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Heilig CE, Horak P, Kreutzfeldt S, Teleanu V, Mock A, Renner M, Bhatti IA, Hutter B, Hüllein J, Fröhlich M, Uhrig S, Süße H, Heiligenthal L, Ochsenreither S, Illert AL, Vogel A, Desuki A, Heinemann V, Heidegger S, Bitzer M, Scheytt M, Brors B, Hübschmann D, Baretton G, Stenzinger A, Steindorf K, Benner A, Jäger D, Heining C, Glimm H, Fröhling S, Schlenk RF. Rationale and design of the CRAFT (Continuous ReAssessment with Flexible ExTension in Rare Malignancies) multicenter phase II trial. ESMO Open 2021; 6:100310. [PMID: 34808524 PMCID: PMC8609144 DOI: 10.1016/j.esmoop.2021.100310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 10/27/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Approvals of cancer therapeutics are primarily disease entity specific. Current molecular diagnostic approaches frequently identify actionable alterations in rare cancers or rare subtypes of common cancers for which the corresponding treatments are not approved and unavailable within clinical trials due to entity-related eligibility criteria. Access may be negotiated with health insurances. However, approval rates vary, and critical information required for a scientific evaluation of treatment-associated risks and benefits is not systematically collected. Thus clinical trials with optimized patient selection and comprehensive molecular characterization are essential for translating experimental treatments into standard care. PATIENTS AND METHODS Continuous ReAssessment with Flexible ExTension in Rare Malignancies (CRAFT) is an open-label phase II trial for adults with pretreated, locally advanced, or metastatic solid tumors. Based on the evaluation by a molecular tumor board, patients are assigned to combinations of six molecularly targeted agents and a programmed death-ligand 1 (PD-L1) antagonist within seven study arms focusing on (i) BRAF V600 mutations; (ii) ERBB2 amplification and/or overexpression, activating ERBB2 mutations; (iii) ALK rearrangements, activating ALK mutations; (iv and v) activating PIK3CA and AKT mutations, other aberrations predicting increased PI3K-AKT pathway activity; (vi) aberrations predicting increased RAF-MEK-ERK pathway activity; (vii) high tumor mutational burden and other alterations predicting sensitivity to PD-L1 inhibition. The primary endpoint is the disease control rate (DCR) at week 16; secondary and exploratory endpoints include the progression-free survival ratio, overall survival, and patient-reported outcomes. Using Simon's optimal two-stage design, 14 patients are accrued for each study arm. If three or fewer patients achieve disease control, the study arm is stopped. Otherwise, 11 additional patients are accrued. If the DCR exceeds 7 of 25 patients, the null hypothesis is rejected for the respective study arm. CONCLUSIONS CRAFT was activated in October 2021 and will recruit at 10 centers in Germany. TRIAL REGISTRATION NUMBERS EudraCT: 2019-003192-18; ClinicalTrials.gov: NCT04551521.
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Affiliation(s)
- C E Heilig
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany; German Cancer Consortium (DKTK), Heidelberg, Germany
| | - P Horak
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany; German Cancer Consortium (DKTK), Heidelberg, Germany
| | - S Kreutzfeldt
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany; German Cancer Consortium (DKTK), Heidelberg, Germany
| | - V Teleanu
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany; German Cancer Consortium (DKTK), Heidelberg, Germany; Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
| | - A Mock
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany; German Cancer Consortium (DKTK), Heidelberg, Germany; Department of Medical Oncology, NCT Heidelberg and Heidelberg University Hospital, Heidelberg, Germany
| | - M Renner
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany; Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - I A Bhatti
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany; German Cancer Consortium (DKTK), Heidelberg, Germany; Department of Medical Oncology, NCT Heidelberg and Heidelberg University Hospital, Heidelberg, Germany
| | - B Hutter
- Computational Oncology Group, Molecular Precision Oncology Program, NCT Heidelberg and DKFZ, Heidelberg, Germany; Division of Applied Bioinformatics, DKFZ, Heidelberg, Germany
| | - J Hüllein
- Computational Oncology Group, Molecular Precision Oncology Program, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - M Fröhlich
- Computational Oncology Group, Molecular Precision Oncology Program, NCT Heidelberg and DKFZ, Heidelberg, Germany; Division of Applied Bioinformatics, DKFZ, Heidelberg, Germany
| | - S Uhrig
- Computational Oncology Group, Molecular Precision Oncology Program, NCT Heidelberg and DKFZ, Heidelberg, Germany; Division of Applied Bioinformatics, DKFZ, Heidelberg, Germany
| | - H Süße
- NCT Trial Center, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - L Heiligenthal
- NCT Trial Center, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - S Ochsenreither
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Berlin, Germany; DKTK, Berlin, Germany
| | - A L Illert
- Comprehensive Cancer Center Freiburg, University of Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Department of Internal Medicine I, University of Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany; DKTK, Freiburg, Germany
| | - A Vogel
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - A Desuki
- University Cancer Center Mainz, Johannes Gutenberg University Mainz, Mainz, Germany; DKTK, Mainz, Germany; Third Medical Department, University Medical Center, Mainz, Germany
| | - V Heinemann
- Department of Medicine III, University Hospital, Ludwig Maximilians University Munich, Munich, Germany; DKTK, Munich, Germany
| | - S Heidegger
- DKTK, Munich, Germany; Department of Medicine III, School of Medicine, Technical University of Munich, Munich, Germany
| | - M Bitzer
- Center for Personalized Medicine, Eberhard-Karls University, Tübingen, Germany; Department of Internal Medicine I, University Hospital, Eberhard-Karls University, Tübingen, Germany; DKTK, Tübingen, Germany
| | - M Scheytt
- Comprehensive Cancer Center Mainfranken, University of Würzburg, Würzburg, Germany; Department of Internal Medicine II, Würzburg University Medical Center, Würzburg, Germany
| | - B Brors
- German Cancer Consortium (DKTK), Heidelberg, Germany; Division of Applied Bioinformatics, DKFZ, Heidelberg, Germany
| | - D Hübschmann
- German Cancer Consortium (DKTK), Heidelberg, Germany; Computational Oncology Group, Molecular Precision Oncology Program, NCT Heidelberg and DKFZ, Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine, Heidelberg, Germany
| | - G Baretton
- Institute for Pathology, Faculty of Medicine Carl Gustav Carus, Technical University Dresden, Dresden, Germany
| | - A Stenzinger
- German Cancer Consortium (DKTK), Heidelberg, Germany; Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - K Steindorf
- Division of Physical Activity, Prevention and Cancer, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - A Benner
- Division of Biostatistics, DKFZ, Heidelberg, Germany
| | - D Jäger
- Department of Medical Oncology, NCT Heidelberg and Heidelberg University Hospital, Heidelberg, Germany
| | - C Heining
- Department of Translational Medical Oncology, NCT Dresden and DKFZ, Dresden, Germany; Center for Personalized Oncology, University Hospital Carl Gustav Carus, Technical University Dresden, Dresden, Germany; DKTK, Dresden, Germany
| | - H Glimm
- Department of Translational Medical Oncology, NCT Dresden and DKFZ, Dresden, Germany; Center for Personalized Oncology, University Hospital Carl Gustav Carus, Technical University Dresden, Dresden, Germany; DKTK, Dresden, Germany
| | - S Fröhling
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany; German Cancer Consortium (DKTK), Heidelberg, Germany
| | - R F Schlenk
- German Cancer Consortium (DKTK), Heidelberg, Germany; Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany; Department of Medical Oncology, NCT Heidelberg and Heidelberg University Hospital, Heidelberg, Germany; NCT Trial Center, NCT Heidelberg and DKFZ, Heidelberg, Germany.
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Elgaafary S, Hlevnjak M, Schulze M, Thewes V, Seitz J, Fremd C, Michel L, Beck K, Pfütze K, Richter D, Wolf S, Pixberg C, Hutter B, Ishaque N, Hirsch S, Gieldon L, Stenzinger A, Springfeld C, Kreutzfeld S, Horak P, Smetanay K, Mavratzas A, Brors B, Kirsten R, Trumpp A, Schütz F, Fröhling S, Sinn HP, Jäger D, Zapatka M, Lichter P, Schneeweiss A. Dauerhaftes Ansprechen auf Olaparib und endokrine Therapie bei einer Patientin mit metastasiertem luminalem Mammakarzinom und gBRCA-Mutation. Geburtshilfe Frauenheilkd 2020. [DOI: 10.1055/s-0040-1714539] [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: 03/22/2023] Open
Affiliation(s)
- S Elgaafary
- Gynäkologische Onkologie, Nationales Zentrum für Tumorerkrankungen (NCT), Universitätsklinikum Heidelberg und Deutsches Krebsforschungszentrum (DKFZ)
- Molekulardiagnostik-Programm, Nationales Zentrum für Tumorerkrankungen (NCT), Universitätsklinikum Heidelberg und Deutsches Krebsforschungszentrum (DKFZ)
| | - M Hlevnjak
- Molekulardiagnostik-Programm, Nationales Zentrum für Tumorerkrankungen (NCT), Universitätsklinikum Heidelberg und Deutsches Krebsforschungszentrum (DKFZ)
- Abteilung für Molekulargenetik, Deutsches Krebskonsortium (DKTK), Deutsches Krebsforschungszentrum (DKFZ)
| | - M Schulze
- Molekulardiagnostik-Programm, Nationales Zentrum für Tumorerkrankungen (NCT), Universitätsklinikum Heidelberg und Deutsches Krebsforschungszentrum (DKFZ)
- Abteilung für Molekulargenetik, Deutsches Krebskonsortium (DKTK), Deutsches Krebsforschungszentrum (DKFZ)
| | - V Thewes
- Gynäkologische Onkologie, Nationales Zentrum für Tumorerkrankungen (NCT), Universitätsklinikum Heidelberg und Deutsches Krebsforschungszentrum (DKFZ)
- Abteilung für Molekulargenetik, Deutsches Krebskonsortium (DKTK), Deutsches Krebsforschungszentrum (DKFZ)
| | - J Seitz
- Gynäkologische Onkologie, Nationales Zentrum für Tumorerkrankungen (NCT), Universitätsklinikum Heidelberg und Deutsches Krebsforschungszentrum (DKFZ)
| | - C Fremd
- Gynäkologische Onkologie, Nationales Zentrum für Tumorerkrankungen (NCT), Universitätsklinikum Heidelberg und Deutsches Krebsforschungszentrum (DKFZ)
| | - L Michel
- Gynäkologische Onkologie, Nationales Zentrum für Tumorerkrankungen (NCT), Universitätsklinikum Heidelberg und Deutsches Krebsforschungszentrum (DKFZ)
| | - K Beck
- Molekulardiagnostik-Programm, Nationales Zentrum für Tumorerkrankungen (NCT), Universitätsklinikum Heidelberg und Deutsches Krebsforschungszentrum (DKFZ)
- Abteilung Translationale Medizinische Onkologie, Nationales Zentrum für Tumorerkrankungen (NCT) Heidelberg/Dresden, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg/Dresden
| | - K Pfütze
- Molekulardiagnostik-Programm, Nationales Zentrum für Tumorerkrankungen (NCT), Universitätsklinikum Heidelberg und Deutsches Krebsforschungszentrum (DKFZ)
| | - D Richter
- Abteilung Translationale Medizinische Onkologie, Nationales Zentrum für Tumorerkrankungen (NCT) Heidelberg/Dresden, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg/Dresden
| | - S Wolf
- Kernfazilität Genomik und Proteomik, Deutsches Krebsforschungszentrum (DKFZ)
| | - C Pixberg
- Gynäkologische Onkologie, Nationales Zentrum für Tumorerkrankungen (NCT), Universitätsklinikum Heidelberg und Deutsches Krebsforschungszentrum (DKFZ)
- Molekulardiagnostik-Programm, Nationales Zentrum für Tumorerkrankungen (NCT), Universitätsklinikum Heidelberg und Deutsches Krebsforschungszentrum (DKFZ)
| | - B Hutter
- Molekulardiagnostik-Programm, Nationales Zentrum für Tumorerkrankungen (NCT), Universitätsklinikum Heidelberg und Deutsches Krebsforschungszentrum (DKFZ)
- Abteilung Angewandte Bioinformatik, Deutsches Krebsforschungszentrum (DKFZ)
| | - N Ishaque
- Molekulardiagnostik-Programm, Nationales Zentrum für Tumorerkrankungen (NCT), Universitätsklinikum Heidelberg und Deutsches Krebsforschungszentrum (DKFZ)
- Abteilung Theoretische Bioinformatik, Deutsches Krebsforschungszentrum (DKFZ)
| | - S Hirsch
- Institut für Humangenetik, Universität Heidelberg
| | - L Gieldon
- Molekulardiagnostik-Programm, Nationales Zentrum für Tumorerkrankungen (NCT), Universitätsklinikum Heidelberg und Deutsches Krebsforschungszentrum (DKFZ)
- Institut für Humangenetik, Universität Heidelberg
| | - A Stenzinger
- Institut für Pathologie, Universitätsklinikum Heidelberg
| | - C Springfeld
- Klinik für Medizinische Onkologie, Nationales Zentrum für Tumorerkrankungen (NCT), Universitätsklinikum Heidelberg
| | - S Kreutzfeld
- Molekulardiagnostik-Programm, Nationales Zentrum für Tumorerkrankungen (NCT), Universitätsklinikum Heidelberg und Deutsches Krebsforschungszentrum (DKFZ)
- Abteilung Translationale Medizinische Onkologie, Nationales Zentrum für Tumorerkrankungen (NCT) Heidelberg/Dresden, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg/Dresden
| | - P Horak
- Abteilung Translationale Medizinische Onkologie, Nationales Zentrum für Tumorerkrankungen (NCT) Heidelberg/Dresden, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg/Dresden
| | - K Smetanay
- Gynäkologische Onkologie, Nationales Zentrum für Tumorerkrankungen (NCT), Universitätsklinikum Heidelberg und Deutsches Krebsforschungszentrum (DKFZ)
| | - A Mavratzas
- Gynäkologische Onkologie, Nationales Zentrum für Tumorerkrankungen (NCT), Universitätsklinikum Heidelberg und Deutsches Krebsforschungszentrum (DKFZ)
| | - B Brors
- Abteilung Angewandte Bioinformatik, Deutsches Krebsforschungszentrum (DKFZ)
| | - R Kirsten
- Liquid Biobank, Nationales Zentrum für Tumorerkrankungen (NCT)
| | - A Trumpp
- Abteilung Stammzellen und Krebs, Deutsches Krebsforschungszentrum (DKFZ) und DKFZ-ZMBH-Bündnis
| | - F Schütz
- Klinik für Gynäkologie und Geburtshilfe, Universitätsklinikum Heidelberg
| | - S Fröhling
- Abteilung Translationale Medizinische Onkologie, Nationales Zentrum für Tumorerkrankungen (NCT) Heidelberg/Dresden, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg/Dresden
| | - H-P Sinn
- Institut für Pathologie, Universitätsklinikum Heidelberg
| | - D Jäger
- Klinik für Medizinische Onkologie, Nationales Zentrum für Tumorerkrankungen (NCT), Universitätsklinikum Heidelberg
| | - M Zapatka
- Abteilung für Molekulargenetik, Deutsches Krebskonsortium (DKTK), Deutsches Krebsforschungszentrum (DKFZ)
| | - P Lichter
- Molekulardiagnostik-Programm, Nationales Zentrum für Tumorerkrankungen (NCT), Universitätsklinikum Heidelberg und Deutsches Krebsforschungszentrum (DKFZ)
- Abteilung für Molekulargenetik, Deutsches Krebskonsortium (DKTK), Deutsches Krebsforschungszentrum (DKFZ)
| | - A Schneeweiss
- Gynäkologische Onkologie, Nationales Zentrum für Tumorerkrankungen (NCT), Universitätsklinikum Heidelberg und Deutsches Krebsforschungszentrum (DKFZ)
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Lang M, Leménager T, Streit F, Fauth-Bühler M, Frank J, Juraeva D, Witt S, Degenhardt F, Hofmann A, Heilmann-Heimbach S, Kiefer F, Brors B, Grabe HJ, John U, Bischof A, Bischof G, Völker U, Homuth G, Beutel M, Lind P, Medland S, Slutske W, Martin N, Völzke H, Nöthen M, Meyer C, Rumpf HJ, Wurst F, Rietschel M, Mann K. Genome-wide association study of pathological gambling. Eur Psychiatry 2020; 36:38-46. [DOI: 10.1016/j.eurpsy.2016.04.001] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 03/09/2016] [Accepted: 04/01/2016] [Indexed: 12/18/2022] Open
Abstract
AbstractBackgroundPathological gambling is a behavioural addiction with negative economic, social, and psychological consequences. Identification of contributing genes and pathways may improve understanding of aetiology and facilitate therapy and prevention. Here, we report the first genome-wide association study of pathological gambling. Our aims were to identify pathways involved in pathological gambling, and examine whether there is a genetic overlap between pathological gambling and alcohol dependence.MethodsFour hundred and forty-five individuals with a diagnosis of pathological gambling according to the Diagnostic and Statistical Manual of Mental Disorders were recruited in Germany, and 986 controls were drawn from a German general population sample. A genome-wide association study of pathological gambling comprising single marker, gene-based, and pathway analyses, was performed. Polygenic risk scores were generated using data from a German genome-wide association study of alcohol dependence.ResultsNo genome-wide significant association with pathological gambling was found for single markers or genes. Pathways for Huntington's disease (P-value = 6.63 × 10−3); 5′-adenosine monophosphate-activated protein kinase signalling (P-value = 9.57 × 10−3); and apoptosis (P-value = 1.75 × 10−2) were significant. Polygenic risk score analysis of the alcohol dependence dataset yielded a one-sided nominal significant P-value in subjects with pathological gambling, irrespective of comorbid alcohol dependence status.ConclusionsThe present results accord with previous quantitative formal genetic studies which showed genetic overlap between non-substance- and substance-related addictions. Furthermore, pathway analysis suggests shared pathology between Huntington's disease and pathological gambling. This finding is consistent with previous imaging studies.
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Horak P, Kreutzfeldt S, Mock A, Heining C, Heilig C, Möhrmann L, Uhrig S, Hübschmann D, Beck K, Richter D, Schlenk R, Klink B, Hutter B, Weichert W, Stenzinger A, Schröck E, Brors B, Glimm H, Fröhling S. Comprehensive genomic and transcriptomic profiling in advanced-stage cancers and rare malignancies: Clinical results from the MASTER trial of the German Cancer Consortium. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz413.085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Mock A, Heilig C, Kreutzfeldt S, Hübschmann D, Heining C, Schröck E, Brors B, Stenzinger A, Jäger D, Schlenk R, Glimm H, Fröhling S, Horak P. Community-driven development of a modified progression-free survival ratio for precision oncology trials. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz413.101] [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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Heilig C, Hübschmann D, Kopp HG, Metzeler K, Richter S, Hermes B, von Bubnoff N, Kindler T, Siveke J, Wagner S, Ochsenreither S, Süße H, Brors B, Benner A, Jäger D, Von Kalle C, Glimm H, Gröschel S, Fröhling S, Schlenk R. Randomized phase II study of trabectedin/olaparib compared to physician’s choice in subjects with previously treated advanced or recurrent solid tumors harboring dna repair deficiencies. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz268.106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Roider T, Frauhammer F, Seufert J, Bordas M, Stolarczyk M, Rabe S, Malm J, Bruch P, Hundemer M, Rippe K, Goeppert B, Seiffert M, Brors B, Mechtersheimer G, Müller-Tidow C, Fröhling S, Schlesner M, Huber W, Anders S, Dietrich S. TRANSCRIPTIONAL AND GENOMIC INTRA-TUMOR HETEROGENEITY DRIVES SUBCLONE SPECIFIC DRUG RESPONSES IN DIFFUSE LARGE B CELL LYMPHOMA. Hematol Oncol 2019. [DOI: 10.1002/hon.45_2629] [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: 11/10/2022]
Affiliation(s)
- T. Roider
- Department of Medicine V; Hematology, Oncology and Rheumatology, University of Heidelberg; Heidelberg Germany
| | - F. Frauhammer
- Centre for Molecular Biology; University of Heidelberg; Heidelberg Germany
| | - J. Seufert
- Bioinformatics and Omics Data Analytics; German Cancer Research Center (DKFZ); Heidelberg Germany
| | - M. Bordas
- Department of Molecular Genetics; German Cancer Research Center (DKFZ); Heidelberg Germany
| | - M. Stolarczyk
- Department of Medicine V; Hematology, Oncology and Rheumatology, University of Heidelberg; Heidelberg Germany
| | - S. Rabe
- Department of Medicine V; Hematology, Oncology and Rheumatology, University of Heidelberg; Heidelberg Germany
| | - J. Malm
- Division of Chromatin Networks; German Cancer Research Center (DKFZ) and Bioquant; Heidelberg Germany
| | - P. Bruch
- Department of Medicine V; Hematology, Oncology and Rheumatology, University of Heidelberg; Heidelberg Germany
| | - M. Hundemer
- Department of Medicine V; Hematology, Oncology and Rheumatology, University of Heidelberg; Heidelberg Germany
| | - K. Rippe
- Division of Chromatin Networks; German Cancer Research Center (DKFZ) and Bioquant; Heidelberg Germany
| | - B. Goeppert
- Institute of Pathology; University of Heidelberg; Heidelberg Germany
| | - M. Seiffert
- Department of Molecular Genetics; German Cancer Research Center (DKFZ); Heidelberg Germany
| | - B. Brors
- Bioinformatics and Omics Data Analytics; German Cancer Research Center (DKFZ); Heidelberg Germany
| | - G. Mechtersheimer
- Institute of Pathology; University of Heidelberg; Heidelberg Germany
| | - C. Müller-Tidow
- Department of Medicine V; Hematology, Oncology and Rheumatology, University of Heidelberg; Heidelberg Germany
| | - S. Fröhling
- Translational Oncology; National Center for Tumor Diseases (NCT); Heidelberg Germany
| | - M. Schlesner
- Bioinformatics and Omics Data Analytics; German Cancer Research Center (DKFZ); Heidelberg Germany
| | - W. Huber
- Genome Biology; European Molecular Biology Laboratory (EMBL); Heidelberg Germany
| | - S. Anders
- Centre for Molecular Biology; University of Heidelberg; Heidelberg Germany
| | - S. Dietrich
- Department of Medicine V; Hematology, Oncology and Rheumatology, University of Heidelberg; Heidelberg Germany
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Abstract
Summary
Objectives:
Many methods for statistical analysis of gene expression studies by DNA microarrays produce lists of genes as output. To understand gene lists in terms of traditional biology, e.g. which pathways may be affected, it is necessary to get appropriate annotations for the probes on an array.
Methods:
Problems arise with the different sources that have been used by manufacturers to design microarray probes, and their association to biological entities like genes, transcripts and proteins. Function annotation is of crucial importance, and systems like Gene Ontology can be used for this purpose. It arranges annotation terms in a hierarchical manner and thus makes annotations in a gene list amenable to automated analysis.
Results:
Several methods for analyses of gene function are described. The hierarchical nature of systems like Gene Ontology particularly suggests using methods from graph theory.
Conclusions:
The main problem in annotating micro-array probes and inferring affected functional modules is the incompleteness and degree of error in current biological databases. Initial approaches to make use of functional annotation exist, but have to be extended, in particular with respect to estimating the statistical significance of results.
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Dieter S, Heining C, Agaimy A, Huebschmann D, Bonekamp D, Hutter B, Ehrenberg K, Fröhlich M, Schlesner M, Scholl C, Schlemmer HP, Wolf S, Mavratzas A, Jung C, Gröschel S, von Kalle C, Eils R, Brors B, Penzel R, Kriegsmann M, Reuss D, Schirmacher P, Stenzinger A, Federspil P, Weichert W, Glimm H, Fröhling S. Mutant KIT as imatinib-sensitive target in metastatic sinonasal carcinoma. Ann Oncol 2017; 28:142-148. [DOI: 10.1093/annonc/mdw446] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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Kurilov R, Juraeva D, Weese D, Klein T, Kapushesky M, Brors B. Drug response prediction system for personalized cancer therapy. Eur J Cancer 2016. [DOI: 10.1016/s0959-8049(16)32838-6] [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: 11/29/2022]
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Vazquez VF, Mughal S, Brors B, Raab M. Characterization of dabrafenib resistance mechanisms in multiple myeloma. Eur J Cancer 2016. [DOI: 10.1016/s0959-8049(16)61411-9] [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: 11/29/2022]
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Czink E, Heining C, Weber TF, Lasitschka F, Schemmer P, Schirmacher P, Weiss KH, Glimm H, Brors B, Weichert W, Jäger D, Fröhling S, Springfeld C. [Durable remission under dual HER2 blockade with Trastuzumab and Pertuzumab in a patient with metastatic gallbladder cancer]. Z Gastroenterol 2016; 54:426-30. [PMID: 27171333 DOI: 10.1055/s-0042-103498] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Gallbladder cancer represents a rare but dismal disease. The only curative option is complete surgical resection, though patients often develop recurrent disease. In patients with advanced biliary tract cancer, the combination of cisplatin and gemcitabine showed a benefit in overall survival compared to gemcitabine alone. However, there is no standardized second-line regimen after treatment failure. We report on a young patient with early recurrence of a gallbladder cancer with cutaneous and peritoneal metastases. Upon identification of an ERBB2 gene amplification within the NCT MASTER (Molecularly Aided Stratification for Tumor Eradication Research) exome sequencing program with resulting overexpression of HER2 in the tumors cells, the patient received a targeted therapy with the HER2 antibodies pertuzumab and trastuzumab in combination with nab-paclitaxel, which led to a durable remission for more than one year. This case report underlines the potential of molecularly aided personalized targeted therapy for patients with biliary tract cancer and the need for respective clinical trials.
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Affiliation(s)
- E Czink
- Universitätsklinikum Heidelberg, Nationales Centrum für Tumorerkrankungen, Abteilung Medizinische Onkologie * Sektion Personalisierte Onkologie
| | - C Heining
- Nationales Centrum für Tumorerkrankungen und Deutsches Krebsforschungszentrum (DKFZ), Abteilung Translationale Onkologie
| | - T F Weber
- Universitätsklinikum Heidelberg, Abteilung Diagnostische und Interventionelle Radiologie
| | - F Lasitschka
- Universitätsklinikum Heidelberg, Pathologisches Institut
| | - P Schemmer
- Universitätsklinikum Heidelberg, Abteilung für Allgemein-, Viszeral- & Transplantationschirurgie
| | - P Schirmacher
- Universitätsklinikum Heidelberg, Pathologisches Institut
| | - K H Weiss
- Universitätsklinikum Heidelberg, Abteilung Gastroenterologie, Infektionskrankheiten, Vergiftungen
| | - H Glimm
- Nationales Centrum für Tumorerkrankungen und Deutsches Krebsforschungszentrum (DKFZ), Abteilung Translationale Onkologie
| | - B Brors
- Deutsches Krebsforschungszentrum (DKFZ), Abteilung Angewandte Bioinformatik
| | - W Weichert
- Universitätsklinikum Heidelberg, Pathologisches Institut
| | - D Jäger
- Universitätsklinikum Heidelberg, Nationales Centrum für Tumorerkrankungen, Abteilung Medizinische Onkologie * Sektion Personalisierte Onkologie
| | - S Fröhling
- Nationales Centrum für Tumorerkrankungen und Deutsches Krebsforschungszentrum (DKFZ), Abteilung Translationale Onkologie
| | - C Springfeld
- Universitätsklinikum Heidelberg, Nationales Centrum für Tumorerkrankungen, Abteilung Medizinische Onkologie * Sektion Personalisierte Onkologie
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14
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Kordes M, Röring M, Heining C, Braun S, Hutter B, Richter D, Geörg C, Scholl C, Gröschel S, Roth W, Rosenwald A, Geissinger E, von Kalle C, Jäger D, Brors B, Weichert W, Grüllich C, Glimm H, Brummer T, Fröhling S. Cooperation of BRAF(F595L) and mutant HRAS in histiocytic sarcoma provides new insights into oncogenic BRAF signaling. Leukemia 2015; 30:937-46. [PMID: 26582644 DOI: 10.1038/leu.2015.319] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Revised: 10/22/2015] [Accepted: 10/26/2015] [Indexed: 12/19/2022]
Abstract
Activating BRAF mutations, in particular V600E/K, drive many cancers and are considered mutually exclusive with mutant RAS, whereas inactivating BRAF mutations in the D(594)F(595)G(596) motif cooperate with RAS via paradoxical MEK/ERK activation. Due to the increasing use of comprehensive tumor genomic profiling, many non-V600 BRAF mutations are being detected whose functional consequences and therapeutic actionability are often unknown. We investigated an atypical BRAF mutation, F595L, which was identified along with mutant HRAS in histiocytic sarcoma and also occurs in epithelial cancers, melanoma and neuroblastoma, and determined its interaction with mutant RAS. Unlike other DFG motif mutants, BRAF(F595L) is a gain-of-function variant with intermediate activity that does not act paradoxically, but nevertheless cooperates with mutant RAS to promote oncogenic signaling, which is efficiently blocked by pan-RAF and MEK inhibitors. Mutation data from patients and cell lines show that BRAF(F595L), as well as other intermediate-activity BRAF mutations, frequently coincide with mutant RAS in various cancers. These data define a distinct class of activating BRAF mutations, extend the spectrum of patients with systemic histiocytoses and other malignancies who are candidates for therapeutic blockade of the RAF-MEK-ERK pathway and underscore the value of comprehensive genomic testing for uncovering the vulnerabilities of individual tumors.
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Affiliation(s)
- M Kordes
- Department of Medical Oncology, National Center for Tumor Diseases (NCT), Heidelberg, Germany.,Department of Internal Medicine VI, Heidelberg University Hospital, Heidelberg, Germany
| | - M Röring
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK), Freiburg, Germany
| | - C Heining
- Department of Translational Oncology, NCT Heidelberg, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Section for Personalized Oncology, Heidelberg University Hospital, Heidelberg, Germany.,DKTK, Heidelberg, Germany
| | - S Braun
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK), Freiburg, Germany
| | - B Hutter
- DKTK, Heidelberg, Germany.,Division of Applied Bioinformatics, DKFZ and NCT Heidelberg, Heidelberg, Germany
| | - D Richter
- Department of Translational Oncology, NCT Heidelberg, German Cancer Research Center (DKFZ), Heidelberg, Germany.,DKTK, Heidelberg, Germany
| | - C Geörg
- Department of Translational Oncology, NCT Heidelberg, German Cancer Research Center (DKFZ), Heidelberg, Germany.,DKTK, Heidelberg, Germany.,DKFZ-Heidelberg Center for Personalized Oncology (HIPO), Heidelberg, Germany
| | - C Scholl
- Department of Translational Oncology, NCT Heidelberg, German Cancer Research Center (DKFZ), Heidelberg, Germany.,DKTK, Heidelberg, Germany
| | - S Gröschel
- Department of Translational Oncology, NCT Heidelberg, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Section for Personalized Oncology, Heidelberg University Hospital, Heidelberg, Germany.,DKTK, Heidelberg, Germany
| | - W Roth
- Institute of Pathology, Heidelberg University Hospital and NCT Heidelberg, Heidelberg, Germany
| | - A Rosenwald
- Institute of Pathology, Comprehensive Cancer Center Mainfranken, University of Würzburg and Würzburg University Hospital, Würzburg, Germany
| | - E Geissinger
- Institute of Pathology, Comprehensive Cancer Center Mainfranken, University of Würzburg and Würzburg University Hospital, Würzburg, Germany
| | - C von Kalle
- Department of Translational Oncology, NCT Heidelberg, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Section for Personalized Oncology, Heidelberg University Hospital, Heidelberg, Germany.,DKTK, Heidelberg, Germany.,DKFZ-Heidelberg Center for Personalized Oncology (HIPO), Heidelberg, Germany
| | - D Jäger
- Department of Medical Oncology, National Center for Tumor Diseases (NCT), Heidelberg, Germany.,Department of Internal Medicine VI, Heidelberg University Hospital, Heidelberg, Germany
| | - B Brors
- DKTK, Heidelberg, Germany.,Division of Applied Bioinformatics, DKFZ and NCT Heidelberg, Heidelberg, Germany
| | - W Weichert
- DKTK, Heidelberg, Germany.,Institute of Pathology, Heidelberg University Hospital and NCT Heidelberg, Heidelberg, Germany
| | - C Grüllich
- Department of Medical Oncology, National Center for Tumor Diseases (NCT), Heidelberg, Germany.,Department of Internal Medicine VI, Heidelberg University Hospital, Heidelberg, Germany
| | - H Glimm
- Department of Translational Oncology, NCT Heidelberg, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Section for Personalized Oncology, Heidelberg University Hospital, Heidelberg, Germany.,DKTK, Heidelberg, Germany
| | - T Brummer
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK), Freiburg, Germany
| | - S Fröhling
- Department of Translational Oncology, NCT Heidelberg, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Section for Personalized Oncology, Heidelberg University Hospital, Heidelberg, Germany.,DKTK, Heidelberg, Germany
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15
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Witt SH, Juraeva D, Sticht C, Strohmaier J, Meier S, Treutlein J, Dukal H, Frank J, Lang M, Deuschle M, Schulze TG, Degenhardt F, Mattheisen M, Brors B, Cichon S, Nöthen MM, Witt CC, Rietschel M. Investigation of manic and euthymic episodes identifies state- and trait-specific gene expression and STAB1 as a new candidate gene for bipolar disorder. Transl Psychiatry 2014; 4:e426. [PMID: 25136889 PMCID: PMC4150244 DOI: 10.1038/tp.2014.71] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 06/23/2014] [Indexed: 12/28/2022] Open
Abstract
Bipolar disorder (BD) is a highly heritable psychiatric disease characterized by recurrent episodes of mania and depression. To identify new BD genes and pathways, the present study employed a three-step approach. First, gene-expression profiles of BD patients were assessed during both a manic and an euthymic phase. These profiles were compared intra-individually and with the gene-expression profiles of controls. Second, those differentially expressed genes that were considered potential trait markers of BD were validated using data from the Psychiatric Genomics Consortiums' genome-wide association study (GWAS) of BD. Third, the implicated molecular mechanisms were investigated using pathway analytical methods. In the present patients, this novel approach identified: (i) sets of differentially expressed genes specific to mania and euthymia; and (ii) a set of differentially expressed genes that were common to both mood states. In the GWAS data integration analysis, one gene (STAB1) remained significant (P=1.9 × 10(-4)) after adjustment for multiple testing. STAB1 is located in close proximity to PBMR1 and the NEK4-ITIH1-ITIH3-ITIH4 region, which are the top findings from GWAS meta-analyses of mood disorder, and a combined BD and schizophrenia data set. Pathway analyses in the mania versus control comparison revealed three distinct clusters of pathways tagging molecular mechanisms implicated in BD, for example, energy metabolism, inflammation and the ubiquitin proteasome system. The present findings suggest that STAB1 is a new and highly promising candidate gene in this region. The combining of gene expression and GWAS data may provide valuable insights into the biological mechanisms of BD.
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Affiliation(s)
- S H Witt
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim/Heidelberg University, Mannheim, Germany,Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim/Heidelberg University, J5, Mannheim 68159, Germany. E-mail:
| | - D Juraeva
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - C Sticht
- Medical Research Center, University Hospital Mannheim, Medical Faculty Mannheim/Heidelberg University, Mannheim, Germany
| | - J Strohmaier
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim/Heidelberg University, Mannheim, Germany
| | - S Meier
- National Center for Register-based Research, Aarhus University, Aarhus C, Denmark
| | - J Treutlein
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim/Heidelberg University, Mannheim, Germany
| | - H Dukal
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim/Heidelberg University, Mannheim, Germany
| | - J Frank
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim/Heidelberg University, Mannheim, Germany
| | - M Lang
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim/Heidelberg University, Mannheim, Germany
| | - M Deuschle
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim/Heidelberg University, Mannheim, Germany
| | - T G Schulze
- Section of Psychiatric Genetics, Department of Psychiatry and Psychotherapy, University Medical Centre Göttingen, Göttingen, Germany
| | - F Degenhardt
- Institute of Human Genetics, University of Bonn, Bonn, Germany,Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
| | - M Mattheisen
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark,Department of Genomic Mathematics, University of Bonn, Bonn, Germany
| | - B Brors
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - S Cichon
- Department of Medical Genetics, University Hospital Basel, Basel, Switzerland
| | - M M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany,Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
| | - C C Witt
- Department of Anaesthesiology and Operative Intensive Care, University Hospital Mannheim, Medical Faculty Mannheim/Heidelberg University, Mannheim, Germany
| | - M Rietschel
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim/Heidelberg University, Mannheim, Germany
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16
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Hauser C, Hutter B, Buchhalter I, Shavinskaya A, Abba M, Yazdanparast H, Eils R, Brors B, Allgayer H. 431: Identification of deregulated genes in colorectal cancer metastasis through whole genome and transcriptome sequencing. Eur J Cancer 2014. [DOI: 10.1016/s0959-8049(14)50385-1] [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: 11/30/2022]
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17
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Treutlein J, Juraeva D, Scholz H, Frank J, Ridinger M, Mann K, Kiefer F, Nöthen M, Brors B, Spanagel R, Rietschel M. Gene-set based analysis for alcohol dependence. Suchttherapie 2013. [DOI: 10.1055/s-0033-1351592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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18
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Sterz C, Oberthuer A, Juraeva D, Schmidt R, Faldum A, Berthold F, Hero B, Brors B, Fischer M. A novel treatment stratification system for current low- and intermediate-risk neuroblastoma patients using gene expression-based classification. Klin Padiatr 2013. [DOI: 10.1055/s-0033-1343642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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19
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Kocak H, Ackermann S, Hero B, Kahlert Y, Oberthuer A, Juraeva D, Roels F, Theissen J, Westermann F, Deubzer H, Ehemann V, Brors B, Odenthal M, Berthold F, Fischer M. Hox-C9 activates the intrinsic pathway of apoptosis and is associated with spontaneous regression in neuroblastoma. Cell Death Dis 2013; 4:e586. [PMID: 23579273 PMCID: PMC3668636 DOI: 10.1038/cddis.2013.84] [Citation(s) in RCA: 163] [Impact Index Per Article: 14.8] [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] [Indexed: 11/09/2022]
Abstract
Neuroblastoma is an embryonal malignancy of the sympathetic nervous system. Spontaneous regression and differentiation of neuroblastoma is observed in a subset of patients, and has been suggested to represent delayed activation of physiologic molecular programs of fetal neuroblasts. Homeobox genes constitute an important family of transcription factors, which play a fundamental role in morphogenesis and cell differentiation during embryogenesis. In this study, we demonstrate that expression of the majority of the human HOX class I homeobox genes is significantly associated with clinical covariates in neuroblastoma using microarray expression data of 649 primary tumors. Moreover, a HOX gene expression-based classifier predicted neuroblastoma patient outcome independently of age, stage and MYCN amplification status. Among all HOX genes, HOXC9 expression was most prominently associated with favorable prognostic markers. Most notably, elevated HOXC9 expression was significantly associated with spontaneous regression in infant neuroblastoma. Re-expression of HOXC9 in three neuroblastoma cell lines led to a significant reduction in cell viability, and abrogated tumor growth almost completely in neuroblastoma xenografts. Neuroblastoma growth arrest was related to the induction of programmed cell death, as indicated by an increase in the sub-G1 fraction and translocation of phosphatidylserine to the outer membrane. Programmed cell death was associated with the release of cytochrome c from the mitochondria into the cytosol and activation of the intrinsic cascade of caspases, indicating that HOXC9 re-expression triggers the intrinsic apoptotic pathway. Collectively, our results show a strong prognostic impact of HOX gene expression in neuroblastoma, and may point towards a role of Hox-C9 in neuroblastoma spontaneous regression.
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Affiliation(s)
- H Kocak
- Children's Hospital, Department of Pediatric Oncology and Hematology and Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
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20
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Jones DTW, Zapatka M, Jäger N, Wang Q, Stuetz A, Rausch T, Benes V, Blake J, Korshunov A, Schmidt M, Bartholomae C, Witt O, Taylor MD, Kalle CV, Brors B, Eils R, Korbel J, Lichter P, Pfister SM. First Results from the International Cancer Genome Consortium PedBrain Tumor Project on Whole-Genome Deep Sequencing in Medulloblastoma. Klin Padiatr 2011. [DOI: 10.1055/s-0031-1292588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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21
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Afanasyeva EA, Mestdagh P, Kumps C, Vandesompele J, Ehemann V, Theissen J, Fischer M, Zapatka M, Brors B, Savelyeva L, Sagulenko V, Speleman F, Schwab M, Westermann F. MicroRNA miR-885-5p targets CDK2 and MCM5, activates p53 and inhibits proliferation and survival. Cell Death Differ 2011; 18:974-84. [PMID: 21233845 PMCID: PMC3131937 DOI: 10.1038/cdd.2010.164] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2010] [Revised: 10/28/2010] [Accepted: 11/02/2010] [Indexed: 12/19/2022] Open
Abstract
Several microRNA (miRNA) loci are found within genomic regions frequently deleted in primary neuroblastoma, including miR-885-5p at 3p25.3. In this study, we demonstrate that miR-885-5p is downregulated on loss of 3p25.3 region in neuroblastoma. Experimentally enforced miR-885-5p expression in neuroblastoma cell lines inhibits proliferation triggering cell cycle arrest, senescence and/or apoptosis. miR-885-5p leads to the accumulation of p53 protein and activates the p53 pathway, resulting in upregulation of p53 targets. Enforced miR-885-5p expression consistently leads to downregulation of cyclin-dependent kinase (CDK2) and mini-chromosome maintenance protein (MCM5). Both genes are targeted by miR-885-5p via predicted binding sites within the 3'-untranslated regions (UTRs) of CDK2 and MCM5. Transcript profiling after miR-885-5p introduction in neuroblastoma cells reveals alterations in expression of multiple genes, including several p53 target genes and a number of factors involved in p53 pathway activity. Taken together, these data provide evidence that miR-885-5p has a tumor suppressive role in neuroblastoma interfering with cell cycle progression and cell survival.
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Affiliation(s)
- E A Afanasyeva
- Department of Tumor Genetics, B030, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg, Germany
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22
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Ackermann S, Hero B, Ehemann V, Kocak H, Oberthuer A, Brors B, Westermann F, Kahlert Y, Odenthal M, Berthold F, Fischer M. Identification and characterization of FoxP1 as a candidate tumor suppressor gene in neuroblastoma. Klin Padiatr 2011. [DOI: 10.1055/s-0031-1277076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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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23
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Feuerborn A, Srivastava PK, Küffer S, Grandy WA, Sijmonsma TP, Gretz N, Brors B, Gröne HJ. The Forkhead factor FoxQ1 influences epithelial differentiation. J Cell Physiol 2011; 226:710-9. [PMID: 20717954 DOI: 10.1002/jcp.22385] [Citation(s) in RCA: 45] [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] [Indexed: 01/12/2023]
Abstract
The Forkhead family of transcription factors comprises numerous members and is implicated in various cellular functions, including cell growth, apoptosis, migration, and differentiation. In this study, we identified the Forkhead factor FoxQ1 as increased in expression during TGF-β1 induced changes in epithelial differentiation, suggesting functional roles of FoxQ1 for epithelial plasticity. The repression of FoxQ1 in mammary epithelial cells led to a change in cell morphology characterized by an increase in cell size, pronounced cell-cell contacts, and an increased expression of several junction proteins (e.g., E-cadherin). In addition, FoxQ1 knock-down cells revealed rearrangements in the actin-cytoskeleton and slowed down cell cycle G1-phase progression. Furthermore, repression of FoxQ1 enhanced the migratory capacity of coherent mammary epithelial cells. Gene expression profiling of NM18 cells indicated that FoxQ1 is a relevant downstream mediator of TGF-β1-induced gene expression changes. This included the differential expression of transcription factors involved in epithelial plasticity, for example, Ets-1, Zeb1, and Zeb2. In summary, this study has elucidated the functional impact of FoxQ1 on epithelial differentiation.
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Affiliation(s)
- A Feuerborn
- Department of Cellular and Molecular Pathology, German Cancer Research Centre (DKFZ), Heidelberg, Germany.
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24
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Oberthuer A, Juraeva D, Li L, Kahlert Y, Westermann F, Eils R, Berthold F, Shi L, Wolfinger RD, Fischer M, Brors B. Comparison of performance of one-color and two-color gene-expression analyses in predicting clinical endpoints of neuroblastoma patients. Pharmacogenomics J 2010; 10:258-66. [PMID: 20676065 PMCID: PMC2920066 DOI: 10.1038/tpj.2010.53] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Microarray-based prediction of clinical endpoints may be performed using either a one-color approach reflecting mRNA abundance in absolute intensity values or a two-color approach yielding ratios of fluorescent intensities. In this study, as part of the MAQC-II project, we systematically compared the classification performance resulting from one- and two-color gene-expression profiles of 478 neuroblastoma samples. In total, 196 classification models were applied to these measurements to predict four clinical endpoints, and classification performances were compared in terms of accuracy, area under the curve, Matthews correlation coefficient and root mean-squared error. Whereas prediction performance varied with distinct clinical endpoints and classification models, equivalent performance metrics were observed for one- and two-color measurements in both internal and external validation. Furthermore, overlap of selected signature genes correlated inversely with endpoint prediction difficulty. In summary, our data strongly substantiate that the choice of platform is not a primary factor for successful gene expression based-prediction of clinical endpoints.
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Affiliation(s)
- A Oberthuer
- Department of Pediatric Oncology and Hematology, Children's Hospital, and Center for Molecular Medicine Cologne (ZMMK), University of Cologne, Köln, Germany
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25
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Oberthuer A, Hero B, Juraeva D, Faldum A, Kahlert Y, Asgharzadeh S, Seeger R, Scaruffi P, Tonini GP, Janoueix-Lerosey I, Delattre O, Schleiermacher G, Vandesompele J, Vermeulen J, Speleman F, Noguera R, Piqueras M, Bénard J, Valent A, Avigad S, Yaniv I, Weber A, Christiansen H, Grundy RG, Schardt K, Schwab M, Eils R, Warnat P, Kaderali L, Simon T, DeCarolis B, Theissen J, Westermann F, Brors B, Berthold F, Fischer M. Gene expression-based classification improves risk estimation of neuroblastoma patients. Klin Padiatr 2010. [DOI: 10.1055/s-0030-1254478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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26
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Effenberger K, Borgen E, Bartkowiak K, zu Eulenburg C, Brors B, Kaaresen R, Nesland J, Pantel K, Naume B. Clinical Relevance of Early Disseminated Breast Cancer Cells Depends on Their Cytokeratin Expression Pattern. Cancer Res 2009. [DOI: 10.1158/0008-5472.sabcs-09-3021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: The factors determining the clinical relevance of disseminated tumor cells (DTC) in breast cancer patients are largely unknown. Here we compared the specificity and clinical performance of two anti-cytokeratin(CK) antibodies frequently used for DTC detection, namely A45-B/B3 (A45) and AE1/AE3 (AE). Additionally we explored the CK gene expression patterns in primary breast tumors.Methods: Specificities of antibodies A45 and AE for selected CKs were assessed by 2-DE western blot analysis. Using these antibodies bone marrow aspirates from 391 breast cancer patients (M0, pT1-3, pN0-3) were screened for the presence of DTC. To obtain prognostic information, patients were followed up over a median of 83 months for time to relapse and 99 months for time to death. Two breast cancer patient datasets (Oslo (n=123), and van de Vijver et al. (NEJM 2002; n=295)) were analysed for CK primary tumor gene expression patterns and grouped by hormone receptor (HR) status of the primary tumors. T-tests and hierarchial clustering analyses were applied.Results: AE detected CK5, CK7, CK8, and CK19, whereas A45 recognized CK7 and CK18. In total, 24 of 391 patients (6.1%) were DTC-positive for A45, and 41 (10.5%) for AE. Although concordance between the two antibodies was 84.4%, overlap among positive cases was only 3.2%. DTC-positivity with AE and A45 was more frequent in patients of higher nodal status (p=0.019 and p=0.036, respectively). Nearly all patients with A45-positive DTC had hormone receptor-positive tumors (23/24), while detection of AE-positive DTC was more frequent among hormone receptor negative patients (p=0.006). Clear differences in primary tumor CK expression patterns between HR+ and HR- tumors were detected in both datasets. Compared to HR- tumors, CKs up-regulated in HR+ tumors were CK8 and 18, in addition CK19 in two datasets, whereas e.g. CK5, CK6, CK7, CK14, CK15, CK16, and CK17 were significantly down-regulated.Survival analyses of all patients revealed shorter distant disease-free survival (p=0.039) for patients with A45-positive DTC, whereas the prognostic relevance of AE-positive DTC was restricted to node positive patients.Conclusion: The clinical utility of immunocytochemical DTC detection depends on the anti-CK antibody used, which may reflect the complex CK composition of DTC. Tumor CK expression patterns and their correlation to antibody-sprecific DTC detection will further be explored by A45- and AE- staining of corresponding patient samples.
Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 3021.
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Affiliation(s)
| | - E. Borgen
- 2The Norwegian Radium Hospital, Oslo University Hospital, Norway
| | - K. Bartkowiak
- 1University Medical Center Hamburg-Eppendorf, Germany
| | | | - B. Brors
- 5Deutsches Krebsforschungsinstitut, Germany
| | - R. Kaaresen
- 4Ulleval Hospital, Oslo University Hospital, Norway
| | - J. Nesland
- 2The Norwegian Radium Hospital, Oslo University Hospital, Norway
| | - K. Pantel
- 1University Medical Center Hamburg-Eppendorf, Germany
| | - B. Naume
- 3The Norwegian Radium Hospital, Oslo University Hospital, University of Oslo, Norway
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27
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Bruns I, Czibere A, Fischer JC, Roels F, Cadeddu RP, Buest S, Bruennert D, Huenerlituerkoglu AN, Stoecklein NH, Singh R, Zerbini LF, Jäger M, Kobbe G, Gattermann N, Kronenwett R, Brors B, Haas R. The hematopoietic stem cell in chronic phase CML is characterized by a transcriptional profile resembling normal myeloid progenitor cells and reflecting loss of quiescence. Leukemia 2009; 23:892-9. [PMID: 19158832 DOI: 10.1038/leu.2008.392] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We found that composition of cell subsets within the CD34+ cell population is markedly altered in chronic phase (CP) chronic myeloid leukemia (CML). Specifically, proportions and absolute cell counts of common myeloid progenitors (CMP) and megakaryocyte-erythrocyte progenitors (MEP) are significantly greater in comparison to normal bone marrow whereas absolute numbers of hematopoietic stem cells (HSC) are equal. To understand the basis for this, we performed gene expression profiling (Affymetrix HU-133A 2.0) of the distinct CD34+ cell subsets from six patients with CP CML and five healthy donors. Euclidean distance analysis revealed a remarkable transcriptional similarity between the CML patients' HSC and normal progenitors, especially CMP. CP CML HSC were transcriptionally more similar to their progeny than normal HSC to theirs, suggesting a more mature phenotype. Hence, the greatest differences between CP CML patients and normal donors were apparent in HSC including downregulation of genes encoding adhesion molecules, transcription factors, regulators of stem-cell fate and inhibitors of cell proliferation in CP CML. Impaired adhesive and migratory capacities were functionally corroborated by fibronectin detachment analysis and transwell assays, respectively. Based on our findings we propose a loss of quiescence of the CML HSC on detachment from the niche leading to expansion of myeloid progenitors.
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Affiliation(s)
- I Bruns
- Department of Hematology, Oncology and Clinical Immunology, Heinrich-Heine-University Düsseldorf, Duesseldorf, Germany.
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28
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Nowacki S, Skowron M, Oberthuer A, Fagin A, Voth H, Brors B, Westermann F, Eggert A, Hero B, Berthold F, Fischer M. Expression of the tumour suppressor gene CADM1 is associated with favourable outcome and inhibits cell survival in neuroblastoma. Oncogene 2007; 27:3329-38. [DOI: 10.1038/sj.onc.1210996] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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29
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Diaz-Blanco E, Bruns I, Neumann F, Fischer JC, Graef T, Rosskopf M, Brors B, Pechtel S, Bork S, Koch A, Baer A, Rohr UP, Kobbe G, von Haeseler A, Gattermann N, Haas R, Kronenwett R. Molecular signature of CD34+ hematopoietic stem and progenitor cells of patients with CML in chronic phase. Leukemia 2007; 21:494-504. [PMID: 17252012 DOI: 10.1038/sj.leu.2404549] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.3] [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: 01/18/2023]
Abstract
In this study, we provide a molecular signature of highly enriched CD34+ cells from bone marrow of untreated patients with chronic myelogenous leukemia (CML) in chronic phase in comparison with normal CD34+ cells using microarrays covering 8746 genes. Expression data reflected several BCR-ABL-induced effects in primary CML progenitors, such as transcriptional activation of the classical mitogen-activated protein kinase pathway and the phosphoinositide-3 kinase/AKT pathway as well as downregulation of the proapoptotic gene IRF8. Moreover, novel transcriptional changes in comparison with normal CD34+ cells were identified. These include upregulation of genes involved in the transforming growth factorbeta pathway, fetal hemoglobin genes, leptin receptor, sorcin, tissue inhibitor of metalloproteinase 1, the neuroepithelial cell transforming gene 1 and downregulation of selenoprotein P. Additionally, genes associated with early hematopoietic stem cells (HSC) and leukemogenesis such as HoxA9 and MEIS1 were transcriptionally activated. Differential expression of differentiation-associated genes suggested an altered composition of the CD34+ cell population in CML. This was confirmed by subset analyses of chronic phase CML CD34+ cells showing an increase of the proportion of megakaryocyte-erythroid progenitors, whereas the proportion of HSC and granulocyte-macrophage progenitors was decreased in CML. In conclusion, our results give novel insights into the biology of CML and could provide the basis for identification of new therapeutic targets.
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MESH Headings
- Antigens, CD34/analysis
- Apoptosis/genetics
- Cell Adhesion/genetics
- Cell Differentiation/genetics
- Cell Division/genetics
- DNA, Complementary/genetics
- DNA, Neoplasm/genetics
- Fusion Proteins, bcr-abl/analysis
- Fusion Proteins, bcr-abl/genetics
- Gene Expression Profiling
- Gene Expression Regulation, Leukemic
- Hematopoietic Stem Cells/chemistry
- Humans
- Intercellular Signaling Peptides and Proteins/biosynthesis
- Intercellular Signaling Peptides and Proteins/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- Leukemia, Myeloid, Chronic-Phase/genetics
- Leukemia, Myeloid, Chronic-Phase/metabolism
- Leukemia, Myeloid, Chronic-Phase/pathology
- Neoplasm Proteins/analysis
- Neoplasm Proteins/biosynthesis
- Neoplasm Proteins/genetics
- Neoplastic Stem Cells/chemistry
- RNA, Messenger/genetics
- RNA, Neoplasm/genetics
- Receptors, Cell Surface/biosynthesis
- Receptors, Cell Surface/genetics
- Receptors, Growth Factor/biosynthesis
- Receptors, Growth Factor/genetics
- Receptors, Leptin
- Signal Transduction/genetics
- Up-Regulation
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Affiliation(s)
- E Diaz-Blanco
- Department of Hematology, Oncology and Clinical Immunology, University of Duesseldorf, Duesseldorf, Germany
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30
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Frank O, Brors B, Fabarius A, Li L, Haak M, Merk S, Schwindel U, Zheng C, Müller MC, Gretz N, Hehlmann R, Hochhaus A, Seifarth W. Gene expression signature of primary imatinib-resistant chronic myeloid leukemia patients. Leukemia 2006; 20:1400-7. [PMID: 16728981 DOI: 10.1038/sj.leu.2404270] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Although the selective tyrosine kinase inhibitor imatinib is successfully used in the treatment of chronic myeloid leukemia (CML), inherent mechanisms confer primary resistance to leukemic patients. In order to search for potentially useful genes in predicting cytogenetic response, a retrospective gene expression study was performed. Leukocyte RNA isolated before imatinib from interferon-alpha-pretreated chronic phase CML patients (n=34) with or without major cytogenetic remission (< or =35% Philadelphia (Ph)+ metaphases) during the first year of treatment was comparatively analyzed using Affymetrix U133A chips. Using support vector machines for gene classification, an outcome-specific gene expression signature consisting of 128 genes was identified. Comparative expression data of specific genes point to changes in apoptosis (e.g. casp9, tumor necrosis factor receptor-associated protein 1, hras), DNA repair (msh3, ddb2), oxidative stress protection (glutathione synthetase, paraoxonase 2, vanin 1) and centrosomes (inhibitor of differentiation-1) within primary resistant patients. Independent statistical approaches and quantitative real-time reverse transcriptase-polymerase chain reaction studies support the clinical relevance of gene profiling. In conclusion, this study establishes a candidate predictor of imatinib resistance in interferon-alpha-pretreated CML patients to be subjected to future investigation in a larger independent patient cohort. The resulting expression signature point to involvement of BCR-ABL-independent mechanisms of resistance.
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Affiliation(s)
- O Frank
- III. Medizinische Klinik, Fakultät für Klinische Medizin Mannheim der Universität Heidelberg, Universitätsklinikum Mannheim der Ruprecht-Karls-Universität Heidelberg, Mannheim, Germany.
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31
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Zheng C, Li L, Haak M, Brors B, Frank O, Giehl M, Fabarius A, Schatz M, Weisser A, Lorentz C, Gretz N, Hehlmann R, Hochhaus A, Seifarth W. Gene expression profiling of CD34+ cells identifies a molecular signature of chronic myeloid leukemia blast crisis. Leukemia 2006; 20:1028-34. [PMID: 16617318 DOI: 10.1038/sj.leu.2404227] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [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: 02/08/2023]
Abstract
Despite recent success in the treatment of early-stage disease, blastic phase (BP) of chronic myeloid leukemia (CML) that is characterized by rapid expansion of therapy-refractory and differentiation-arrested blasts, remains a therapeutic challenge. The development of resistance upon continuous administration of imatinib mesylate is associated with poor prognosis pointing to the need for alternative therapeutic strategies and a better understanding of the molecular mechanisms underlying disease progression. To identify transcriptional signatures that may explain pathological characteristics and aggressive behavior of BP blasts, we performed comparative gene expression profiling on CD34+ Ph+ cells purified from patients with untreated newly diagnosed chronic phase CML (CP, n=11) and from patients in BP (n=9) using Affymetrix oligonucleotide arrays. Supervised microarray data analysis revealed 114 differentially expressed genes (P<10(-4)), 34 genes displaying more than two-fold transcriptional changes when comparing CP and BP groups. While 24 of these genes were downregulated, 10 genes, especially suppressor of cytokine signalling 2 (SOCS2), CAMPATH-1 antigen (CD52), and four human leukocyte antigen-related genes were strongly overexpressed in BP. Expression of selected genes was validated by real-time-polymerase chain reaction and flow cytometry. Our data suggest the existence of a common gene expression profile of CML-BP and provide new insight into the molecular phenotype of blasts associated with disease progression and high malignancy.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Antigens, CD/genetics
- Antigens, CD34/biosynthesis
- Antigens, CD34/genetics
- Antigens, Differentiation, B-Lymphocyte/genetics
- Antigens, Neoplasm/genetics
- Blast Crisis/genetics
- Blast Crisis/pathology
- CD52 Antigen
- Cell Separation
- Cell Transformation, Neoplastic/genetics
- Female
- Flow Cytometry
- Gene Expression Profiling
- Glycoproteins/genetics
- Histocompatibility Antigens Class II/genetics
- Humans
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/diagnosis
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- Leukemia, Myeloid, Chronic-Phase/genetics
- Leukemia, Myeloid, Chronic-Phase/pathology
- Male
- Middle Aged
- Oligonucleotide Array Sequence Analysis
- Reverse Transcriptase Polymerase Chain Reaction
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Affiliation(s)
- C Zheng
- III. Medizinische Universitätsklinik, Fakultät für Klinische Medizin Mannheim der Ruprecht-Karls-Universität Heidelberg, Mannheim, Germany
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32
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Lin J, Zeller S, Huber J, Dietrich N, Feng Y, Vom Hagen F, Ozog M, Ivaschenko Y, Brors B, Hammes HP. Gene expression and neovascularization: analysis of mouse retinae by gene microarray. DIABETOL STOFFWECHS 2006. [DOI: 10.1055/s-2006-943846] [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: 10/19/2022]
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33
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Schneeweiss A, Thuerigen O, Toedt G, Warnat P, Hahn M, Rudlowski C, Benner A, Brors B, Sohn C, Lichter P. Gene expression profiles predict pathologic complete response to preoperative chemotherapy with gemcitabine, epirubicin and docetaxel in primary breast cancer. J Clin Oncol 2005. [DOI: 10.1200/jco.2005.23.16_suppl.2001] [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: 11/20/2022] Open
Affiliation(s)
- A. Schneeweiss
- Univ, Heidelberg, Germany; German Cancer Research Ctr, Heidelberg, Germany
| | - O. Thuerigen
- Univ, Heidelberg, Germany; German Cancer Research Ctr, Heidelberg, Germany
| | - G. Toedt
- Univ, Heidelberg, Germany; German Cancer Research Ctr, Heidelberg, Germany
| | - P. Warnat
- Univ, Heidelberg, Germany; German Cancer Research Ctr, Heidelberg, Germany
| | - M. Hahn
- Univ, Heidelberg, Germany; German Cancer Research Ctr, Heidelberg, Germany
| | - C. Rudlowski
- Univ, Heidelberg, Germany; German Cancer Research Ctr, Heidelberg, Germany
| | - A. Benner
- Univ, Heidelberg, Germany; German Cancer Research Ctr, Heidelberg, Germany
| | - B. Brors
- Univ, Heidelberg, Germany; German Cancer Research Ctr, Heidelberg, Germany
| | - C. Sohn
- Univ, Heidelberg, Germany; German Cancer Research Ctr, Heidelberg, Germany
| | - P. Lichter
- Univ, Heidelberg, Germany; German Cancer Research Ctr, Heidelberg, Germany
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34
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Neumann F, Teutsch N, Kliszewski S, Bork S, Steidl U, Brors B, Schimkus N, Roes N, Germing U, Hildebrandt B, Royer-Pokora B, Eils R, Gattermann N, Haas R, Kronenwett R. Gene expression profiling of Philadelphia chromosome (Ph)-negative CD34+ hematopoietic stem and progenitor cells of patients with Ph-positive CML in major molecular remission during therapy with imatinib. Leukemia 2005; 19:458-60. [PMID: 15618956 DOI: 10.1038/sj.leu.2403615] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
MESH Headings
- Adult
- Aged
- Antigens, CD34/biosynthesis
- Antigens, CD34/genetics
- Antigens, CD34/immunology
- Benzamides
- Female
- Fusion Proteins, bcr-abl/genetics
- Gene Expression Profiling
- Hematopoietic Stem Cells/immunology
- Hematopoietic Stem Cells/metabolism
- Humans
- Imatinib Mesylate
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/immunology
- Leukemia, Myeloid, Chronic-Phase/drug therapy
- Leukemia, Myeloid, Chronic-Phase/genetics
- Male
- Middle Aged
- Philadelphia Chromosome
- Phylogeny
- Piperazines/therapeutic use
- Protein-Tyrosine Kinases/antagonists & inhibitors
- Pyrimidines/therapeutic use
- Remission Induction/methods
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35
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Brors B. Microarray annotation and biological information on function. Methods Inf Med 2005; 44:468-72. [PMID: 16113775] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
OBJECTIVES Many methods for statistical analysis of gene expression studies by DNA microarrays produce lists of genes as output. To understand gene lists in terms of traditional biology, e.g. which pathways may be affected, it is necessary to get appropriate annotations for the probes on an array. METHODS Problems arise with the different sources that have been used by manufacturers to design microarray probes, and their association to biological entities like genes, transcripts and proteins. Function annotation is of crucial importance, and systems like Gene Ontology can be used for this purpose. It arranges annotation terms in a hierarchical manner and thus makes annotations in a gene list amenable to automated analysis. RESULTS Several methods for analyses of gene function are described. The hierarchical nature of systems like Gene Ontology particularly suggests using methods from graph theory. CONCLUSIONS The main problem in annotating microarray probes and inferring affected functional modules is the incompleteness and degree of error in current biological databases. Initial approaches to make use of functional annotation exist, but have to be extended, in particular with respect to estimating the statistical significance of results.
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Affiliation(s)
- B Brors
- Dept. Theoretical Bioinformatics, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
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36
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Schramm A, Schulte JH, Klein-Hitpass L, Havers W, Sieverts H, Berwanger B, Christiansen H, Simon T, Berthold F, Warnat P, Brors B, Eils J, Eils R, Eggert A. Prediction of clinical outcome and biological characterization of neuroblastoma by expression profiling. Klin Padiatr 2004. [DOI: 10.1055/s-2004-828592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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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Abstract
Correspondence analysis is an explorative computational method for the study of associations between variables. Much like principal component analysis, it displays a low-dimensional projection of the data, e.g., into a plane. It does this, though, for two variables simultaneously, thus revealing associations between them. Here, we demonstrate the applicability of correspondence analysis to and high value for the analysis of microarray data, displaying associations between genes and experiments. To introduce the method, we show its application to the well-known Saccharomyces cerevisiae cell-cycle synchronization data by Spellman et al. [Spellman, P. T., Sherlock, G., Zhang, M. Q., Iyer, V. R., Anders, K., Eisen, M. B., Brown, P. O., Botstein, D. & Futcher, B. (1998) Mol. Biol. Cell 9, 3273-3297], allowing for comparison with their visualization of this data set. Furthermore, we apply correspondence analysis to a non-time-series data set of our own, thus supporting its general applicability to microarray data of different complexity, underlying structure, and experimental strategy (both two-channel fluorescence-tag and radioactive labeling).
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Affiliation(s)
- K Fellenberg
- Department of Theoretical Bioinformatics, German Cancer Research Center, PO 101949, D-69009 Heidelberg, Germany
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Rasmussen T, Scheide D, Brors B, Kintscher L, Weiss H, Friedrich T. Identification of Two Tetranuclear FeS Clusters on the Ferredoxin-Type Subunit of NADH:Ubiquinone Oxidoreductase (Complex I). Biochemistry 2001; 40:6124-31. [PMID: 11352750 DOI: 10.1021/bi0026977] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.7] [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: 11/30/2022]
Abstract
The proton-translocating NADH:ubiquinone oxidoreductase of respiratory chains (complex I) contains one flavin mononucleotide and five EPR-detectable iron-sulfur clusters as redox groups. Because of the number of conserved motifs typical for binding iron-sulfur clusters and the high content of iron and acid-labile sulfide of complex I preparations, it is predicted that complex I contains additional clusters which have not yet been detected by EPR spectroscopy. To search for such clusters, we used a combination of UV/vis and EPR spectroscopy to study complex I from Neurospora crassa and Escherichia coli adjusted to distinct redox states. We detected a UV/vis redox difference spectrum characterized by negative absorbances at 325 and 425 nm that could not be assigned to the known redox groups. Redox titration was used to determine the pH-independent midpoint potential to be -270 mV, being associated with the transfer of two electrons. Comparison with UV/vis difference spectra obtained from complex I fragments and related enzymes showed that this group is localized on subunit Nuo21.3c of the N. crassa or NuoI of the E. coli complex I, respectively. This subunit (the bovine TYKY) belongs to a family of 8Fe-ferredoxins which contain two tetranuclear iron-sulfur clusters as redox groups. We detected EPR signals in a fragment of complex I which we attribute to the novel FeS clusters of complex I.
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Affiliation(s)
- T Rasmussen
- Institut für Biochemie, Heinrich-Heine-Universität, Universitätsstrasse 1, 40225 Düsseldorf, Germany
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39
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Beissbarth T, Fellenberg K, Brors B, Arribas-Prat R, Boer J, Hauser NC, Scheideler M, Hoheisel JD, Schütz G, Poustka A, Vingron M. Processing and quality control of DNA array hybridization data. Bioinformatics 2000; 16:1014-22. [PMID: 11159313 DOI: 10.1093/bioinformatics/16.11.1014] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.1] [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: 11/14/2022] Open
Abstract
MOTIVATION The technology of hybridization to DNA arrays is used to obtain the expression levels of many different genes simultaneously. It enables searching for genes that are expressed specifically under certain conditions. However, the technology produces large amounts of data demanding computational methods for their analysis. It is necessary to find ways to compare data from different experiments and to consider the quality and reproducibility of the data. RESULTS Data analyzed in this paper have been generated by hybridization of radioactively labeled targets to DNA arrays spotted on nylon membranes. We introduce methods to compare the intensity values of several hybridization experiments. This is essential to find differentially expressed genes or to do pattern analysis. We also discuss possibilities for quality control of the acquired data. AVAILABILITY http://www.dkfz.de/tbi CONTACT M.Vingron@dkfz-heidelberg.de
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Affiliation(s)
- T Beissbarth
- Abt. Theoretische Bioinformatik, Deutsches Krebsforschungszentrum, INF 280, D-69120 Heidelberg, Germany
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40
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Friedrich T, Brors B, Hellwig P, Kintscher L, Rasmussen T, Scheide D, Schulte U, Mäntele W, Weiss H. Characterization of two novel redox groups in the respiratory NADH:ubiquinone oxidoreductase (complex I). Biochim Biophys Acta 2000; 1459:305-9. [PMID: 11004444 DOI: 10.1016/s0005-2728(00)00165-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The proton-pumping NADH:ubiquinone oxidoreductase is the first of the respiratory chain complexes in many bacteria and mitochondria of most eukaryotes. The bacterial complex consists of 14 different subunits. Seven peripheral subunits bear all known redox groups of complex I, namely one FMN and five EPR-detectable iron-sulfur (FeS) clusters. The remaining seven subunits are hydrophobic proteins predicted to fold into 54 alpha-helices across the membrane. Little is known about their function, but they are most likely involved in proton translocation. The mitochondrial complex contains in addition to the homologues of these 14 subunits at least 29 additional proteins that do not directly participate in electron transfer and proton translocation. A novel redox group has been detected in the Neurospora crassa complex, in an amphipathic fragment of the Escherichia coli complex I and in a related hydrogenase and ferredoxin by means of UV/Vis spectroscopy. This group is made up by the two tetranuclear FeS clusters located on NuoI (the bovine TYKY) which have not been detected by EPR spectroscopy yet. Furthermore, we present evidence for the existence of a novel redox group located in the membrane arm of the complex. Partly reduced complex I equilibrated to a redox potential of -150 mV gives a UV/Vis redox difference spectrum that cannot be attributed to the known cofactors. Electrochemical titration of this absorption reveals a midpoint potential of -80 mV. This group is believed to transfer electrons from the high potential FeS cluster to ubiquinone.
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Affiliation(s)
- T Friedrich
- Institut für Biochemie, Universität Düsseldorf, Universitätsstrasse, Germany.
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41
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Schulte U, Haupt V, Abelmann A, Fecke W, Brors B, Rasmussen T, Friedrich T, Weiss H. A reductase/isomerase subunit of mitochondrial NADH:ubiquinone oxidoreductase (complex I) carries an NADPH and is involved in the biogenesis of the complex. J Mol Biol 1999; 292:569-80. [PMID: 10497022 DOI: 10.1006/jmbi.1999.3096] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Respiratory chains of bacteria and mitochondria contain closely related forms of the proton-pumping NADH:ubiquinone oxidoreductase, or complex I. The bacterial complex I consists of 14 subunits, whereas the mitochondrial complex contains some 25 extra subunits in addition to the homologues of the bacterial subunits. One of these extra subunits with a molecular mass of 40 kDa belongs to a heterogeneous family of reductases/isomerases with a conserved nucleotide binding site. We deleted this subunit in Neurospora crassa by gene disruption. In the mutant nuo 40, a complex I lacking the 40 kDa subunit is assembled. The mutant complex I does not contain tightly bound NADPH present in wild-type complex I. This NADPH cofactor is not connected to the respiratory electron pathway of complex I. The mutant complex has normal NADH dehydrogenase activity and contains the redox groups known for wild-type complex I, one flavin mononucleotide and four iron-sulfur clusters detectable by electron paramagnetic resonance spectroscopy. In the mutant complex these groups are all readily reduced by NADH. However, the mutant complex is not capable of reducing ubiquinone. A recently described redox group identified in wild-type complex I by UV-visible spectroscopy is not detectable in the mutant complex. We propose that the reductase/isomerase subunit with its NADPH cofactor takes part in the biosynthesis of this new redox group.
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Affiliation(s)
- U Schulte
- Institut für Biochemie, Heinrich-Heine-Universität, Düsseldorf, Germany.
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42
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Friedrich T, Abelmann A, Brors B, Guénebaut V, Kintscher L, Leonard K, Rasmussen T, Scheide D, Schlitt A, Schulte U, Weiss H. Redox components and structure of the respiratory NADH:ubiquinone oxidoreductase (complex I). Biochim Biophys Acta 1998; 1365:215-9. [PMID: 9693737 DOI: 10.1016/s0005-2728(98)00070-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The proton-pumping NADH:ubiquinone oxidoreductase is the first complex in the respiratory chains of many purple bacteria and of mitochondria of most eucaryotes. The bacterial complex consists of 14 different subunits. The mitochondrial complex contains at least 29 additional proteins that do not directly participate in electron transfer and proton translocation. We analysed electron micrographs of isolated and negatively stained complex I particles from Escherichia coli and Neurospora crassa and obtained three-dimensional models of both complexes at medium resolution. Both have the same L-shaped overall structure with a peripheral arm protruding into the aqueous phase and a membrane arm extending into the membrane. The two arms of the bacterial complex are only slightly shorter than those of the mitochondrial complex although the protein mass of the former is only half of that of the latter. The presence of a novel redox group in the membrane arm of the complex is discussed. This group has been detected in the N. crassa complex by means of UV-visible spectroscopy. After reduction with an excess of NADH and reoxidation by the lactate dehydrogenase reaction, a reduced-minus-oxidized difference spectrum was obtained that cannot be attributed to the known cofactors flavin mononucleotide (FMN) and the FeS clusters N1, N2, N3 and N4. Due to its positive midpoint potential the novel group is believed to transfer electrons from the FeS clusters to ubiquinone. Its role in proton translocation is discussed.
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Affiliation(s)
- T Friedrich
- Institut für Biochemie, Universität Düsseldorf, Germany.
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Schulte U, Abelmann A, Amling N, Brors B, Friedrich T, Kintscher L, Rasmussen T, Weiss H. Search for novel redox groups in mitochondrial NADH:ubiquinone oxidoreductase (complex I) by diode array UV/VIS spectroscopy. Biofactors 1998; 8:177-86. [PMID: 9914816 DOI: 10.1002/biof.5520080303] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The proton-translocating NADH:ubiquinone oxidoreductase of mitochondria (complex I) is a large L-shaped multisubunit complex. The peripheral matrix arm contains one FMN and a number of iron-sulfur (FeS) clusters and is involved in NADH oxidation and electron transfer to the membrane intrinsic arm. There, following a yet unknown mechanism, the redox-driven proton translocation and the ubiquinone reduction take place. Redox groups that would be able to link electron transfer with proton translocation have not been found so far in the membrane arm. We searched for such groups in complex I isolated from Neurospora crassa. Under anaerobic conditions, the preparation was analyzed in different redox states by means of UV/VIS and EPR spectroscopy. Absorption bands in the UV/VIS redox difference spectra were found which cannot be attributed to the FMN or the EPR detectable FeS clusters. The existence of two novel groups is postulated and their possible locations in the electron pathway and their roles in proton translocation are discussed.
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Affiliation(s)
- U Schulte
- Institut für Biochemie, Heinrich-Heine-Universität Düsseldorf, Germany.
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Schneider R, Brors B, Bürger F, Camrath S, Weiss H. Two genes of the putative mitochondrial fatty acid synthase in the genome of Saccharomyces cerevisiae. Curr Genet 1997; 32:384-8. [PMID: 9388293 DOI: 10.1007/s002940050292] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.6] [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: 02/05/2023]
Abstract
In order to find further genes of the mitochondrial fatty acid synthase, we searched the genome of Saccharomyces cerevisiae for sequences that are homologous to conserved regions of bacterial fatty acid synthase genes. We found the gene products of ORF YKL055c (EMBL Accession No. X75781) and of YOR221C (EMBL Accession No. X92441) to be homologous to bacterial 3-oxoacyl-(acyl carrier protein) reductases and to malonyl-CoA:ACP-transferases, respectively. We disrupted these two genes which in both cases led to a respiratory deficient phenotype, as is the case for the genes encoding a mitochondrial acyl carrier protein and a beta-ketoacyl-ACP synthase. We propose to call the above mentioned genes OAR1 [3-oxo-acyl-(acyl carrier protein) reductase] and MCT1 (malonyl-CoA:ACP transferase). They are presumed to be part of a type-II mitochondrial fatty acid synthase, a relic of the endosymbiontic origin of mitochondria, delivering substrates for phospholipid re-modelling and/or repair.
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Affiliation(s)
- R Schneider
- Institut für Biochemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany.
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Abstract
Genes that encode mitochondrial homologues to the bacterial enzymes of fatty acid synthesis were found in various eukaryotic species. Inactivation of these genes leads to a disturbed mitochondrial respiration and an increase in mitochondrial lysophospholipids. We postulate that there is a mitochondrial biosynthetic system providing fatty acids for phospholipid repair. The mitochondrial acyl carrier protein may also play another role, supporting the formation of the respiratory NADH:ubiquinone oxidoreductase.
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Affiliation(s)
- R Schneider
- Institut für Biochemie, Heinrich-Heine-Universität Düsseldorf, Germany.
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