen processing and presentation machinery in colon and ovarian cancer cells. PLoS One 2020; 15:e0243944. [PMID: 33301506 PMCID: PMC7728177 DOI: 10.1371/journal.pone.0243944] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Koch A, Jeschke J, Van Criekinge W, van Engeland M, De Meyer T. MEXPRESS update 2019. Nucleic Acids Res 2020; 47:W561-W565. [PMID: 31114869 PMCID: PMC6602516 DOI: 10.1093/nar/gkz445] [Citation(s) in RCA: 151] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 05/07/2019] [Accepted: 05/15/2019] [Indexed: 01/22/2023] Open
Abstract
The recent growth in the number of publicly available cancer omics databases has been accompanied by the development of various tools that allow researchers to visually explore these data. In 2015, we built MEXPRESS, an online tool for the integration and visualization of gene expression, DNA methylation and clinical data from The Cancer Genome Atlas (TCGA), a large collection of publicly available multi-omics cancer data. MEXPRESS addresses the need for an easy-to-use, interactive application that allows researchers to identify dysregulated genes and their clinical relevance in cancer. Furthermore, while other tools typically do not support integrated visualization of expression and DNA methylation data in combination with the precise genomic location of the methylation, MEXPRESS is unique in how it depicts these diverse data types together. Motivated by the large number of users MEXPRESS has managed to attract over the past 3 years and the recent migration of all TCGA data to a new data portal, we developed a new version of MEXPRESS (https://mexpress.be). It contains the latest TCGA data, additional types of omics and clinical data and extra functionality, allowing users to explore mechanisms of gene dysregulation beyond expression and DNA methylation.
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Affiliation(s)
- Alexander Koch
- Department of Pathology, GROW School for Oncology and Developmental Biology, Maastricht University, 6229 ER Maastricht, the Netherlands
| | - Jana Jeschke
- Laboratory of Cancer Epigenetics, Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Wim Van Criekinge
- Department of Data Analysis and Mathematical Modelling, Ghent University, 9000 Ghent, Belgium
| | - Manon van Engeland
- Department of Pathology, GROW School for Oncology and Developmental Biology, Maastricht University, 6229 ER Maastricht, the Netherlands
| | - Tim De Meyer
- Department of Data Analysis and Mathematical Modelling, Ghent University, 9000 Ghent, Belgium.,CRIG - Cancer Research Institute Ghent, Ghent University, 9000 Ghent, Belgium
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Jeschke J, Bizet M, Desmedt C, Calonne E, Dedeurwaerder S, Garaud S, Koch A, Larsimont D, Salgado R, Van den Eynden G, Willard Gallo K, Bontempi G, Defrance M, Sotiriou C, Fuks F. DNA methylation-based immune response signature improves patient diagnosis in multiple cancers. J Clin Invest 2017; 127:3090-3102. [PMID: 28714863 DOI: 10.1172/jci91095] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 05/26/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The tumor immune response is increasingly associated with better clinical outcomes in breast and other cancers. However, the evaluation of tumor-infiltrating lymphocytes (TILs) relies on histopathological measurements with limited accuracy and reproducibility. Here, we profiled DNA methylation markers to identify a methylation of TIL (MeTIL) signature that recapitulates TIL evaluations and their prognostic value for long-term outcomes in breast cancer (BC). METHODS MeTIL signature scores were correlated with clinical endpoints reflecting overall or disease-free survival and a pathologic complete response to preoperative anthracycline therapy in 3 BC cohorts from the Jules Bordet Institute in Brussels and in other cancer types from The Cancer Genome Atlas. RESULTS The MeTIL signature measured TIL distributions in a sensitive manner and predicted survival and response to chemotherapy in BC better than did histopathological assessment of TILs or gene expression-based immune markers, respectively. The MeTIL signature also improved the prediction of survival in other malignancies, including melanoma and lung cancer. Furthermore, the MeTIL signature predicted differences in survival for malignancies in which TILs were not known to have a prognostic value. Finally, we showed that MeTIL markers can be determined by bisulfite pyrosequencing of small amounts of DNA from formalin-fixed, paraffin-embedded tumor tissue, supporting clinical applications for this methodology. CONCLUSIONS This study highlights the power of DNA methylation to evaluate tumor immune responses and the potential of this approach to improve the diagnosis and treatment of breast and other cancers. FUNDING This work was funded by the Fonds National de la Recherche Scientifique (FNRS) and Télévie, the INNOVIRIS Brussels Region BRUBREAST Project, the IUAP P7/03 program, the Belgian "Foundation against Cancer," the Breast Cancer Research Foundation (BCRF), and the Fonds Gaston Ithier.
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Affiliation(s)
- Jana Jeschke
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Martin Bizet
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles and Vrije Universiteit Brussel, Brussels, Belgium.,Machine Learning Group, Computer Science Department
| | - Christine Desmedt
- Breast Cancer Translational Research Laboratory, Jules Bordet Institute, and
| | - Emilie Calonne
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Sarah Dedeurwaerder
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Soizic Garaud
- Molecular Immunology Unit, Jules Bordet Institute, Université Libre de Bruxelles, Brussels, Belgium
| | - Alexander Koch
- Laboratory of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Denis Larsimont
- Breast Cancer Translational Research Laboratory, Jules Bordet Institute, and
| | - Roberto Salgado
- Breast Cancer Translational Research Laboratory, Jules Bordet Institute, and
| | - Gert Van den Eynden
- Breast Cancer Translational Research Laboratory, Jules Bordet Institute, and
| | - Karen Willard Gallo
- Molecular Immunology Unit, Jules Bordet Institute, Université Libre de Bruxelles, Brussels, Belgium
| | - Gianluca Bontempi
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles and Vrije Universiteit Brussel, Brussels, Belgium.,Machine Learning Group, Computer Science Department
| | - Matthieu Defrance
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles and Vrije Universiteit Brussel, Brussels, Belgium
| | - Christos Sotiriou
- Breast Cancer Translational Research Laboratory, Jules Bordet Institute, and
| | - François Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
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Siebenkäs C, Chiappinelli KB, Guzzetta AA, Sharma A, Jeschke J, Vatapalli R, Baylin SB, Ahuja N. Inhibiting DNA methylation activates cancer testis antigens and expression of the antigen processing and presentation machinery in colon and ovarian cancer cells. PLoS One 2017. [PMID: 28622390 PMCID: PMC5473589 DOI: 10.1371/journal.pone.0179501] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Innovative therapies for solid tumors are urgently needed. Recently, therapies that harness the host immune system to fight cancer cells have successfully treated a subset of patients with solid tumors. These responses have been strong and durable but observed in subsets of patients. Work from our group and others has shown that epigenetic therapy, specifically inhibiting the silencing DNA methylation mark, activates immune signaling in tumor cells and can sensitize to immune therapy in murine models. Here we show that colon and ovarian cancer cell lines exhibit lower expression of transcripts involved in antigen processing and presentation to immune cells compared to normal tissues. In addition, treatment with clinically relevant low doses of DNMT inhibitors (that remove DNA methylation) increases expression of both antigen processing and presentation and Cancer Testis Antigens in these cell lines. We confirm that treatment with DNMT inhibitors upregulates expression of the antigen processing and presentation molecules B2M, CALR, CD58, PSMB8, PSMB9 at the RNA and protein level in a wider range of colon and ovarian cancer cell lines and treatment time points than had been described previously. In addition, we show that DNMTi treatment upregulates many Cancer Testis Antigens common to both colon and ovarian cancer. This increase of both antigens and antigen presentation by epigenetic therapy may be one mechanism to sensitize patients to immune therapies.
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Affiliation(s)
- Cornelia Siebenkäs
- Department of Surgery, The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Katherine B. Chiappinelli
- Department of Microbiology, Immunology, & Tropical Medicine, The George Washington University, Washington, District of Columbia, United States of America
- * E-mail: (NA); (KBC)
| | - Angela A. Guzzetta
- Department of Surgery, The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Surgery, The University of Texas Southwestern Medical School, Dallas, Texas, United States of America
| | - Anup Sharma
- Department of Surgery, The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Jana Jeschke
- Department of Surgery, The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Rajita Vatapalli
- Department of Surgery, The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Urology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Stephen B. Baylin
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Nita Ahuja
- Department of Surgery, The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- * E-mail: (NA); (KBC)
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van Vlodrop IJH, Joosten SC, De Meyer T, Smits KM, Van Neste L, Melotte V, Baldewijns MMLL, Schouten LJ, van den Brandt PA, Jeschke J, Yi JM, Schuebel KE, Ahuja N, Herman JG, Aarts MJ, Bosman FT, Van Criekinge W, van Engeland M. A Four-Gene Promoter Methylation Marker Panel Consisting of GREM1, NEURL, LAD1, and NEFH Predicts Survival of Clear Cell Renal Cell Cancer Patients. Clin Cancer Res 2017; 23:2006-2018. [PMID: 27756787 DOI: 10.1158/1078-0432.ccr-16-1236] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 09/02/2016] [Accepted: 09/24/2016] [Indexed: 11/16/2022]
Abstract
Purpose: The currently used prognostic models for patients with nonmetastatic clear cell renal cell carcinoma (ccRCC) are based on clinicopathologic features and might be improved by adding molecular markers. Epigenetic alterations occur frequently in ccRCC and are promising biomarkers. The aim of this study is to identify prognostic promoter methylation markers for ccRCC.Experimental Design: We integrated data generated by massive parallel sequencing of methyl-binding domain enriched DNA and microarray-based RNA expression profiling of 5-aza-2'-deoxycytidine-treated ccRCC cell lines to comprehensively characterize the ccRCC methylome. A selection of the identified methylation markers was evaluated in two independent series of primary ccRCC (n = 150 and n = 185) by methylation-specific PCR. Kaplan-Meier curves and log-rank tests were used to estimate cause-specific survival. HRs and corresponding 95% confidence intervals (CI) were assessed using Cox proportional hazard models. To assess the predictive capacity and fit of models combining several methylation markers, HarrellC statistic and the Akaike Information Criterion were used.Results: We identified four methylation markers, that is, GREM1, NEURL, LAD1, and NEFH, that individually predicted prognosis of patients with ccRCC. The four markers combined were associated with poorer survival in two independent patient series (HR, 3.64; 95% CI, 1.02-13.00 and HR, 7.54; 95% CI, 2.68-21.19). These findings were confirmed in a third series of ccRCC cases from The Cancer Genome Atlas (HR, 3.60; 95% CI, 2.02-6.40).Conclusions: A four-gene promoter methylation marker panel consisting of GREM1, NEURL, LAD1, and NEFH predicts outcome of patients with ccRCC and might be used to improve current prognostic models. Clin Cancer Res; 23(8); 2006-18. ©2016 AACR.
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Affiliation(s)
- Iris J H van Vlodrop
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Sophie C Joosten
- Division of Medical Oncology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Tim De Meyer
- BioBix: Laboratory of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium
| | - Kim M Smits
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
- Department of Radiation Oncology (MAASTRO), GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Leander Van Neste
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Veerle Melotte
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Marcella M L L Baldewijns
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Leo J Schouten
- Department of Epidemiology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Piet A van den Brandt
- Department of Epidemiology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Jana Jeschke
- The Sidney Kimmel Comprehensive Cancer Center at the Johns Hopkins University School of Medicine, Baltimore, Maryland
- Laboratory of Cancer Epigenetics, Faculty of Medicine, Université Libre de Bruxelles, Brussels, Belgium
| | - Joo Mi Yi
- Research Institute, Dongnam Institute of Radiological and Medical Sciences (DIRAMS), Jangan-eup, Gijang-gun, Busan, Korea
| | - Kornel E Schuebel
- The Sidney Kimmel Comprehensive Cancer Center at the Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Nita Ahuja
- The Sidney Kimmel Comprehensive Cancer Center at the Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Maureen J Aarts
- Division of Medical Oncology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Fred T Bosman
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Wim Van Criekinge
- BioBix: Laboratory of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium
| | - Manon van Engeland
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands.
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10
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Calmon MF, Jeschke J, Zhang W, Dhir M, Siebenkäs C, Herrera A, Tsai HC, O'Hagan HM, Pappou EP, Hooker CM, Fu T, Schuebel KE, Gabrielson E, Rahal P, Herman JG, Baylin SB, Ahuja N. Epigenetic silencing of neurofilament genes promotes an aggressive phenotype in breast cancer. Epigenetics 2016; 10:622-32. [PMID: 25985363 DOI: 10.1080/15592294.2015.1050173] [Citation(s) in RCA: 18] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Neurofilament heavy polypeptide (NEFH) has recently been identified as a candidate DNA hypermethylated gene within the functional breast cancer hypermethylome. NEFH exists in a complex with neurofilament medium polypeptide (NEFM) and neurofilament light polypeptide (NEFL) to form neurofilaments, which are structural components of the cytoskeleton in mature neurons. Recent studies reported the deregulation of these proteins in several malignancies, suggesting that neurofilaments may have a role in other cell types as well. Using a comprehensive approach, we studied the epigenetic inactivation of neurofilament genes in breast cancer and the functional significance of this event. We report that DNA methylation-associated silencing of NEFH, NEFL, and NEFM in breast cancer is frequent, cancer-specific, and correlates with clinical features of disease progression. DNA methylation-mediated inactivation of these genes occurs also in multiple other cancer histologies including pancreas, gastric, and colon. Restoration of NEFH function, the major subunit of the neurofilament complex, reduces proliferation and growth of breast cancer cells and arrests them in Go/G1 phase of the cell cycle along with a reduction in migration and invasion. These findings suggest that DNA methylation-mediated silencing of the neurofilament genes NEFH, NEFM, and NEFL are frequent events that may contribute to the progression of breast cancer and possibly other malignancies.
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11
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Koch A, De Meyer T, Jeschke J, Van Criekinge W. MEXPRESS: visualizing expression, DNA methylation and clinical TCGA data. BMC Genomics 2015; 16:636. [PMID: 26306699 PMCID: PMC4549898 DOI: 10.1186/s12864-015-1847-z] [Citation(s) in RCA: 221] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 08/14/2015] [Indexed: 12/21/2022] Open
Abstract
Background In recent years, increasing amounts of genomic and clinical cancer data have become publically available through large-scale collaborative projects such as The Cancer Genome Atlas (TCGA). However, as long as these datasets are difficult to access and interpret, they are essentially useless for a major part of the research community and their scientific potential will not be fully realized. To address these issues we developed MEXPRESS, a straightforward and easy-to-use web tool for the integration and visualization of the expression, DNA methylation and clinical TCGA data on a single-gene level (http://mexpress.be). Results In comparison to existing tools, MEXPRESS allows researchers to quickly visualize and interpret the different TCGA datasets and their relationships for a single gene, as demonstrated for GSTP1 in prostate adenocarcinoma. We also used MEXPRESS to reveal the differences in the DNA methylation status of the PAM50 marker gene MLPH between the breast cancer subtypes and how these differences were linked to the expression of MPLH. Conclusions We have created a user-friendly tool for the visualization and interpretation of TCGA data, offering clinical researchers a simple way to evaluate the TCGA data for their genes or candidate biomarkers of interest. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1847-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexander Koch
- Department of Mathematical Modeling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium. .,Department of Mathematical Modeling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
| | - Tim De Meyer
- Department of Mathematical Modeling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium.
| | - Jana Jeschke
- Laboratory of Cancer Epigenetics, Université Libre de Bruxelles, Brussels, Belgium.
| | - Wim Van Criekinge
- Department of Mathematical Modeling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium.
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12
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Delatte B, Jeschke J, Defrance M, Bachman M, Creppe C, Calonne E, Bizet M, Deplus R, Marroquí L, Libin M, Ravichandran M, Mascart F, Eizirik DL, Murrell A, Jurkowski TP, Fuks F. Genome-wide hydroxymethylcytosine pattern changes in response to oxidative stress. Sci Rep 2015; 5:12714. [PMID: 26239807 PMCID: PMC4523844 DOI: 10.1038/srep12714] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 07/01/2015] [Indexed: 12/21/2022] Open
Abstract
The TET enzymes convert methylcytosine to the newly discovered base hydroxymethylcytosine. While recent reports suggest that TETs may play a role in response to oxidative stress, this role remains uncertain, and results lackin vivomodels. Here we show a global decrease of hydroxymethylcytosine in cells treated with buthionine sulfoximine, and in mice depleted for the major antioxidant enzymesGPx1 and 2. Furthermore, genome-wide profiling revealed differentially hydroxymethylated regions in coding genes, and intriguingly in microRNA genes, both involved in response to oxidative stress. These results thus suggest a profound effect ofin vivooxidative stress on the global hydroxymethylome.
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Affiliation(s)
- Benjamin Delatte
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB, 1070 Brussels, Belgium
| | - Jana Jeschke
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB, 1070 Brussels, Belgium
| | - Matthieu Defrance
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB, 1070 Brussels, Belgium
| | - Martin Bachman
- CRUK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Catherine Creppe
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB, 1070 Brussels, Belgium
| | - Emilie Calonne
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB, 1070 Brussels, Belgium
| | - Martin Bizet
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB, 1070 Brussels, Belgium
| | - Rachel Deplus
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB, 1070 Brussels, Belgium
| | - Laura Marroquí
- ULB, Center for Diabetes Research, Faculty of Medicine, ULB, 1070 Brussels, Belgium
| | - Myriam Libin
- Laboratory of Vaccinology and Mucosal Immunity, Faculty of Medicine, ULB, 1070 Brussels, Belgium
| | | | - Françoise Mascart
- Laboratory of Vaccinology and Mucosal Immunity, Faculty of Medicine, ULB, 1070 Brussels, Belgium
| | - Decio L Eizirik
- ULB, Center for Diabetes Research, Faculty of Medicine, ULB, 1070 Brussels, Belgium
| | - Adele Murrell
- CRUK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Tomasz P Jurkowski
- Institute of Biochemistry, Stuttgart University, 70569 Stuttgart, Germany
| | - François Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB, 1070 Brussels, Belgium
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13
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Deckers IAG, Schouten LJ, Van Neste L, van Vlodrop IJH, Soetekouw PMMB, Baldewijns MMLL, Jeschke J, Ahuja N, Herman JG, van den Brandt PA, van Engeland M. Promoter Methylation of CDO1 Identifies Clear-Cell Renal Cell Cancer Patients with Poor Survival Outcome. Clin Cancer Res 2015; 21:3492-500. [PMID: 25904753 PMCID: PMC4612631 DOI: 10.1158/1078-0432.ccr-14-2049] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 04/10/2015] [Indexed: 12/31/2022]
Abstract
PURPOSE In this era of molecular diagnostics, prediction of clear-cell renal cell cancer (ccRCC) survival requires optimization, as current prognostic markers fail to determine individual patient outcome. Epigenetic events are promising molecular markers. Promoter CpG island methylation of cysteine dioxygenase type 1 (CDO1), which was identified as prognostic marker for breast cancer, is studied as a potential marker for ccRCC survival. EXPERIMENTAL DESIGN We collected primary tissues of 365 ccRCC cases identified within the prospective Netherlands Cohort Study (NLCS). In this population-based series, CDO1 promoter methylation was observed in 124 of 324 (38.3%) patients with successful methylation-specific PCR analysis. Kaplan-Meier curves and Wilcoxon tests were used to evaluate 10-year ccRCC-specific survival. Cox regression analysis was used to obtain crude and multivariate HRs and 95% confidence intervals (CI). The relative prognostic value of multivariate models with and without CDO1 promoter methylation was compared using likelihood-ratio tests. RESULTS Patients with CDO1 promoter methylation have a significantly poorer survival than those without (Wilcoxon P = 0.006). Differences in survival were independent of other prognostic factors, including age and sex (HR, 1.66; 95% CI, 1.12-2.45) and TNM stage, tumor size, and Fuhrman grade (HR, 1.89; 95% CI, 1.25-2.85). Multivariate models performed better with than without CDO1 promoter methylation status (likelihood-ratio P = 0.003). Survival curves were validated in an independent series of 280 ccRCC cases from The Cancer Genome Atlas (TCGA; Wilcoxon P < 0.001). CONCLUSIONS CDO1 promoter methylation may not substitute common prognostic makers to predict ccRCC survival, but offers additional, relevant prognostic information, indicating that it might be a novel molecular marker to determine ccRCC prognosis.
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Affiliation(s)
- Ivette A G Deckers
- Department of Epidemiology, School for Oncology and Developmental Biology (GROW), Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Leo J Schouten
- Department of Epidemiology, School for Oncology and Developmental Biology (GROW), Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Leander Van Neste
- Department of Pathology, School for Oncology and Developmental Biology (GROW), Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Iris J H van Vlodrop
- Department of Pathology, School for Oncology and Developmental Biology (GROW), Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Patricia M M B Soetekouw
- Division of Medical Oncology, Department of Internal Medicine, School for Oncology and Developmental Biology (GROW), Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Marcella M L L Baldewijns
- Department of Pathology, School for Oncology and Developmental Biology (GROW), Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Jana Jeschke
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland. Laboratory of Cancer Epigenetics, Faculty of Medicine, Université Libre de Bruxelles, Brussels, Belgium
| | - Nita Ahuja
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland. Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland. Department of Urology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - James G Herman
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Piet A van den Brandt
- Department of Epidemiology, School for Oncology and Developmental Biology (GROW), Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Manon van Engeland
- Department of Pathology, School for Oncology and Developmental Biology (GROW), Maastricht University Medical Centre, Maastricht, the Netherlands.
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14
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Jeschke J, Collignon E, Fuks F. DNA methylome profiling beyond promoters - taking an epigenetic snapshot of the breast tumor microenvironment. FEBS J 2014; 282:1801-14. [PMID: 25331982 DOI: 10.1111/febs.13125] [Citation(s) in RCA: 22] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 10/06/2014] [Accepted: 10/19/2014] [Indexed: 12/22/2022]
Abstract
Breast cancer, one of the most common and deadliest malignancies in developed countries, is a remarkably heterogeneous disease, which is clinically reflected by patients who display similar pathological features but respond differently to treatments. In the search for mediators of responsiveness, the tumor microenvironment (TME), in particular tumor-associated immune cells, has been pushed into the spotlight as it has become clear that the TME is an active component of breast cancer disease that affects clinical outcomes. Thus, the characterization of the TME in terms of cell identities and their frequencies has generated a great deal of interest. The common methods currently used for this purpose are either limited in accuracy or application, and DNA methylation has recently been proposed as an alternative approach. The aim of this review is to discuss DNA methylation profiling beyond promoters as a potential clinical tool for TME characterization and cell typing within tumors. With respect to this, we review the role of DNA methylation in breast cancer and cell-lineage specification, as well as inform about the composition and clinical relevance of the TME.
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Affiliation(s)
- Jana Jeschke
- Laboratory of Cancer Epigenetics, Université Libre de Bruxelles, Brussels, Belgium
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15
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Jeschke J, Kurylo D. The Effect of Priming on Contour Integration Training. J Vis 2014. [DOI: 10.1167/14.10.1160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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16
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Jeschke J, Defrance M, Desmedt C, Bizet M, Dedeurwaerder S, Calonne E, Sotiriou C, Fuks F. A Novel Methylation Signature that Reflects Intratumoral Lymphocyte Infiltration in Breast Cancer and Predicts for Response to Anthracycline Treatment. Ann Oncol 2014. [DOI: 10.1093/annonc/mdu066.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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17
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Sun L, Guzzetta AA, Fu T, Chen J, Jeschke J, Kwak R, Vatapalli R, Baylin SB, Iacobuzio-Donahue CA, Wolfgang CL, Ahuja N. CpG island methylator phenotype and its association with malignancy in sporadic duodenal adenomas. Epigenetics 2014; 9:738-46. [PMID: 24518818 DOI: 10.4161/epi.28082] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [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: 12/20/2022] Open
Abstract
CpG island methylator phenotype (CIMP) has been found in multiple precancerous and cancerous lesions, including colorectal adenomas, colorectal cancers, and duodenal adenocarcinomas. There are no reports in the literature of a relationship between CIMP status and clinicopathologic features of sporadic duodenal adenomas. This study sought to elucidate the role of methylation in duodenal adenomas and correlate it with KRAS and BRAF mutations. CIMP+ (with more than 2 markers methylated) was seen in 33.3% of duodenal adenomas; 61% of these CIMP+ adenomas were CIMP-high (with more than 3 markers methylated). Furthermore, CIMP+ status significantly correlated with older age of patients, larger size and villous type of tumor, coexistent dysplasia and periampullary location. MLH1 methylation was seen in 11.1% of duodenal adenomas and was significantly associated with CIMP+ tumors, while p16 methylation was an infrequent event. KRAS mutations were frequent and seen in 26.3% of adenomas; however, no BRAF mutations were detected. Furthermore, CIMP-high status was associated with larger size and villous type of tumor and race (non-white). These results suggest that CIMP+ duodenal adenomas may have a higher risk for developing malignancy and may require more aggressive management and surveillance.
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Affiliation(s)
- Lifeng Sun
- Department of Surgical Oncology; Second Affiliated Hospital; Zhejiang University School of Medicine; Hangzhou, PR China; Department of Surgery; The Sidney Kimmel Comprehensive Cancer Center; The Johns Hopkins University School of Medicine; Baltimore, MD USA
| | - Angela A Guzzetta
- Department of Surgery; The Sidney Kimmel Comprehensive Cancer Center; The Johns Hopkins University School of Medicine; Baltimore, MD USA
| | - Tao Fu
- Department of Surgery; The Sidney Kimmel Comprehensive Cancer Center; The Johns Hopkins University School of Medicine; Baltimore, MD USA; Department of Urology; The Sidney Kimmel Comprehensive Cancer Center; The Johns Hopkins University School of Medicine; Baltimore, MD USA; Department of Gastrointestinal Surgery; Daping Hospital; Third Military Medical University; Chongqing, PR China
| | - Jinming Chen
- Department of Surgical Oncology; Second Affiliated Hospital; Zhejiang University School of Medicine; Hangzhou, PR China; Department of Surgery; The Sidney Kimmel Comprehensive Cancer Center; The Johns Hopkins University School of Medicine; Baltimore, MD USA
| | - Jana Jeschke
- Department of Surgery; The Sidney Kimmel Comprehensive Cancer Center; The Johns Hopkins University School of Medicine; Baltimore, MD USA
| | - Ruby Kwak
- Department of Surgery; The Sidney Kimmel Comprehensive Cancer Center; The Johns Hopkins University School of Medicine; Baltimore, MD USA
| | - Rajita Vatapalli
- Department of Surgery; The Sidney Kimmel Comprehensive Cancer Center; The Johns Hopkins University School of Medicine; Baltimore, MD USA
| | - Stephen B Baylin
- Department of Surgery; The Sidney Kimmel Comprehensive Cancer Center; The Johns Hopkins University School of Medicine; Baltimore, MD USA
| | - Christine A Iacobuzio-Donahue
- Department of Pathology; The Sidney Kimmel Comprehensive Cancer Center; The Johns Hopkins University School of Medicine; Baltimore, MD USA
| | - Christopher L Wolfgang
- Department of Surgery; The Sidney Kimmel Comprehensive Cancer Center; The Johns Hopkins University School of Medicine; Baltimore, MD USA; Department of Oncology; The Sidney Kimmel Comprehensive Cancer Center; The Johns Hopkins University School of Medicine; Baltimore, MD USA
| | - Nita Ahuja
- Department of Surgery; The Sidney Kimmel Comprehensive Cancer Center; The Johns Hopkins University School of Medicine; Baltimore, MD USA; Department of Oncology; The Sidney Kimmel Comprehensive Cancer Center; The Johns Hopkins University School of Medicine; Baltimore, MD USA; Department of Urology; The Sidney Kimmel Comprehensive Cancer Center; The Johns Hopkins University School of Medicine; Baltimore, MD USA; Department of Gastrointestinal Surgery; Daping Hospital; Third Military Medical University; Chongqing, PR China
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18
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Di Cello F, Cope L, Li H, Jeschke J, Wang W, Baylin SB, Zahnow CA. Methylation of the claudin 1 promoter is associated with loss of expression in estrogen receptor positive breast cancer. PLoS One 2013; 8:e68630. [PMID: 23844228 PMCID: PMC3701071 DOI: 10.1371/journal.pone.0068630] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 05/31/2013] [Indexed: 12/31/2022] Open
Abstract
Downregulation of the tight junction protein claudin 1 is a frequent event in breast cancer and is associated with recurrence, metastasis, and reduced survival, suggesting a tumor suppressor role for this protein. Tumor suppressor genes are often epigenetically silenced in cancer. Downregulation of claudin 1 via DNA promoter methylation may thus be an important determinant in breast cancer development and progression. To investigate if silencing of claudin 1 has an epigenetic etiology in breast cancer we compared gene expression and methylation data from 217 breast cancer samples and 40 matched normal samples available through the Cancer Genome Atlas (TCGA). Moreover, we analyzed claudin 1 expression and methylation in 26 breast cancer cell lines. We found that methylation of the claudin 1 promoter CpG island is relatively frequent in estrogen receptor positive (ER+) breast cancer and is associated with low claudin 1 expression. In contrast, the claudin 1 promoter was not methylated in most of the ER-breast cancers samples and some of these tumors overexpress claudin 1. In addition, we observed that the demethylating agents, azacitidine and decitabine can upregulate claudin 1 expression in breast cancer cell lines that have a methylated claudin 1 promoter. Taken together, our results indicate that DNA promoter methylation is causally associated with downregulation of claudin 1 in a subgroup of breast cancer that includes mostly ER+ tumors, and suggest that epigenetic therapy to restore claudin 1 expression might represent a viable therapeutic strategy in this subtype of breast cancer.
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Affiliation(s)
- Francescopaolo Di Cello
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
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19
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Jeschke J, O'Hagan HM, Zhang W, Vatapalli R, Calmon MF, Danilova L, Nelkenbrecher C, Van Neste L, Bijsmans ITGW, Van Engeland M, Gabrielson E, Schuebel KE, Winterpacht A, Baylin SB, Herman JG, Ahuja N. Frequent inactivation of cysteine dioxygenase type 1 contributes to survival of breast cancer cells and resistance to anthracyclines. Clin Cancer Res 2013; 19:3201-11. [PMID: 23630167 DOI: 10.1158/1078-0432.ccr-12-3751] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
PURPOSE Genome-wide DNA methylation analyses have identified hundreds of candidate DNA-hypermethylated genes in cancer. Comprehensive functional analyses provide an understanding of the biologic significance of this vast amount of DNA methylation data that may allow the determination of key epigenetic events associated with tumorigenesis. EXPERIMENTAL DESIGN To study mechanisms of cysteine dioxygenase type 1 (CDO1) inactivation and its functional significance in breast cancer in a comprehensive manner, we screened for DNA methylation and gene mutations in primary breast cancers and analyzed growth, survival, and reactive oxygen species (ROS) production in breast cancer cells with restored CDO1 function in the context of anthracycline treatment. RESULTS DNA methylation-associated silencing of CDO1 in breast cancer is frequent (60%), cancer specific, and correlates with disease progression and outcome. CDO1 function can alternatively be silenced by repressive chromatin, and we describe protein-damaging missense mutations in 7% of tumors without DNA methylation. Restoration of CDO1 function in breast cancer cells increases levels of ROS and leads to reduced viability and growth, as well as sensitization to anthracycline treatment. Priming with 5-azacytidine of breast cancer cells with epigenetically silenced CDO1 resulted in restored expression and increased sensitivity to anthracyclines. CONCLUSION We report that silencing of CDO1 is a critical epigenetic event that contributes to the survival of oxidative-stressed breast cancer cells through increased detoxification of ROS and thus leads to the resistance to ROS-generating chemotherapeutics including anthracyclines. Our study shows the importance of CDO1 inactivation in breast cancer and its clinical potential as a biomarker and therapeutic target to overcome resistance to anthracyclines.
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Affiliation(s)
- Jana Jeschke
- Department of Surgery, Johns Hopkins University, Baltimore, Maryland 21287, USA
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20
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Fu T, Guzzetta AA, Jeschke J, Vatapalli R, Dave P, Hooker CM, Morgan R, Iacobuzio-Donahue CA, Liu B, Ahuja N. KRAS G>A mutation favors poor tumor differentiation but may not be associated with prognosis in patients with curatively resected duodenal adenocarcinoma. Int J Cancer 2013; 132:2502-9. [PMID: 23065691 DOI: 10.1002/ijc.27910] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Accepted: 09/10/2012] [Indexed: 12/24/2022]
Abstract
KRAS mutations have been found in duodenal adenocarcinomas and may have prognostic significance. The purpose of this study was to classify clinicopathological characteristics, microsatellite instability and KRAS mutations and identify possible prognostic role of KRAS mutations in duodenal adenocarcinomas. Demographics, tumor characteristics and survival were recorded for 78 patients with duodenal adenocarcinomas (Stages I-III). KRAS mutations were detected in 27 (34.6%) cases, of which the majority (74.1%) were G>A transitions. Multivariate logistic regression analysis showed that KRAS G>A mutation was significantly associated with late stage (p = 0.025) and poor tumor differentiation (p = 0.035), when compared with wild-type and other than G>A mutations. KRAS G>A mutation carriers were at increased risk for distant relapse (p = 0.022) and had significantly shorter overall survival (OS; log-rank p = 0.045) and a trend toward shorter relapse-free survival (RFS; log-rank p = 0.062) when compared with those who did not carry the KRAS G>A mutation. In multivariate analyses, there was a significant correlation between ≥ 3 positive lymph nodes and poor OS (p < 0.001) and RFS (p = 0.001) and KRAS G>A mutation carriers demonstrated no effect on clinical outcome. In conclusion, KRAS G>A mutation correlates significantly with late stage and poor tumor differentiation in duodenal adenocarcinoma. Among patients who undergo a curative resection of duodenal adenocarcinoma, KRAS G>A mutation carriers will more likely experience distant relapse but may not exhibit a poor prognosis. The number of positive lymph nodes should be incorporated in future staging systems.
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Affiliation(s)
- Tao Fu
- Department of Gastrointestinal Surgery, Daping Hospital, Third Military Medical University, Chongqing 400042, China
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21
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Fu T, Pappou EP, Guzzetta AA, Jeschke J, Kwak R, Dave P, Hooker CM, Morgan R, Baylin SB, Iacobuzio-Donahue CA, Wolfgang CL, Ahuja N. CpG island methylator phenotype-positive tumors in the absence of MLH1 methylation constitute a distinct subset of duodenal adenocarcinomas and are associated with poor prognosis. Clin Cancer Res 2012; 18:4743-52. [PMID: 22825585 DOI: 10.1158/1078-0432.ccr-12-0707] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
PURPOSE Little information is available on genetic and epigenetic changes in duodenal adenocarcinomas. The purpose was to identify possible subsets of duodenal adenocarcinomas based on microsatellite instability (MSI), DNA methylation, mutations in the KRAS and BRAF genes, clinicopathologic features, and prognosis. EXPERIMENTAL DESIGN Demographics, tumor characteristics, and survival were available for 99 duodenal adenocarcinoma patients. Testing for KRAS and BRAF mutations, MSI, MLH1 methylation, and CpG island methylator phenotype (CIMP) status was conducted. A Cox proportional hazard model was built to predict survival. RESULTS CIMP(+) was detected in 27 of 99 (27.3%) duodenal adenocarcinomas and was associated with MSI (P = 0.011) and MLH1 methylation (P < 0.001), but not with KRAS mutations (P = 0.114), as compared with CIMP(-) tumors. No BRAF V600E mutation was detected. Among the CIMP(+) tumors, 15 (55.6%) were CIMP(+)/MLH1-unmethylated (MLH1-U). Kaplan-Meier analysis showed that tumors classified by CIMP, CIMP/MLH1 methylation status, or CIMP/MSI status could predict overall survival (OS; P = 0.047, 0.002, and 0.002, respectively), whereas CIMP/MLH1 methylation status could also predict time-to-recurrence (TTR; P = 0.016). In multivariate analysis, CIMP/MLH1 methylation status showed a significant prognostic value in both OS (P < 0.001) and TTR (P = 0.023). Patients with CIMP(+)/MLH1-U tumors had the worst OS and TTR. CONCLUSIONS Our results showed existence of CIMP in duodenal adenocarcinomas. The combination of CIMP(+)/MLH1-U seems to be independently associated with poor prognosis in patients with duodenal adenocarcinomas. This study also suggests that BRAF mutations are not involved in duodenal tumorigenesis, MSI, or CIMP development.
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Affiliation(s)
- Tao Fu
- Department of Surgery, Johns Hopkins University, Baltimore, MD 21287, USA
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22
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Jeschke J, Van Neste L, Glöckner SC, Dhir M, Calmon MF, Deregowski V, Van Criekinge W, Vlassenbroeck I, Koch A, Chan TA, Cope L, Hooker CM, Schuebel KE, Gabrielson E, Winterpacht A, Baylin SB, Herman JG, Ahuja N. Biomarkers for detection and prognosis of breast cancer identified by a functional hypermethylome screen. Epigenetics 2012; 7:701-9. [PMID: 22647880 DOI: 10.4161/epi.20445] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Breast cancer (BC) is a disease with diverse tumor heterogeneity, which challenges conventional approaches to develop biomarkers for early detection and prognosis. To identify effective biomarkers, we performed a genome-wide screen for functional methylation changes in BC, i.e., genes silenced by promoter hypermethylation, using a functionally proven gene expression approach. A subset of candidate hypermethylated genes were validated in primary BCs and tested as markers for detection and prognosis prediction of BC. We identified 33 cancer specific methylated genes and, among these, two categories of genes: (1) highly frequent methylated genes that detect early stages of BC. Within that category, we have identified the combination of NDRG2 and HOXD1 as the most sensitive (94%) and specific (90%) gene combination for detection of BC; (2) genes that show stage dependent methylation frequency pattern, which are candidates to help delineate BC prognostic signatures. For this category, we found that methylation of CDO1, CKM, CRIP1, KL and TAC1 correlated with clinical prognostic variables and was a significant prognosticator for poor overall survival in BC patients. CKM [Hazard ratio (HR) = 2.68] and TAC1 (HR = 7.73) were the strongest single markers and the combination of both (TAC1 and CKM) was associated with poor overall survival independent of age and stage in our training (HR = 1.92) and validation cohort (HR = 2.87). Our study demonstrates an efficient method to utilize functional methylation changes in BC for the development of effective biomarkers for detection and prognosis prediction of BC.
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Affiliation(s)
- Jana Jeschke
- Department of Surgery, Johns Hopkins University, Baltimore, MD, USA
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23
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Jeschke J, O'Hagan H, Zhang W, Calmon MF, Dhir M, van Neste L, Bijsmans I, Gabrielson E, Schuebel KE, Baylin SB, Winterpacht A, Herman JG, Ahuja N. Abstract 94: Epigenetic silencing of CDO1 sustains viability of breast cancer cells via the reduction of cellular ROS. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-94] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Approaches to analyze genome-wide methylation changes have become an extraordinary useful tool to identify thousands of new candidate hypermethylated genes in cancer. Numerous comprehensive approaches have been initiated to begin to understand the biological significance of the vast amount of methylation data generated and by this, novel tumor suppressor genes, biomarkers for early detection and prognosis prediction of cancer, and molecular mechanisms underlying tumor growth control have been discovered. In this study, we explore the candidate hypermethylated gene Cysteine Dioxygenase Type 1 (CDO1), which was recently identified in breast cancer using a functionally proven genome-wide gene expression approach. Here, we show that the epigenetic inactivation of CDO1 enhances tumor growth and sustains viability of breast cancer cells via the reduction of cellular ROS. Moreover, we observed a cancer stage-dependent increase in CDO1 methylation frequency (DCIS: 50%, stage 1-2: 65% and stage 3-4: 90%) that coincides with elevated oxidative stress levels in advanced cancers. These findings support the hypothesis that cancer cells upregulate their antioxidant capacity in adaptation to intrinsic oxidative stress. Lastly, we correlated CDO1 methylation status with clinicopathologic patient characteristics in a cohort of 186 patients. Methylation of CDO1 is significantly associated with prognostic parameters such as tumor stage, lymphovascular and perinodal invasion and predicts worse patient outcome.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 94. doi:1538-7445.AM2012-94
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Affiliation(s)
| | | | - Wei Zhang
- 1Johns Hopkins University, Baltimore, MD
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- 1Johns Hopkins University, Baltimore, MD
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Jeschke J, Ostermann D, Krieg R. Critical strains and necking phenomena for different steel sheet specimens under uniaxial loading. Nuclear Engineering and Design 2011. [DOI: 10.1016/j.nucengdes.2011.03.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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25
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Dhir M, Yachida S, Van Neste L, Glöckner SC, Jeschke J, Pappou EP, Montgomery EA, Herman JG, Baylin SB, Iacobuzio-Donahue C, Ahuja N. Sessile serrated adenomas and classical adenomas: an epigenetic perspective on premalignant neoplastic lesions of the gastrointestinal tract. Int J Cancer 2011; 129:1889-98. [PMID: 21154739 DOI: 10.1002/ijc.25847] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2010] [Accepted: 11/02/2010] [Indexed: 12/11/2022]
Abstract
The diagnosis of sessile serrated adenomas (SSAs) is challenging, and there is a great deal of interobserver variability amongst pathologists in differentiating SSAs from hyperplastic polyps (HPPs). The aim of this study was (i) to assess the utility of epigenetic changes such as DNA methylation in differentiating SSAs from HPPs and (ii) to identify common methylation based molecular markers potentially useful for early detection of premalignant neoplastic lesions of gastrointestinal tract. A total of 97 primary patient adenoma samples were obtained from The Johns Hopkins Hospital pathology archive with IRB approval and HIPAA compliance. We analyzed the promoter associated CpG island methylation status of 17 genes using nested multiplex methylation specific PCR (MSP). Methylation of CDX2, hMLH1 and TLR2 was detected in SSAs and SSAs with dysplasia but not in HPPs. A subset of genes including EVL, GATAs (4 and 5), HIN-1, SFRPs (1, 2, 4 and 5), SOX17 and SYNE1 were methylated frequently in all premalignant gastrointestinal adenomas including tubular adenomas, villous adenomas, SSAs and SSAs with dysplasia but infrequently in non-premalignant polyps such as HPPs. Methylation of CDX2, hMLH1 and TLR2 may be of diagnostic utility in differentiating, histologically challenging cases of SSAs from HPPs. Genes such as EVL, GATAs, HIN-1, SFRPs, SOX17 and SYNE1, which are frequently methylated in all types of tested premalignant adenomas, may be useful as biomarkers in stool-based strategies for early detection of these adenomas and CRCs in future.
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Affiliation(s)
- Mashaal Dhir
- Department of Surgery, Johns Hopkins University, Baltimore 21287, MD, USA
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26
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Yi JM, Dhir M, Van Neste L, Downing SR, Jeschke J, Glöckner SC, de Freitas Calmon M, Hooker CM, Funes JM, Boshoff C, Smits KM, van Engeland M, Weijenberg MP, Iacobuzio-Donahue CA, Herman JG, Schuebel KE, Baylin SB, Ahuja N. Genomic and epigenomic integration identifies a prognostic signature in colon cancer. Clin Cancer Res 2011; 17:1535-45. [PMID: 21278247 DOI: 10.1158/1078-0432.ccr-10-2509] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
PURPOSE The importance of genetic and epigenetic alterations maybe in their aggregate role in altering core pathways in tumorigenesis. EXPERIMENTAL DESIGN Merging genome-wide genomic and epigenomic alterations, we identify key genes and pathways altered in colorectal cancers (CRC). DNA methylation analysis was tested for predicting survival in CRC patients using Cox proportional hazard model. RESULTS We identified 29 low frequency-mutated genes that are also inactivated by epigenetic mechanisms in CRC. Pathway analysis showed the extracellular matrix (ECM) remodeling pathway is silenced in CRC. Six ECM pathway genes were tested for their prognostic potential in large CRC cohorts (n = 777). DNA methylation of IGFBP3 and EVL predicted for poor survival (IGFBP3: HR = 2.58, 95% CI: 1.37-4.87, P = 0.004; EVL: HR = 2.48, 95% CI: 1.07-5.74, P = 0.034) and simultaneous methylation of multiple genes predicted significantly worse survival (HR = 8.61, 95% CI: 2.16-34.36, P < 0.001 for methylation of IGFBP3, EVL, CD109, and FLNC). DNA methylation of IGFBP3 and EVL was validated as a prognostic marker in an independent contemporary-matched cohort (IGFBP3 HR = 2.06, 95% CI: 1.04-4.09, P = 0.038; EVL HR = 2.23, 95% CI: 1.00-5.0, P = 0.05) and EVL DNA methylation remained significant in a secondary historical validation cohort (HR = 1.41, 95% CI: 1.05-1.89, P = 0.022). Moreover, DNA methylation of selected ECM genes helps to stratify the high-risk stage 2 colon cancers patients who would benefit from adjuvant chemotherapy (HR: 5.85, 95% CI: 2.03-16.83, P = 0.001 for simultaneous methylation of IGFBP3, EVL, and CD109). CONCLUSIONS CRC that have silenced genes in ECM pathway components show worse survival suggesting that our finding provides novel prognostic biomarkers for CRC and reflects the high importance of integrative analyses linking genetic and epigenetic abnormalities with pathway disruption in cancer.
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Affiliation(s)
- Joo Mi Yi
- Department of Oncology, Johns Hopkins University, Baltimore, Maryland 20892-8110, USA
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Engelhardt TO, Jeschke J, Piza-Katzer H. [About the self-reported quality of life after amputation of the hand in patients with upper extremity tumors]. HANDCHIR MIKROCHIR P 2008; 40:23-30. [PMID: 18322896 DOI: 10.1055/s-2007-989452] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
PURPOSE/BACKGROUND Amputation proximal to the wrist may be oncologically dictated in cases of upper extremity soft tissue sarcoma and aggressive fibromatosis. Literature on functional long-term results and patient-oriented assessment is sparse. Our study is concerned with subjective impressions of quality of life and upper extremity health status and their importance in the evaluation and interpretation of results after amputation of the hand. PATIENTS/METHODS Between 1999 and 2007, 14 patients (6 females/8 males; average age: 25 years) were operated because of a soft tissue sarcoma (n = 11) or aggressive fibromatosis (n = 3). Ten patients underwent limb-sparing surgery. There were two amputations at the level of the forearm. Local recurrence following forequarter amputation due to aggressive fibromatosis required reoperation in another patient. A heterotopic replantation after resection was carried out in one patient. In patients with amputations, the self-reported upper extremity-specific health status and quality of life were measured with the DASH score. Disturbances in body image and symptoms of depression were assessed psychiatrically. RESULTS In two cases with amputations, minimal impairments in everyday life and a high reported quality of life were observed (DASH scores: 3,5). CONCLUSION Self-reported upper extremity health status and quality of life following amputation of the hand can be in contrast to the objective pathology. In patient-oriented assessment of results, individual psychosocial factors that may affect results must be taken into consideration. They also must not be neglected when determining whether patients are suitable candidates for prosthetic devices.
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Affiliation(s)
- T O Engelhardt
- Universitätsklinik für Plastische und Wiederherstellungschirurgie, Medizinische Universität Innsbruck, Anichstrasse 35, Innsbruck, Austria
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Schwabegger A, Jeschke J, Del Frari B. A Rounded Dissector to Reduce Complications in the Minimally Invasive Repair (Nuss) of Pectus Excavatum in Adolescents and Adults. Thorac Cardiovasc Surg 2008; 56:118-20. [DOI: 10.1055/s-2007-965379] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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29
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Jeschke J, Engelhardt TO, Piza-Katzer H. [Optimal result after ear reconstruction following a dog bite injury]. Unfallchirurg 2007; 110:789-91. [PMID: 17581732 DOI: 10.1007/s00113-007-1274-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
A case of a young woman is reported who lost a big part of the right auricle by a dog bite. An aesthetically satisfying immediate reconstruction after refixation of the deep-ithelialised amputated helical rim could be achieved with the aid of a temporal fascial island flap and full thickness skin grafts.
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Affiliation(s)
- J Jeschke
- Universitätsklinik für Plastische und Wiederherstellungschirurgie, Ludwig-Boltzmann-Institut für Qualitätssicherung in der Plastischen- und Wiederherstellungschirurgie, Medizinische Universität, Anichstrasse 35, A-6020, Innsbruck, Osterreich
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Abstract
A case of a mechanic and motorcyclist is reported who developed unilateral chronic exertional compartment syndrome of the flexor muscles in the forearm. After years of discomfort and medical check-ups, a subcutaneous fasciotomy of the superficial compartments of the flexor muscles in the forearm led to a complete relief of symptoms, which allowed the patient unrestricted activity.
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Affiliation(s)
- J Jeschke
- Universitätsklinik für Plastische und Wiederherstellungschirurgie, Medizinische Universität Innsbruck, Osterreich.
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31
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32
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Schroeder RJ, Hauff P, Bartels T, Vogel K, Jeschke J, Hidajat N, Maeurer J. Tumor vascularization in experimental melanomas: correlation between unenhanced and contrast enhanced power Doppler imaging and histological grading. Ultrasound Med Biol 2001; 27:761-771. [PMID: 11516536 DOI: 10.1016/s0301-5629(01)00363-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The purpose of this study was to evaluate the reliability of unenhanced and enhanced power Doppler sonography in visualization of intratumoral angioneogenesis. Thirty-seven malignant melanomas, which had been implanted intra- or subcutaneously in 22 mice, were examined. Various B-mode criteria, power Doppler criteria and spectral Doppler parameters were evaluated before and after IV-application of the d-galactose-based contrast agent Levovist. After sonographic examination, all tumors were analyzed histologically with semiquantitative grading of tumoral vascularization. Unenhanced, in 70% of the tumors, no intratumoral vessels were visible using power Doppler, but only in 11% of the intracutaneous and in 0% of the subcutaneous after injection of the contrast agent. The enhanced mode was definitely superior to unenhanced Doppler in showing the intratumoral vascularity. The intratumoral vascular structure could be sufficiently analyzed in 30% of all tumors by unenhanced Doppler, but in 92% enhanced. The mean percentage vessel area increased about 433% after application of Levovist (intracutaneous: 485%, subcutaneous: 280%). Despite the missing direct correlation between the sonographically and histologically determined grade of tumor vascularization (Pearson's correlation unenhanced 0,356, p <.05/enhanced 0.395, p <.05), the correlation between the percentage vessel area and the histologic grade of vascularization was improved after application of the contrast agent (Pearson's correlation unenhanced 0.347, p <.05/enhanced 0.686, p <.01). We did not find a significant direct correlation between histologically and sonographically determined degree of vascularization. However, the correlation was improved using a d-galactose-based signal-enhancing agent in power Doppler sonography.
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Affiliation(s)
- R J Schroeder
- Department of Radiology, Charité-Virchow University Hospital, Berlin, Germany.
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33
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Jeschke J, Nekola J, Chlumský J. [Doping in sports]. Cas Lek Cesk 1999; 138:291-7. [PMID: 10422337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
The first organized doping controls were carried out in the 1970s. In 1993, the Czech Antidoping Charter was signed and the Antidoping Committee was established. The medical commission of International Olympic Committee decides, which substances and methods are prohibited. The current classification is as follows: I. prohibited classes of substances--stimulants, narcotics, anabolic agents, diuretics and some hormones. II. prohibited methods--blood doping and pharmaceutical, chemical or physical manipulation. III. classes of drugs subject to certain restrictions--alcohol, marijuana, local anesthetics, corticosteroids and beta blockers. All substances are characterized from the ergogenic viewpoint and health risks are particularly emphasized. In practice, doping control starts by drawing the athletes and ends by urine sample analysis in a special laboratory. In case of positive results, the sportsman is banned from sports activity for 3 months, 2 years or for the rest of his life. In 24 worldwide laboratories in 1995 93,938 urine samples were analyzed. 1516 (1.61%) proved to be positive, including 986 anabolic steroid use. In 1997, the Czech laboratory carried out 843 checks, of which 15 (1.7%) were positive. The largest positive doping group were body builders. Doping poses a major risk among junior sportsmen. Prevalence worldwide is estimated at 2-10% of the male population. In the future a severe antidoping attitude, as well as antidoping enlightenment, are certain to continue. By these standards the activity of the Czech Antidoping Committee is on a very high level.
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Affiliation(s)
- J Jeschke
- Oddĕlení tĕlovýchovného lékarství FN, Plzen
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34
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Jeschke J. [The narcotics situation from the viewpoint of the German Federal Criminal Police Office]. Offentl Gesundheitswes 1986; 48:395-403. [PMID: 2945135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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35
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Smíd J, Jeschke J, Zeman V, Kubín Z. [Effect of metipranolol (Trimepranol Spofa) on changes in selected hemodynamic indicators during physical exercise. I. Dynamic loading]. Vnitr Lek 1983; 29:862-8. [PMID: 6138899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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36
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Hůla J, Kucera M, Jeschke J. [The position of noninvasive diagnosis and work capacity determination in patients after myocardial infarct]. Vnitr Lek 1982; 28:1161-5. [PMID: 7157693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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37
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Pokorná I, Jeschke J, Zeman V. [Our experience with the examination of the spine in sportsmen (author's transl)]. Acta Chir Orthop Traumatol Cech 1980; 47:328-32. [PMID: 7424467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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38
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Polácková J, Bocková E, Jeschke J, Kucera M, Kotál L, Kubín Z, Sedivec V. [Camp concentration of training character as one of the possibilities of rehabilitation of psychological condition of patients subsequent to myocardial infarction (author's transl)]. Cesk Psychiatr 1979; 75:375-81. [PMID: 535090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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39
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Smíd J, Kucera M, Kubín Z, Jeschke J. [Changes in systolic time intervals during rest and after exercise during long-term rehabilitation for myocardial infarct]. Vnitr Lek 1979; 25:1048-54. [PMID: 516485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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40
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Kotál L, Kuŭcera M, Polácková J, Bocková E, Jeschke J, Kubín Z. [Sex problems in post-infarction patients' rehabilitation (author's transl)]. Cesk Psychiatr 1978; 74:193-9. [PMID: 737798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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41
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Kotál L, Polácková J, Bocková E, Kucera M, Kubín Z, Jeschke J. [Prevention of sexual disorders in men following myocardial infarction]. Cas Lek Cesk 1978; 117:559-62. [PMID: 566616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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42
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Kucera M, Polácková J, Paceltová L, Joachimsthaler J, Jeschke J, Suchan J. [Social and economic problems of patients after myocardial infarction (author's transl)]. Cas Lek Cesk 1976; 115:919-23. [PMID: 963717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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43
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Karlícek V, Topolcan O, Jeschke J. [Plasmatic immunoreactive insulin in trained athletes]. Cas Lek Cesk 1976; 115:324-6. [PMID: 1260800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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44
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Holecek V, Jeschke J, Kucera M, Suchan J. [Osmotic pressure in the blood and urine after loading in patients rehabilitated after myocardial infarct]. Vnitr Lek 1975; 21:1065-8. [PMID: 1198950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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45
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Kucera M, Jeschke J, Suchan J, Hůla J, Holecek V, Sova J. [Results of complex rehabilitation care for patients after myocardial infarct]. Vnitr Lek 1975; 21:567-73. [PMID: 1136204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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46
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Polácková J, Kucera M, Paceltová L, Suchmanová V, Jeschke J. [Influence of training camps on psychical state of post-infarction patients (author's transl)]. Cas Lek Cesk 1975; 114:560-2. [PMID: 1139600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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47
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Jeschke J, Kucera M, Zeman V, Suchan J, Holecek V, Paceltová L, Polácková J, Cepeláková H. [Experience with training camps for patients after myocardial infarction (author's transl)]. Cas Lek Cesk 1975; 114:555-60. [PMID: 1139599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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48
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Kucera M, Joachimsthaler J, Suchan J, Jeschke J, Chaloupková E, Polácková J. [A method for working capacity examination in post-infarction patients (author's transl)]. Cas Lek Cesk 1975; 114:49-51. [PMID: 1116165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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49
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Kucera M, Chaloupková E, Joachimsthaler J, Jeschke J. [Changes in the pulse rate during work in patients after myocardial infarction (author's transl)]. Cas Lek Cesk 1974; 113:996-8. [PMID: 4408829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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50
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Karlícek V, Topolcan O, Sova J, Kucera M, Jeschke J, Suchan J. [Insulin and long-term therapeutic exercise in patients after myocardial infarction (author's transl)]. Cas Lek Cesk 1974; 113:569-70. [PMID: 4451932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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