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Diexer S, Klee B, Gottschick C, Broda A, Purschke O, Binder M, Gekle M, Girndt M, Hoell JI, Moor I, Sedding D, Rosendahl J, Mikolajczyk R. Insights into early recovery from Long COVID-results from the German DigiHero Cohort. Sci Rep 2024; 14:8569. [PMID: 38609482 PMCID: PMC11015032 DOI: 10.1038/s41598-024-59122-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 04/08/2024] [Indexed: 04/14/2024] Open
Abstract
65 million people worldwide are estimated to suffer from long-term symptoms after their SARS-CoV-2 infection (Long COVID). However, there is still little information about the early recovery among those who initially developed Long COVID, i.e. had symptoms 4-12 weeks after infection but no symptoms after 12 weeks. We aimed to identify associated factors with this early recovery. We used data from SARS-CoV-2-infected individuals from the DigiHero study. Participants provided information about their SARS-CoV-2 infections and symptoms at the time of infection, 4-12 weeks, and more than 12 weeks post-infection. We performed multivariable logistic regression to identify factors associated with early recovery from Long COVID and principal component analysis (PCA) to identify groups among symptoms. 5098 participants reported symptoms at 4-12 weeks after their SARS-CoV-2 infection, of which 2441 (48%) reported no symptoms after 12 weeks. Men, younger participants, individuals with mild course of acute infection, individuals infected with the Omicron variant, and individuals who did not seek medical care in the 4-12 week period after infection had a higher chance of early recovery. In the PCA, we identified four distinct symptom groups. Our results indicate differential risk of continuing symptoms among individuals who developed Long COVID. The identified risk factors are similar to those for the development of Long COVID, so people with these characteristics are at higher risk not only for developing Long COVID, but also for longer persistence of symptoms. Those who sought medical help were also more likely to have persistent symptoms.
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Affiliation(s)
- Sophie Diexer
- Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Interdisciplinary Centre for Health Sciences, Medical Faculty of the Martin Luther University Halle-Wittenberg, Magdeburger Str. 8, 06112, Halle (Saale), Germany
| | - Bianca Klee
- Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Interdisciplinary Centre for Health Sciences, Medical Faculty of the Martin Luther University Halle-Wittenberg, Magdeburger Str. 8, 06112, Halle (Saale), Germany
| | - Cornelia Gottschick
- Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Interdisciplinary Centre for Health Sciences, Medical Faculty of the Martin Luther University Halle-Wittenberg, Magdeburger Str. 8, 06112, Halle (Saale), Germany
| | - Anja Broda
- Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Interdisciplinary Centre for Health Sciences, Medical Faculty of the Martin Luther University Halle-Wittenberg, Magdeburger Str. 8, 06112, Halle (Saale), Germany
| | - Oliver Purschke
- Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Interdisciplinary Centre for Health Sciences, Medical Faculty of the Martin Luther University Halle-Wittenberg, Magdeburger Str. 8, 06112, Halle (Saale), Germany
| | - Mascha Binder
- Department of Internal Medicine IV, Oncology/Haematology, Martin Luther University Halle-Wittenberg, Ernst-Grube-Str. 40, 06120, Halle (Saale), Germany
- Division of Medical Oncology, University Hospital Basel, Basel, Switzerland, Petersgraben 4, 4031, Basel, Switzerland
| | - Michael Gekle
- Julius-Bernstein-Institute of Physiology, Medical Faculty of the Martin Luther University Halle-Wittenberg, Magdeburger Str. 6, 06110, Halle (Saale), Germany
| | - Matthias Girndt
- Department of Internal Medicine II, Martin Luther University Halle-Wittenberg, Ernst-Grube-Str. 40, 06120, Halle (Saale), Germany
| | - Jessica I Hoell
- Paediatric Haematology and Oncology, Martin Luther University Halle-Wittenberg, Ernst-Grube-Str. 40, 06120, Halle (Saale), Germany
| | - Irene Moor
- Institute for Medical Sociology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 8, 06112, Halle (Saale), Germany
| | - Daniel Sedding
- Mid-German Heart Centre, Department of Cardiology and Intensive Care Medicine, University Hospital, Martin Luther University Halle-Wittenberg, Ernst-Grube-Str. 40, 06120, Halle (Saale), Germany
| | - Jonas Rosendahl
- Department of Internal Medicine I, Martin Luther University Halle-Wittenberg, Ernst-Grube-Str. 40, 06120, Halle (Saale), Germany
| | - Rafael Mikolajczyk
- Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Interdisciplinary Centre for Health Sciences, Medical Faculty of the Martin Luther University Halle-Wittenberg, Magdeburger Str. 8, 06112, Halle (Saale), Germany.
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2
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Fischer C, Willscher E, Paschold L, Gottschick C, Klee B, Diexer S, Bosurgi L, Dutzmann J, Sedding D, Frese T, Girndt M, Hoell JI, Gekle M, Addo MM, Schulze Zur Wiesch J, Mikolajczyk R, Binder M, Schultheiß C. SARS-CoV-2 vaccination may mitigate dysregulation of IL-1/IL-18 and gastrointestinal symptoms of the post-COVID-19 condition. NPJ Vaccines 2024; 9:23. [PMID: 38316833 PMCID: PMC10844289 DOI: 10.1038/s41541-024-00815-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 01/24/2024] [Indexed: 02/07/2024] Open
Abstract
The rapid development of safe and effective vaccines helped to prevent severe disease courses after SARS-CoV-2 infection and to mitigate the progression of the COVID-19 pandemic. While there is evidence that vaccination may reduce the risk of developing post-COVID-19 conditions (PCC), this effect may depend on the viral variant. Therapeutic effects of post-infection vaccination have been discussed but the data for individuals with PCC remains inconclusive. In addition, extremely rare side effects after SARS-CoV-2 vaccination may resemble the heterogeneous PCC phenotype. Here, we analyze the plasma levels of 25 cytokines and SARS-CoV-2 directed antibodies in 540 individuals with or without PCC relative to one or two mRNA-based COVID-19 vaccinations as well as in 20 uninfected individuals one month after their initial mRNA-based COVID-19 vaccination. While none of the SARS-CoV-2 naïve individuals reported any persisting sequelae or exhibited PCC-like dysregulation of plasma cytokines, we detected lower levels of IL-1β and IL-18 in patients with ongoing PCC who received one or two vaccinations at a median of six months after infection as compared to unvaccinated PCC patients. This reduction correlated with less frequent reporting of persisting gastrointestinal symptoms. These data suggest that post-infection vaccination in patients with PCC might be beneficial in a subgroup of individuals displaying gastrointestinal symptoms.
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Affiliation(s)
- Claudia Fischer
- Division of Medical Oncology, University Hospital Basel, Basel, Switzerland
- Laboratory of Translational Immuno-Oncology, Department of Biomedicine, University, and University Hospital Basel, Basel, Switzerland
| | - Edith Willscher
- Department of Internal Medicine IV, Oncology/Hematology, Martin Luther University Halle-Wittenberg, Halle, (Saale), Germany
| | - Lisa Paschold
- Department of Internal Medicine IV, Oncology/Hematology, Martin Luther University Halle-Wittenberg, Halle, (Saale), Germany
| | - Cornelia Gottschick
- Institute for Medical Epidemiology, Biometrics, and Informatics (IMEBI), Interdisciplinary Center for Health Sciences, Medical School of the Martin Luther University Halle-Wittenberg, Halle, (Saale), Germany
| | - Bianca Klee
- Institute for Medical Epidemiology, Biometrics, and Informatics (IMEBI), Interdisciplinary Center for Health Sciences, Medical School of the Martin Luther University Halle-Wittenberg, Halle, (Saale), Germany
| | - Sophie Diexer
- Institute for Medical Epidemiology, Biometrics, and Informatics (IMEBI), Interdisciplinary Center for Health Sciences, Medical School of the Martin Luther University Halle-Wittenberg, Halle, (Saale), Germany
| | - Lidia Bosurgi
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Protozoa Immunology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Jochen Dutzmann
- Mid-German Heart Center, Department of Cardiology and Intensive Care Medicine, University Hospital, Martin Luther University Halle-Wittenberg, Halle, (Saale), Germany
| | - Daniel Sedding
- Mid-German Heart Center, Department of Cardiology and Intensive Care Medicine, University Hospital, Martin Luther University Halle-Wittenberg, Halle, (Saale), Germany
| | - Thomas Frese
- Institute of General Practice and Family Medicine, Martin-Luther-University Halle-Wittenberg, Halle, (Saale), Germany
| | - Matthias Girndt
- Department of Internal Medicine II, Martin Luther University Halle-Wittenberg, Halle, (Saale), Germany
| | - Jessica I Hoell
- Pediatric Hematology and Oncology, Martin Luther University Halle-Wittenberg, Halle, (Saale), Germany
| | - Michael Gekle
- Julius Bernstein-Institute of Physiology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, Halle, (Saale), Germany
| | - Marylyn M Addo
- I. Department of Internal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Braunschweig, Germany
- University Medical Center Hamburg-Eppendorf, Institute for Infection Research and Vaccine Development (IIRVD), Hamburg, Germany
| | | | - Rafael Mikolajczyk
- Institute for Medical Epidemiology, Biometrics, and Informatics (IMEBI), Interdisciplinary Center for Health Sciences, Medical School of the Martin Luther University Halle-Wittenberg, Halle, (Saale), Germany
| | - Mascha Binder
- Division of Medical Oncology, University Hospital Basel, Basel, Switzerland
- Laboratory of Translational Immuno-Oncology, Department of Biomedicine, University, and University Hospital Basel, Basel, Switzerland
| | - Christoph Schultheiß
- Division of Medical Oncology, University Hospital Basel, Basel, Switzerland.
- Laboratory of Translational Immuno-Oncology, Department of Biomedicine, University, and University Hospital Basel, Basel, Switzerland.
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3
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Diexer S, Klee B, Gottschick C, Xu C, Broda A, Purschke O, Binder M, Frese T, Girndt M, Hoell JI, Moor I, Gekle M, Mikolajczyk R. Association between virus variants, vaccination, previous infections, and post-COVID-19 risk. Int J Infect Dis 2023; 136:14-21. [PMID: 37634619 DOI: 10.1016/j.ijid.2023.08.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/19/2023] [Accepted: 08/23/2023] [Indexed: 08/29/2023] Open
Abstract
OBJECTIVES The SARS-CoV-2 Omicron variant has spread rapidly and has been the dominant variant since 2022. The course of acute infection, in a vaccinated population, with Omicron is milder compared with earlier variants. However, little is known about how the occurrence of long-term symptoms after Omicron infection compared with other variants is modulated by previous infections and/or vaccinations. METHODS Participants of the DigiHero study provided information about their SARS-CoV-2 infections, vaccinations, and symptoms 12 or more weeks after infection (post-COVID-19 condition - PCC). RESULTS Participants infected with wildtype SARS-CoV-2 had the highest PCC risk (adjusted odds ratio [aOR] 6.44, 95% confidence interval (CI): 5.49; 7.56), followed by participants infected with Alpha and Delta compared with the reference group (individuals infected with Omicron having received three or more vaccinations). Among those infected with a specific variant, the number of preceding vaccinations was not associated with a risk reduction for PCC, whereas previous infection was strongly associated with a lower PCC risk (aOR 0.14, 95% CI 0.07; 0.25). CONCLUSIONS While infection with Omicron is less likely to result in PCC compared with previous variants, lack of protection by vaccination suggests a substantial challenge for the healthcare system during the early endemic period. In the midterm, the protective effects of previous infections can reduce the burden of PCC.
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Affiliation(s)
- Sophie Diexer
- Institute for Medical Epidemiology, Biometrics, and Informatics (IMEBI), Interdisciplinary Centre for Health Sciences, Medical Faculty of the Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Bianca Klee
- Institute for Medical Epidemiology, Biometrics, and Informatics (IMEBI), Interdisciplinary Centre for Health Sciences, Medical Faculty of the Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Cornelia Gottschick
- Institute for Medical Epidemiology, Biometrics, and Informatics (IMEBI), Interdisciplinary Centre for Health Sciences, Medical Faculty of the Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Chao Xu
- Institute for Medical Epidemiology, Biometrics, and Informatics (IMEBI), Interdisciplinary Centre for Health Sciences, Medical Faculty of the Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Anja Broda
- Institute for Medical Epidemiology, Biometrics, and Informatics (IMEBI), Interdisciplinary Centre for Health Sciences, Medical Faculty of the Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Oliver Purschke
- Institute for Medical Epidemiology, Biometrics, and Informatics (IMEBI), Interdisciplinary Centre for Health Sciences, Medical Faculty of the Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Mascha Binder
- Department of Internal Medicine IV, Oncology/Haematology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Thomas Frese
- Institute of General Practice and Family Medicine, Interdisciplinary Centre for Health Sciences, Medical Faculty of the Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Matthias Girndt
- Department of Internal Medicine II, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Jessica I Hoell
- Paediatric Haematology and Oncology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Irene Moor
- Institute for Medical Sociology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Michael Gekle
- Julius-Bernstein-Institute of Physiology, Medical Faculty of the Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Rafael Mikolajczyk
- Institute for Medical Epidemiology, Biometrics, and Informatics (IMEBI), Interdisciplinary Centre for Health Sciences, Medical Faculty of the Martin Luther University Halle-Wittenberg, Halle (Saale), Germany.
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4
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Klee B, Diexer S, Sarajan MH, Glaser N, Binder M, Frese T, Girndt M, Sedding D, Hoell JI, Moor I, Gekle M, Mikolajczyk R, Gottschick C. Regional Differences in Uptake of Vaccination against COVID-19 and Influenza in Germany: Results from the DigiHero Cohort. Vaccines (Basel) 2023; 11:1640. [PMID: 38005973 PMCID: PMC10674575 DOI: 10.3390/vaccines11111640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/17/2023] [Accepted: 10/24/2023] [Indexed: 11/26/2023] Open
Abstract
During the COVID-19 pandemic in Germany, vaccination uptake exhibited considerable regional disparities. To assess the factors contributing to this variation, we examined the association of sociodemographic variables with COVID-19, COVID-19 booster, and influenza vaccination status within a cohort of 37,078 participants from 13 German federal states in the digital health cohort study commonly known as DigiHero. Our findings revealed variations in vaccination rates based on sociodemographic factors. However, these factors had limited explanatory power regarding regional differences in vaccine uptake. In contrast, we found substantial correlations between regional support of specific parties during the last local elections and the vaccination uptake at the level of each administrative district. In conclusion, sociodemographic factors alone did not suffice to explain the regional disparities in vaccine uptake. Political stances can play a major role, although the current investigation did not assess individual political orientations but rather used only an ecological approach.
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Affiliation(s)
- Bianca Klee
- Institute for Medical Epidemiology, Biometry and Informatics (IMEBI), Interdisciplinary Centre for Health Sciences, Medical Faculty of the Martin Luther University Halle-Wittenberg, Magdeburger Str. 8, 06112 Halle (Saale), Germany; (B.K.); (S.D.); (M.H.S.); (N.G.)
| | - Sophie Diexer
- Institute for Medical Epidemiology, Biometry and Informatics (IMEBI), Interdisciplinary Centre for Health Sciences, Medical Faculty of the Martin Luther University Halle-Wittenberg, Magdeburger Str. 8, 06112 Halle (Saale), Germany; (B.K.); (S.D.); (M.H.S.); (N.G.)
| | - Myka Harun Sarajan
- Institute for Medical Epidemiology, Biometry and Informatics (IMEBI), Interdisciplinary Centre for Health Sciences, Medical Faculty of the Martin Luther University Halle-Wittenberg, Magdeburger Str. 8, 06112 Halle (Saale), Germany; (B.K.); (S.D.); (M.H.S.); (N.G.)
| | - Nadine Glaser
- Institute for Medical Epidemiology, Biometry and Informatics (IMEBI), Interdisciplinary Centre for Health Sciences, Medical Faculty of the Martin Luther University Halle-Wittenberg, Magdeburger Str. 8, 06112 Halle (Saale), Germany; (B.K.); (S.D.); (M.H.S.); (N.G.)
| | - Mascha Binder
- Department of Internal Medicine IV, Oncology/Haematology, Martin Luther University Halle-Wittenberg, Ernst-Grube-Str. 40, 06120 Halle (Saale), Germany;
| | - Thomas Frese
- Institute of General Practice and Family Medicine, Interdisciplinary Centre for Health Sciences, Medical Faculty of the Martin Luther University Halle-Wittenberg, Magdeburger Str. 8, 06112 Halle (Saale), Germany;
| | - Matthias Girndt
- Department of Internal Medicine II, Martin Luther University Halle-Wittenberg, Ernst-Grube-Str. 40, 06120 Halle (Saale), Germany;
| | - Daniel Sedding
- Mid-German Heart Centre, Department of Cardiology and Intensive Care Medicine, University Hospital, Martin Luther University Halle-Wittenberg, Ernst-Grube-Str. 40, 06120 Halle (Saale), Germany;
| | - Jessica I. Hoell
- Paediatric Haematology and Oncology, Martin Luther University Halle-Wittenberg, Ernst-Grube-Str. 40, 06120 Halle (Saale), Germany;
| | - Irene Moor
- Institute for Medical Sociology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 8, 06112 Halle (Saale), Germany;
| | - Michael Gekle
- Julius-Bernstein-Institute of Physiology, Medical Faculty of the Martin Luther University Halle-Wittenberg, Magdeburger Str. 6, 06110 Halle (Saale), Germany;
| | - Rafael Mikolajczyk
- Institute for Medical Epidemiology, Biometry and Informatics (IMEBI), Interdisciplinary Centre for Health Sciences, Medical Faculty of the Martin Luther University Halle-Wittenberg, Magdeburger Str. 8, 06112 Halle (Saale), Germany; (B.K.); (S.D.); (M.H.S.); (N.G.)
| | - Cornelia Gottschick
- Institute for Medical Epidemiology, Biometry and Informatics (IMEBI), Interdisciplinary Centre for Health Sciences, Medical Faculty of the Martin Luther University Halle-Wittenberg, Magdeburger Str. 8, 06112 Halle (Saale), Germany; (B.K.); (S.D.); (M.H.S.); (N.G.)
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5
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Bamezai S, Pulikkottil AJ, Yadav T, Vegi NM, Mueller J, Mark J, Mandal T, Feder K, Ihme S, Song C, Rosler R, Wiese S, Hoell JI, Kloetgen A, Karsan A, Kumari A, Wojenski L, Sinha AU, Gonzalez-Menendez I, Quintanilla-Martinez L, Donato E, Trumpp A, Kruse E, Hamperl S, Zou L, Rawat VPS, Buske C. A noncanonical enzymatic function of PIWIL4 maintains genomic integrity and leukemic growth in AML. Blood 2023; 142:90-105. [PMID: 37146239 DOI: 10.1182/blood.2022018651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 03/03/2023] [Accepted: 03/29/2023] [Indexed: 05/07/2023] Open
Abstract
RNA-binding proteins (RBPs) form a large and diverse class of factors, many members of which are overexpressed in hematologic malignancies. RBPs participate in various processes of messenger RNA (mRNA) metabolism and prevent harmful DNA:RNA hybrids or R-loops. Here, we report that PIWIL4, a germ stem cell-associated RBP belonging to the RNase H-like superfamily, is overexpressed in patients with acute myeloid leukemia (AML) and is essential for leukemic stem cell function and AML growth, but dispensable for healthy human hematopoietic stem cells. In AML cells, PIWIL4 binds to a small number of known piwi-interacting RNA. Instead, it largely interacts with mRNA annotated to protein-coding genic regions and enhancers that are enriched for genes associated with cancer and human myeloid progenitor gene signatures. PIWIL4 depletion in AML cells downregulates the human myeloid progenitor signature and leukemia stem cell (LSC)-associated genes and upregulates DNA damage signaling. We demonstrate that PIWIL4 is an R-loop resolving enzyme that prevents R-loop accumulation on a subset of AML and LSC-associated genes and maintains their expression. It also prevents DNA damage, replication stress, and activation of the ATR pathway in AML cells. PIWIL4 depletion potentiates sensitivity to pharmacological inhibition of the ATR pathway and creates a pharmacologically actionable dependency in AML cells.
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Affiliation(s)
- Shiva Bamezai
- Institute of Experimental Cancer Research, University Hospital of Ulm, Ulm, Germany
| | | | - Tribhuwan Yadav
- Department of Pathology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA
| | - Naidu M Vegi
- Institute of Experimental Cancer Research, University Hospital of Ulm, Ulm, Germany
| | - Julia Mueller
- Institute of Experimental Cancer Research, University Hospital of Ulm, Ulm, Germany
| | - Jasmin Mark
- Institute of Experimental Cancer Research, University Hospital of Ulm, Ulm, Germany
| | - Tamoghna Mandal
- Institute of Experimental Cancer Research, University Hospital of Ulm, Ulm, Germany
- Department of Oncology Pathology, Karolinska Institute, Stockholm, Sweden
| | - Kristin Feder
- Institute of Experimental Cancer Research, University Hospital of Ulm, Ulm, Germany
| | - Susann Ihme
- Institute of Experimental Cancer Research, University Hospital of Ulm, Ulm, Germany
| | - Chenlin Song
- Division of Molecular Biology of the Cell II, German Cancer Research Center, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Reinhild Rosler
- Core Unit Mass Spectrometry and Proteomics, Faculty of Natural Science, Ulm University, Ulm, Germany
| | - Sebastian Wiese
- Core Unit Mass Spectrometry and Proteomics, Faculty of Natural Science, Ulm University, Ulm, Germany
| | - Jessica I Hoell
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany
- Department of Pediatric Hematology and Oncology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Andreas Kloetgen
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Aly Karsan
- Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, BC, Canada
| | | | | | | | - Irene Gonzalez-Menendez
- Institute of Pathology and Neuropathology, Eberhard Karls University of Tübingen and Comprehensive Cancer Center, University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180), Image-Guided and Functionally Instructed Tumor Therapies, University of Tübingen, Tübingen, Germany
| | - Leticia Quintanilla-Martinez
- Institute of Pathology and Neuropathology, Eberhard Karls University of Tübingen and Comprehensive Cancer Center, University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180), Image-Guided and Functionally Instructed Tumor Therapies, University of Tübingen, Tübingen, Germany
| | - Elisa Donato
- HI-STEM-Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH, Heidelberg, Germany
- Division of Stem Cells and Cancer, German Cancer Research Center and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Andreas Trumpp
- HI-STEM-Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH, Heidelberg, Germany
- Division of Stem Cells and Cancer, German Cancer Research Center and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Elisabeth Kruse
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
| | - Stephan Hamperl
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
| | - Lee Zou
- Department of Pathology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA
| | - Vijay P S Rawat
- Institute of Experimental Cancer Research, University Hospital of Ulm, Ulm, Germany
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Christian Buske
- Institute of Experimental Cancer Research, University Hospital of Ulm, Ulm, Germany
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6
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Gottschick C, Diexer S, Massag J, Klee B, Broda A, Purschke O, Binder M, Sedding D, Frese T, Girndt M, Hoell JI, Michl P, Gekle M, Mikolajczyk R. Mental health in Germany in the first weeks of the Russo-Ukrainian war. BJPsych Open 2023; 9:e66. [PMID: 37057843 PMCID: PMC10134205 DOI: 10.1192/bjo.2023.21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/15/2023] Open
Abstract
BACKGROUND In the connected world, although societies are not directly involved in a military conflict, they are exposed to media reports of violence. AIMS We assessed the effects of such exposures on mental health in Germany during the military conflict in Ukraine. METHOD We used the German population-based cohort for digital health research, DigiHero, launching a survey on the eighth day of the Russo-Ukrainian war. Of the 27 509 cohort participants from the general population, 19 444 (70.7%) responded within 17 days. We measured mental health and fear of the impact of war compared with other fears (natural disasters or health-related). RESULTS In a subsample of 4441 participants assessed twice, anxiety in the population (measured by the Generalised Anxiety Disorder-7 screener) was higher in the first weeks of war than during the strongest COVID-19 restrictions. Anxiety was elevated across the whole age spectrum, and the mean was above the cut-off for mild anxiety. Over 95% of participants expressed various degrees of fear of the impact of war, whereas the percentage for other investigated fears was 0.47-0.82. A one-point difference in the fear of the impact of war was associated with a 2.5 point (95% CI 2.42-2.58) increase in anxiety (11.9% of the maximum anxiety score). For emotional distress, the increase was 0.67 points (0.66-0.68) (16.75% of the maximum score). CONCLUSIONS The population in Germany reacted to the Russo-Ukrainian war with substantial distress, exceeding reactions during the strongest restrictions in the COVID-19 pandemic. Fear of the impact of war was associated with worse mental health.
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Affiliation(s)
- Cornelia Gottschick
- Institute for Medical Epidemiology, Biometry and Informatics, Interdisciplinary Centre for Health Sciences, Medical Faculty of the Martin-Luther-University Halle-Wittenberg, Germany
| | - Sophie Diexer
- Institute for Medical Epidemiology, Biometry and Informatics, Interdisciplinary Centre for Health Sciences, Medical Faculty of the Martin-Luther-University Halle-Wittenberg, Germany
| | - Janka Massag
- Institute for Medical Epidemiology, Biometry and Informatics, Interdisciplinary Centre for Health Sciences, Medical Faculty of the Martin-Luther-University Halle-Wittenberg, Germany
| | - Bianca Klee
- Institute for Medical Epidemiology, Biometry and Informatics, Interdisciplinary Centre for Health Sciences, Medical Faculty of the Martin-Luther-University Halle-Wittenberg, Germany
| | - Anja Broda
- Institute for Medical Epidemiology, Biometry and Informatics, Interdisciplinary Centre for Health Sciences, Medical Faculty of the Martin-Luther-University Halle-Wittenberg, Germany
| | - Oliver Purschke
- Institute for Medical Epidemiology, Biometry and Informatics, Interdisciplinary Centre for Health Sciences, Medical Faculty of the Martin-Luther-University Halle-Wittenberg, Germany
| | - Mascha Binder
- Department of Internal Medicine IV - Oncology/Haematology, Martin-Luther-University Halle-Wittenberg, Germany
| | - Daniel Sedding
- Mid-German Heart Centre, Department of Cardiology and Intensive Care Medicine, University Hospital, Martin-Luther-University Halle-Wittenberg, Germany
| | - Thomas Frese
- Institute of General Practice and Family Medicine, Interdisciplinary Centre for Health Sciences, Medical Faculty of the Martin-Luther-University Halle-Wittenberg, Germany
| | - Matthias Girndt
- Department of Internal Medicine II, Martin-Luther-University Halle-Wittenberg, Germany
| | - Jessica I Hoell
- Paediatric Haematology and Oncology, Martin-Luther-University Halle-Wittenberg, Germany
| | - Patrick Michl
- Department of Internal Medicine I, Martin-Luther-University Halle-Wittenberg, Germany
| | - Michael Gekle
- Julius Bernstein-Institute of Physiology, Faculty of Medicine, Martin-Luther-University Halle-Wittenberg, Germany
| | - Rafael Mikolajczyk
- Institute for Medical Epidemiology, Biometry and Informatics, Interdisciplinary Centre for Health Sciences, Medical Faculty of the Martin-Luther-University Halle-Wittenberg, Germany
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Gerstung M, Jolly C, Leshchiner I, Dentro SC, Gonzalez S, Rosebrock D, Mitchell TJ, Rubanova Y, Anur P, Yu K, Tarabichi M, Deshwar A, Wintersinger J, Kleinheinz K, Vázquez-García I, Haase K, Jerman L, Sengupta S, Macintyre G, Malikic S, Donmez N, Livitz DG, Cmero M, Demeulemeester J, Schumacher S, Fan Y, Yao X, Lee J, Schlesner M, Boutros PC, Bowtell DD, Zhu H, Getz G, Imielinski M, Beroukhim R, Sahinalp SC, Ji Y, Peifer M, Markowetz F, Mustonen V, Yuan K, Wang W, Morris QD, Spellman PT, Wedge DC, Van Loo P, Tarabichi M, Wintersinger J, Deshwar AG, Yu K, Gonzalez S, Rubanova Y, Macintyre G, Adams DJ, Anur P, Beroukhim R, Boutros PC, Bowtell DD, Campbell PJ, Cao S, Christie EL, Cmero M, Cun Y, Dawson KJ, Demeulemeester J, Donmez N, Drews RM, Eils R, Fan Y, Fittall M, Garsed DW, Getz G, Ha G, Imielinski M, Jerman L, Ji Y, Kleinheinz K, Lee J, Lee-Six H, Livitz DG, Malikic S, Markowetz F, Martincorena I, Mitchell TJ, Mustonen V, Oesper L, Peifer M, Peto M, Raphael BJ, Rosebrock D, Sahinalp SC, Salcedo A, Schlesner M, Schumacher S, Sengupta S, Shi R, Shin SJ, Spiro O, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Stein LD, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Vázquez-García I, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Vembu S, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Wheeler DA, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Yang TP, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Yao X, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Yuan K, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Zhu H, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Wang W, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Morris QD, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Spellman PT, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Wedge DC, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Van Loo P, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Spellman PT, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Wedge DC, Shorser SI, Short C, Shrestha R, Shringarpure SS, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts AM, Sieverling L, Van Loo P, Signoretti S, Sikora KO, Simbolo M, Simon R, Simons JV, Simpson JT, Simpson PT, Singer S, Sinnott-Armstrong N, Sipahimalani P, Aaltonen LA, Skelly TJ, Smid M, Smith J, Smith-McCune K, Socci ND, Sofia HJ, Soloway MG, Song L, Sood AK, Sothi S, Abascal F, Sotiriou C, Soulette CM, Span PN, Spellman PT, Sperandio N, Spillane AJ, Spiro O, Spring J, Staaf J, Stadler PF, Abeshouse A, Staib P, Stark SG, Stebbings L, Stefánsson ÓA, Stegle O, Stein LD, Stenhouse A, Stewart C, Stilgenbauer S, Stobbe MD, Aburatani H, Stratton MR, Stretch JR, Struck AJ, Stuart JM, Stunnenberg HG, Su H, Su X, Sun RX, Sungalee S, Susak H, Adams DJ, Suzuki A, Sweep F, Szczepanowski M, Sültmann H, Yugawa T, Tam A, Tamborero D, Tan BKT, Tan D, Tan P, Agrawal N, Tanaka H, Taniguchi H, Tanskanen TJ, Tarabichi M, Tarnuzzer R, Tarpey P, Taschuk ML, Tatsuno K, Tavaré S, Taylor DF, Ahn KS, Taylor-Weiner A, Teague JW, Teh BT, Tembe V, Temes J, Thai K, Thayer SP, Thiessen N, Thomas G, Thomas S, Ahn SM, Thompson A, Thompson AM, Thompson JFF, Thompson RH, Thorne H, Thorne LB, Thorogood A, Tiao G, Tijanic N, Timms LE, Aikata H, Tirabosco R, Tojo M, Tommasi S, Toon CW, Toprak UH, Torrents D, Tortora G, Tost J, Totoki Y, Townend D, Akbani R, Traficante N, Treilleux I, Trotta JR, Trümper LHP, Tsao M, Tsunoda T, Tubio JMC, Tucker O, Turkington R, Turner DJ, Akdemir KC, Tutt A, Ueno M, Ueno NT, Umbricht C, Umer HM, Underwood TJ, Urban L, Urushidate T, Ushiku T, Uusküla-Reimand L, Al-Ahmadie H, Valencia A, Van Den Berg DJ, Van Laere S, Van Loo P, Van Meir EG, Van den Eynden GG, Van der Kwast T, Vasudev N, Vazquez M, Vedururu R, Al-Sedairy ST, Veluvolu U, Vembu S, Verbeke LPC, Vermeulen P, Verrill C, Viari A, Vicente D, Vicentini C, VijayRaghavan K, Viksna J, Al-Shahrour F, Vilain RE, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell NM, Waddell N, Wadelius C, Alawi M, Wadi L, Wagener R, Wala JA, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Albert M, Waring PM, Warnatz HJ, Warrell J, Warren AY, Waszak SM, Wedge DC, Weichenhan D, Weinberger P, Weinstein JN, Weischenfeldt J, Aldape K, Weisenberger DJ, Welch I, Wendl MC, Werner J, Whalley JP, Wheeler DA, Whitaker HC, Wigle D, Wilkerson MD, Williams A, Alexandrov LB, Wilmott JS, Wilson GW, Wilson JM, Wilson RK, Winterhoff B, Wintersinger JA, Wiznerowicz M, Wolf S, Wong BH, Wong T, Ally A, Wong W, Woo Y, Wood S, Wouters BG, Wright AJ, Wright DW, Wright MH, Wu CL, Wu DY, Wu G, Alsop K, Wu J, Wu K, Wu Y, Wu Z, Xi L, Xia T, Xiang Q, Xiao X, Xing R, Xiong H, Alvarez EG, Xu Q, Xu Y, Xue H, Yachida S, Yakneen S, Yamaguchi R, Yamaguchi TN, Yamamoto M, Yamamoto S, Yamaue H, Amary F, Yang F, Yang H, Yang JY, Yang L, Yang L, Yang S, Yang TP, Yang Y, Yao X, Yaspo ML, Amin SB, Yates L, Yau C, Ye C, Ye K, Yellapantula VD, Yoon CJ, Yoon SS, Yousif F, Yu J, Yu K, Aminou B, Yu W, Yu Y, Yuan K, Yuan Y, Yuen D, Yung CK, Zaikova O, Zamora J, Zapatka M, Zenklusen JC, Ammerpohl O, Zenz T, Zeps N, Zhang CZ, Zhang F, Zhang H, Zhang H, Zhang H, Zhang J, Zhang J, Zhang J, Anderson MJ, Zhang X, Zhang X, Zhang Y, Zhang Z, Zhao Z, Zheng L, Zheng X, Zhou W, Zhou Y, Zhu B, Ang Y, Zhu H, Zhu J, Zhu S, Zou L, Zou X, deFazio A, van As N, van Deurzen CHM, van de Vijver MJ, van’t Veer L, Antonello D, von Mering C, Anur P, Aparicio S, Appelbaum EL, Arai Y, Aretz A, Arihiro K, Ariizumi SI, Armenia J, Arnould L, Asa S, Assenov Y, Atwal G, Aukema S, Auman JT, Aure MRR, Awadalla P, Aymerich M, Bader GD, Baez-Ortega A, Bailey MH, Bailey PJ, Balasundaram M, Balu S, Bandopadhayay P, Banks RE, Barbi S, Barbour AP, Barenboim J, Barnholtz-Sloan J, Barr H, Barrera E, Bartlett J, Bartolome J, Bassi C, Bathe OF, Baumhoer D, Bavi P, Baylin SB, Bazant W, Beardsmore D, Beck TA, Behjati S, Behren A, Niu B, Bell C, Beltran S, Benz C, Berchuck A, Bergmann AK, Bergstrom EN, Berman BP, Berney DM, Bernhart SH, Beroukhim R, Berrios M, Bersani S, Bertl J, Betancourt M, Bhandari V, Bhosle SG, Biankin AV, Bieg M, Bigner D, Binder H, Birney E, Birrer M, Biswas NK, Bjerkehagen B, Bodenheimer T, Boice L, Bonizzato G, De Bono JS, Boot A, Bootwalla MS, Borg A, Borkhardt A, Boroevich KA, Borozan I, Borst C, Bosenberg M, Bosio M, Boultwood J, Bourque G, Boutros PC, Bova GS, Bowen DT, Bowlby R, Bowtell DDL, Boyault S, Boyce R, Boyd J, Brazma A, Brennan P, Brewer DS, Brinkman AB, Bristow RG, Broaddus RR, Brock JE, Brock M, Broeks A, Brooks AN, Brooks D, Brors B, Brunak S, Bruxner TJC, Bruzos AL, Buchanan A, Buchhalter I, Buchholz C, Bullman S, Burke H, Burkhardt B, Burns KH, Busanovich J, Bustamante CD, Butler AP, Butte AJ, Byrne NJ, Børresen-Dale AL, Caesar-Johnson SJ, Cafferkey A, Cahill D, Calabrese C, Caldas C, Calvo F, Camacho N, Campbell PJ, Campo E, Cantù C, Cao S, Carey TE, Carlevaro-Fita J, Carlsen R, Cataldo I, Cazzola M, Cebon J, Cerfolio R, Chadwick DE, Chakravarty D, Chalmers D, Chan CWY, Chan K, Chan-Seng-Yue M, Chandan VS, Chang DK, Chanock SJ, Chantrill LA, Chateigner A, Chatterjee N, Chayama K, Chen HW, Chen J, Chen K, Chen Y, Chen Z, Cherniack AD, Chien J, Chiew YE, Chin SF, Cho J, Cho S, Choi JK, Choi W, Chomienne C, Chong Z, Choo SP, Chou A, Christ AN, Christie EL, Chuah E, Cibulskis C, Cibulskis K, Cingarlini S, Clapham P, Claviez A, Cleary S, Cloonan N, Cmero M, Collins CC, Connor AA, Cooke SL, Cooper CS, Cope L, Corbo V, Cordes MG, Cordner SM, Cortés-Ciriano I, Covington K, Cowin PA, Craft B, Craft D, Creighton CJ, Cun Y, Curley E, Cutcutache I, Czajka K, Czerniak B, Dagg RA, Danilova L, Davi MV, Davidson NR, Davies H, Davis IJ, Davis-Dusenbery BN, Dawson KJ, De La Vega FM, De Paoli-Iseppi R, Defreitas T, Tos APD, Delaneau O, Demchok JA, Demeulemeester J, Demidov GM, Demircioğlu D, Dennis NM, Denroche RE, Dentro SC, Desai N, Deshpande V, Deshwar AG, Desmedt C, Deu-Pons J, Dhalla N, Dhani NC, Dhingra P, Dhir R, DiBiase A, Diamanti K, Ding L, Ding S, Dinh HQ, Dirix L, Doddapaneni H, Donmez N, Dow MT, Drapkin R, Drechsel O, Drews RM, Serge S, Dudderidge T, Dueso-Barroso A, Dunford AJ, Dunn M, Dursi LJ, Duthie FR, Dutton-Regester K, Eagles J, Easton DF, Edmonds S, Edwards PA, Edwards SE, Eeles RA, Ehinger A, Eils J, Eils R, El-Naggar A, Eldridge M, Ellrott K, Erkek S, Escaramis G, Espiritu SMG, Estivill X, Etemadmoghadam D, Eyfjord JE, Faltas BM, Fan D, Fan Y, Faquin WC, Farcas C, Fassan M, Fatima A, Favero F, Fayzullaev N, Felau I, Fereday S, Ferguson ML, Ferretti V, Feuerbach L, Field MA, Fink JL, Finocchiaro G, Fisher C, Fittall MW, Fitzgerald A, Fitzgerald RC, Flanagan AM, Fleshner NE, Flicek P, Foekens JA, Fong KM, Fonseca NA, Foster CS, Fox NS, Fraser M, Frazer S, Frenkel-Morgenstern M, Friedman W, Frigola J, Fronick CC, Fujimoto A, Fujita M, Fukayama M, Fulton LA, Fulton RS, Furuta M, Futreal PA, Füllgrabe A, Gabriel SB, Gallinger S, Gambacorti-Passerini C, Gao J, Gao S, Garraway L, Garred Ø, Garrison E, Garsed DW, Gehlenborg N, Gelpi JLL, George J, Gerhard DS, Gerhauser C, Gershenwald JE, Gerstein M, Gerstung M, Getz G, Ghori M, Ghossein R, Giama NH, Gibbs RA, Gibson B, Gill AJ, Gill P, Giri DD, Glodzik D, Gnanapragasam VJ, Goebler ME, Goldman MJ, Gomez C, Gonzalez S, Gonzalez-Perez A, Gordenin DA, Gossage J, Gotoh K, Govindan R, Grabau D, Graham JS, Grant RC, Green AR, Green E, Greger L, Grehan N, Grimaldi S, Grimmond SM, Grossman RL, Grundhoff A, Gundem G, Guo Q, Gupta M, Gupta S, Gut IG, Gut M, Göke J, Ha G, Haake A, Haan D, Haas S, Haase K, Haber JE, Habermann N, Hach F, Haider S, Hama N, Hamdy FC, Hamilton A, Hamilton MP, Han L, Hanna GB, Hansmann M, Haradhvala NJ, Harismendy O, Harliwong I, Harmanci AO, Harrington E, Hasegawa T, Haussler D, Hawkins S, Hayami S, Hayashi S, Hayes DN, Hayes SJ, Hayward NK, Hazell S, He Y, Heath AP, Heath SC, Hedley D, Hegde AM, Heiman DI, Heinold MC, Heins Z, Heisler LE, Hellstrom-Lindberg E, Helmy M, Heo SG, Hepperla AJ, Heredia-Genestar JM, Herrmann C, Hersey P, Hess JM, Hilmarsdottir H, Hinton J, Hirano S, Hiraoka N, Hoadley KA, Hobolth A, Hodzic E, Hoell JI, Hoffmann S, Hofmann O, Holbrook A, Holik AZ, Hollingsworth MA, Holmes O, Holt RA, Hong C, Hong EP, Hong JH, Hooijer GK, Hornshøj H, Hosoda F, Hou Y, Hovestadt V, Howat W, Hoyle AP, Hruban RH, Hu J, Hu T, Hua X, Huang KL, Huang M, Huang MN, Huang V, Huang Y, Huber W, Hudson TJ, Hummel M, Hung JA, Huntsman D, Hupp TR, Huse J, Huska MR, Hutter B, Hutter CM, Hübschmann D, Iacobuzio-Donahue CA, Imbusch CD, Imielinski M, Imoto S, Isaacs WB, Isaev K, Ishikawa S, Iskar M, Islam SMA, Ittmann M, Ivkovic S, Izarzugaza JMG, Jacquemier J, Jakrot V, Jamieson NB, Jang GH, Jang SJ, Jayaseelan JC, Jayasinghe R, Jefferys SR, Jegalian K, Jennings JL, Jeon SH, Jerman L, Ji Y, Jiao W, Johansson PA, Johns AL, Johns J, Johnson R, Johnson TA, Jolly C, Joly Y, Jonasson JG, Jones CD, Jones DR, Jones DTW, Jones N, Jones SJM, Jonkers J, Ju YS, Juhl H, Jung J, Juul M, Juul RI, Juul S, Jäger N, Kabbe R, Kahles A, Kahraman A, Kaiser VB, Kakavand H, Kalimuthu S, von Kalle C, Kang KJ, Karaszi K, Karlan B, Karlić R, Karsch D, Kasaian K, Kassahn KS, Katai H, Kato M, Katoh H, Kawakami Y, Kay JD, Kazakoff SH, Kazanov MD, Keays M, Kebebew E, Kefford RF, Kellis M, Kench JG, Kennedy CJ, Kerssemakers JNA, Khoo D, Khoo V, Khuntikeo N, Khurana E, Kilpinen H, Kim HK, Kim HL, Kim HY, Kim H, Kim J, Kim J, Kim JK, Kim Y, King TA, Klapper W, Kleinheinz K, Klimczak LJ, Knappskog S, Kneba M, Knoppers BM, Koh Y, Komorowski J, Komura D, Komura M, Kong G, Kool M, Korbel JO, Korchina V, Korshunov A, Koscher M, Koster R, Kote-Jarai Z, Koures A, Kovacevic M, Kremeyer B, Kretzmer H, Kreuz M, Krishnamurthy S, Kube D, Kumar K, Kumar P, Kumar S, Kumar Y, Kundra R, Kübler K, Küppers R, Lagergren J, Lai PH, Laird PW, Lakhani SR, Lalansingh CM, Lalonde E, Lamaze FC, Lambert A, Lander E, Landgraf P, Landoni L, Langerød A, Lanzós A, Larsimont D, Larsson E, Lathrop M, Lau LMS, Lawerenz C, Lawlor RT, Lawrence MS, Lazar AJ, Lazic AM, Le X, Lee D, Lee D, Lee EA, Lee HJ, Lee JJK, Lee JY, Lee J, Lee MTM, Lee-Six H, Lehmann KV, Lehrach H, Lenze D, Leonard CR, Leongamornlert DA, Leshchiner I, Letourneau L, Letunic I, Levine DA, Lewis L, Ley T, Li C, Li CH, Li HI, Li J, Li L, Li S, Li S, Li X, Li X, Li X, Li Y, Liang H, Liang SB, Lichter P, Lin P, Lin Z, Linehan WM, Lingjærde OC, Liu D, Liu EM, Liu FFF, Liu F, Liu J, Liu X, Livingstone J, Livitz D, Livni N, Lochovsky L, Loeffler M, Long GV, Lopez-Guillermo A, Lou S, Louis DN, Lovat LB, Lu Y, Lu YJ, Lu Y, Luchini C, Lungu I, Luo X, Luxton HJ, Lynch AG, Lype L, López C, López-Otín C, Ma EZ, Ma Y, MacGrogan G, MacRae S, Macintyre G, Madsen T, Maejima K, Mafficini A, Maglinte DT, Maitra A, Majumder PP, Malcovati L, Malikic S, Malleo G, Mann GJ, Mantovani-Löffler L, Marchal K, Marchegiani G, Mardis ER, Margolin AA, Marin MG, Markowetz F, Markowski J, Marks J, Marques-Bonet T, Marra MA, Marsden L, Martens JWM, Martin S, Martin-Subero JI, Martincorena I, Martinez-Fundichely A, Maruvka YE, Mashl RJ, Massie CE, Matthew TJ, Matthews L, Mayer E, Mayes S, Mayo M, Mbabaali F, McCune K, McDermott U, McGillivray PD, McLellan MD, McPherson JD, McPherson JR, McPherson TA, Meier SR, Meng A, Meng S, Menzies A, Merrett ND, Merson S, Meyerson M, Meyerson W, Mieczkowski PA, Mihaiescu GL, Mijalkovic S, Mikkelsen T, Milella M, Mileshkin L, Miller CA, Miller DK, Miller JK, Mills GB, Milovanovic A, Minner S, Miotto M, Arnau GM, Mirabello L, Mitchell C, Mitchell TJ, Miyano S, Miyoshi N, Mizuno S, Molnár-Gábor F, Moore MJ, Moore RA, Morganella S, Morris QD, Morrison C, Mose LE, Moser CD, Muiños F, Mularoni L, Mungall AJ, Mungall K, Musgrove EA, Mustonen V, Mutch D, Muyas F, Muzny DM, Muñoz A, Myers J, Myklebost O, Möller P, Nagae G, Nagrial AM, Nahal-Bose HK, Nakagama H, Nakagawa H, Nakamura H, Nakamura T, Nakano K, Nandi T, Nangalia J, Nastic M, Navarro A, Navarro FCP, Neal DE, Nettekoven G, Newell F, Newhouse SJ, Newton Y, Ng AWT, Ng A, Nicholson J, Nicol D, Nie Y, Nielsen GP, Nielsen MM, Nik-Zainal S, Noble MS, Nones K, Northcott PA, Notta F, O’Connor BD, O’Donnell P, O’Donovan M, O’Meara S, O’Neill BP, O’Neill JR, Ocana D, Ochoa A, Oesper L, Ogden C, Ohdan H, Ohi K, Ohno-Machado L, Oien KA, Ojesina AI, Ojima H, Okusaka T, Omberg L, Ong CK, Ossowski S, Ott G, Ouellette BFF, P’ng C, Paczkowska M, Paiella S, Pairojkul C, Pajic M, Pan-Hammarström Q, Papaemmanuil E, Papatheodorou I, Paramasivam N, Park JW, Park JW, Park K, Park K, Park PJ, Parker JS, Parsons SL, Pass H, Pasternack D, Pastore A, Patch AM, Pauporté I, Pea A, Pearson JV, Pedamallu CS, Pedersen JS, Pederzoli P, Peifer M, Pennell NA, Perou CM, Perry MD, Petersen GM, Peto M, Petrelli N, Petryszak R, Pfister SM, Phillips M, Pich O, Pickett HA, Pihl TD, Pillay N, Pinder S, Pinese M, Pinho AV. Author Correction: The evolutionary history of 2,658 cancers. Nature 2023; 614:E42. [PMID: 36697833 PMCID: PMC9931577 DOI: 10.1038/s41586-022-05601-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK. .,European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany. .,Wellcome Sanger Institute, Cambridge, UK.
| | - Clemency Jolly
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Ignaty Leshchiner
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Stefan C. Dentro
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK ,grid.4991.50000 0004 1936 8948Big Data Institute, University of Oxford, Oxford, UK
| | - Santiago Gonzalez
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Daniel Rosebrock
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Thomas J. Mitchell
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934University of Cambridge, Cambridge, UK
| | - Yulia Rubanova
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Pavana Anur
- grid.5288.70000 0000 9758 5690Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR USA
| | - Kaixian Yu
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Maxime Tarabichi
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Amit Deshwar
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Jeff Wintersinger
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Kortine Kleinheinz
- grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Heidelberg University, Heidelberg, Germany
| | - Ignacio Vázquez-García
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934University of Cambridge, Cambridge, UK
| | - Kerstin Haase
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Lara Jerman
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK ,grid.8954.00000 0001 0721 6013University of Ljubljana, Ljubljana, Slovenia
| | - Subhajit Sengupta
- grid.240372.00000 0004 0400 4439NorthShore University HealthSystem, Evanston, IL USA
| | - Geoff Macintyre
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Salem Malikic
- grid.61971.380000 0004 1936 7494Simon Fraser University, Burnaby, British Columbia Canada ,grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada
| | - Nilgun Donmez
- grid.61971.380000 0004 1936 7494Simon Fraser University, Burnaby, British Columbia Canada ,grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada
| | - Dimitri G. Livitz
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Marek Cmero
- grid.1008.90000 0001 2179 088XUniversity of Melbourne, Melbourne, Victoria Australia ,grid.1042.70000 0004 0432 4889Walter and Eliza Hall Institute, Melbourne, Victoria Australia
| | - Jonas Demeulemeester
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK ,grid.5596.f0000 0001 0668 7884University of Leuven, Leuven, Belgium
| | - Steven Schumacher
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Yu Fan
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Xiaotong Yao
- grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA ,grid.429884.b0000 0004 1791 0895New York Genome Center, New York, NY USA
| | - Juhee Lee
- grid.205975.c0000 0001 0740 6917University of California Santa Cruz, Santa Cruz, CA USA
| | - Matthias Schlesner
- grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Paul C. Boutros
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.419890.d0000 0004 0626 690XOntario Institute for Cancer Research, Toronto, Ontario Canada ,grid.19006.3e0000 0000 9632 6718University of California, Los Angeles, CA USA
| | - David D. Bowtell
- grid.1055.10000000403978434Peter MacCallum Cancer Centre, Melbourne, Victoria Australia
| | - Hongtu Zhu
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Gad Getz
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.32224.350000 0004 0386 9924Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA USA ,grid.32224.350000 0004 0386 9924Department of Pathology, Massachusetts General Hospital, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Marcin Imielinski
- grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA ,grid.429884.b0000 0004 1791 0895New York Genome Center, New York, NY USA
| | - Rameen Beroukhim
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA
| | - S. Cenk Sahinalp
- grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada ,grid.411377.70000 0001 0790 959XIndiana University, Bloomington, IN USA
| | - Yuan Ji
- grid.240372.00000 0004 0400 4439NorthShore University HealthSystem, Evanston, IL USA ,grid.170205.10000 0004 1936 7822The University of Chicago, Chicago, IL USA
| | - Martin Peifer
- grid.6190.e0000 0000 8580 3777University of Cologne, Cologne, Germany
| | - Florian Markowetz
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Ville Mustonen
- grid.7737.40000 0004 0410 2071University of Helsinki, Helsinki, Finland
| | - Ke Yuan
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK ,grid.8756.c0000 0001 2193 314XUniversity of Glasgow, Glasgow, UK
| | - Wenyi Wang
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Quaid D. Morris
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | | | - Paul T. Spellman
- grid.5288.70000 0000 9758 5690Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR USA
| | - David C. Wedge
- grid.4991.50000 0004 1936 8948Big Data Institute, University of Oxford, Oxford, UK ,grid.454382.c0000 0004 7871 7212Oxford NIHR Biomedical Research Centre, Oxford, UK
| | - Peter Van Loo
- The Francis Crick Institute, London, UK. .,University of Leuven, Leuven, Belgium.
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Calabrese C, Davidson NR, Demircioğlu D, Fonseca NA, He Y, Kahles A, Lehmann KV, Liu F, Shiraishi Y, Soulette CM, Urban L, Greger L, Li S, Liu D, Perry MD, Xiang Q, Zhang F, Zhang J, Bailey P, Erkek S, Hoadley KA, Hou Y, Huska MR, Kilpinen H, Korbel JO, Marin MG, Markowski J, Nandi T, Pan-Hammarström Q, Pedamallu CS, Siebert R, Stark SG, Su H, Tan P, Waszak SM, Yung C, Zhu S, Awadalla P, Creighton CJ, Meyerson M, Ouellette BFF, Wu K, Yang H, Brazma A, Brooks AN, Göke J, Rätsch G, Schwarz RF, Stegle O, Zhang Z, Wu K, Yang H, Fonseca NA, Kahles A, Lehmann KV, Urban L, Soulette CM, Shiraishi Y, Liu F, He Y, Demircioğlu D, Davidson NR, Calabrese C, Zhang J, Perry MD, Xiang Q, Greger L, Li S, Liu D, Stark SG, Zhang F, Amin SB, Bailey P, Chateigner A, Cortés-Ciriano I, Craft B, Erkek S, Frenkel-Morgenstern M, Goldman M, Hoadley KA, Hou Y, Huska MR, Khurana E, Kilpinen H, Korbel JO, Lamaze FC, Li C, Li X, Li X, Liu X, Marin MG, Markowski J, Nandi T, Nielsen MM, Ojesina AI, Pan-Hammarström Q, Park PJ, Pedamallu CS, Pedersen JS, Pederzoli P, Peifer M, Pennell NA, Perou CM, Perry MD, Petersen GM, Peto M, Petrelli N, Pedamallu CS, Petryszak R, Pfister SM, Phillips M, Pich O, Pickett HA, Pihl TD, Pillay N, Pinder S, Pinese M, Pinho AV, Pedersen JS, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Siebert R, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Su H, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Tan P, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Teh BT, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Wang J, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Waszak SM, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Xiong H, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Yakneen S, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Ye C, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Yung C, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Zhang X, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Zheng L, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Zhu J, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Zhu S, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Awadalla P, Shorser SI, Short C, Shrestha R, Shringarpure SS, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts AM, Sieverling L, Creighton CJ, Signoretti S, Sikora KO, Simbolo M, Simon R, Simons JV, Simpson JT, Simpson PT, Singer S, Sinnott-Armstrong N, Sipahimalani P, Meyerson M, Skelly TJ, Smid M, Smith J, Smith-McCune K, Socci ND, Sofia HJ, Soloway MG, Song L, Sood AK, Sothi S, Ouellette BFF, Sotiriou C, Soulette CM, Span PN, Spellman PT, Sperandio N, Spillane AJ, Spiro O, Spring J, Staaf J, Stadler PF, Wu K, Staib P, Stark SG, Stebbings L, Stefánsson ÓA, Stegle O, Stein LD, Stenhouse A, Stewart C, Stilgenbauer S, Stobbe MD, Yang H, Stratton MR, Stretch JR, Struck AJ, Stuart JM, Stunnenberg HG, Su H, Su X, Sun RX, Sungalee S, Susak H, Göke J, Suzuki A, Sweep F, Szczepanowski M, Sültmann H, Yugawa T, Tam A, Tamborero D, Tan BKT, Tan D, Tan P, Schwarz RF, Tanaka H, Taniguchi H, Tanskanen TJ, Tarabichi M, Tarnuzzer R, Tarpey P, Taschuk ML, Tatsuno K, Tavaré S, Taylor DF, Stegle O, Taylor-Weiner A, Teague JW, Teh BT, Tembe V, Temes J, Thai K, Thayer SP, Thiessen N, Thomas G, Thomas S, Zhang Z, Thompson A, Thompson AM, Thompson JFF, Thompson RH, Thorne H, Thorne LB, Thorogood A, Tiao G, Tijanic N, Timms LE, Brazma A, Tirabosco R, Tojo M, Tommasi S, Toon CW, Toprak UH, Torrents D, Tortora G, Tost J, Totoki Y, Townend D, Rätsch G, Traficante N, Treilleux I, Trotta JR, Trümper LHP, Tsao M, Tsunoda T, Tubio JMC, Tucker O, Turkington R, Turner DJ, Brooks AN, Tutt A, Ueno M, Ueno NT, Umbricht C, Umer HM, Underwood TJ, Urban L, Urushidate T, Ushiku T, Uusküla-Reimand L, Brazma A, Valencia A, Van Den Berg DJ, Van Laere S, Van Loo P, Van Meir EG, Van den Eynden GG, Van der Kwast T, Vasudev N, Vazquez M, Vedururu R, Brooks AN, Veluvolu U, Vembu S, Verbeke LPC, Vermeulen P, Verrill C, Viari A, Vicente D, Vicentini C, VijayRaghavan K, Viksna J, Göke J, Vilain RE, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell NM, Waddell N, Wadelius C, Rätsch G, Wadi L, Wagener R, Wala JA, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Schwarz RF, Waring PM, Warnatz HJ, Warrell J, Warren AY, Waszak SM, Wedge DC, Weichenhan D, Weinberger P, Weinstein JN, Weischenfeldt J, Stegle O, Weisenberger DJ, Welch I, Wendl MC, Werner J, Whalley JP, Wheeler DA, Whitaker HC, Wigle D, Wilkerson MD, Williams A, Zhang Z, Wilmott JS, Wilson GW, Wilson JM, Wilson RK, Winterhoff B, Wintersinger JA, Wiznerowicz M, Wolf S, Wong BH, Wong T, Aaltonen LA, Wong W, Woo Y, Wood S, Wouters BG, Wright AJ, Wright DW, Wright MH, Wu CL, Wu DY, Wu G, Abascal F, Wu J, Wu K, Wu Y, Wu Z, Xi L, Xia T, Xiang Q, Xiao X, Xing R, Xiong H, Abeshouse A, Xu Q, Xu Y, Xue H, Yachida S, Yakneen S, Yamaguchi R, Yamaguchi TN, Yamamoto M, Yamamoto S, Yamaue H, Aburatani H, Yang F, Yang H, Yang JY, Yang L, Yang L, Yang S, Yang TP, Yang Y, Yao X, Yaspo ML, Adams DJ, Yates L, Yau C, Ye C, Ye K, Yellapantula VD, Yoon CJ, Yoon SS, Yousif F, Yu J, Yu K, Agrawal N, Yu W, Yu Y, Yuan K, Yuan Y, Yuen D, Yung CK, Zaikova O, Zamora J, Zapatka M, Zenklusen JC, Ahn KS, Zenz T, Zeps N, Zhang CZ, Zhang F, Zhang H, Zhang H, Zhang H, Zhang J, Zhang J, Zhang J, Ahn SM, Zhang X, Zhang X, Zhang Y, Zhang Z, Zhao Z, Zheng L, Zheng X, Zhou W, Zhou Y, Zhu B, Aikata H, Zhu H, Zhu J, Zhu S, Zou L, Zou X, deFazio A, van As N, van Deurzen CHM, van de Vijver MJ, van’t Veer L, Akbani R, von Mering C, Akdemir KC, Al-Ahmadie H, Al-Sedairy ST, Al-Shahrour F, Alawi M, Albert M, Aldape K, Alexandrov LB, Ally A, Alsop K, Alvarez EG, Amary F, Amin SB, Aminou B, Ammerpohl O, Anderson MJ, Ang Y, Antonello D, Anur P, Aparicio S, Appelbaum EL, Arai Y, Aretz A, Arihiro K, Ariizumi SI, Armenia J, Arnould L, Asa S, Assenov Y, Atwal G, Aukema S, Auman JT, Aure MRR, Awadalla P, Aymerich M, Bader GD, Baez-Ortega A, Bailey MH, Bailey PJ, Balasundaram M, Balu S, Bandopadhayay P, Banks RE, Barbi S, Barbour AP, Barenboim J, Barnholtz-Sloan J, Barr H, Barrera E, Bartlett J, Bartolome J, Bassi C, Bathe OF, Baumhoer D, Bavi P, Baylin SB, Bazant W, Beardsmore D, Beck TA, Behjati S, Behren A, Niu B, Bell C, Beltran S, Benz C, Berchuck A, Bergmann AK, Bergstrom EN, Berman BP, Berney DM, Bernhart SH, Beroukhim R, Berrios M, Bersani S, Bertl J, Betancourt M, Bhandari V, Bhosle SG, Biankin AV, Bieg M, Bigner D, Binder H, Birney E, Birrer M, Biswas NK, Bjerkehagen B, Bodenheimer T, Boice L, Bonizzato G, De Bono JS, Boot A, Bootwalla MS, Borg A, Borkhardt A, Boroevich KA, Borozan I, Borst C, Bosenberg M, Bosio M, Boultwood J, Bourque G, Boutros PC, Bova GS, Bowen DT, Bowlby R, Bowtell DDL, Boyault S, Boyce R, Boyd J, Brazma A, Brennan P, Brewer DS, Brinkman AB, Bristow RG, Broaddus RR, Brock JE, Brock M, Broeks A, Brooks AN, Brooks D, Brors B, Brunak S, Bruxner TJC, Bruzos AL, Buchanan A, Buchhalter I, Buchholz C, Bullman S, Burke H, Burkhardt B, Burns KH, Busanovich J, Bustamante CD, Butler AP, Butte AJ, Byrne NJ, Børresen-Dale AL, Caesar-Johnson SJ, Cafferkey A, Cahill D, Calabrese C, Caldas C, Calvo F, Camacho N, Campbell PJ, Campo E, Cantù C, Cao S, Carey TE, Carlevaro-Fita J, Carlsen R, Cataldo I, Cazzola M, Cebon J, Cerfolio R, Chadwick DE, Chakravarty D, Chalmers D, Chan CWY, Chan K, Chan-Seng-Yue M, Chandan VS, Chang DK, Chanock SJ, Chantrill LA, Chateigner A, Chatterjee N, Chayama K, Chen HW, Chen J, Chen K, Chen Y, Chen Z, Cherniack AD, Chien J, Chiew YE, Chin SF, Cho J, Cho S, Choi JK, Choi W, Chomienne C, Chong Z, Choo SP, Chou A, Christ AN, Christie EL, Chuah E, Cibulskis C, Cibulskis K, Cingarlini S, Clapham P, Claviez A, Cleary S, Cloonan N, Cmero M, Collins CC, Connor AA, Cooke SL, Cooper CS, Cope L, Corbo V, Cordes MG, Cordner SM, Cortés-Ciriano I, Covington K, Cowin PA, Craft B, Craft D, Creighton CJ, Cun Y, Curley E, Cutcutache I, Czajka K, Czerniak B, Dagg RA, Danilova L, Davi MV, Davidson NR, Davies H, Davis IJ, Davis-Dusenbery BN, Dawson KJ, De La Vega FM, De Paoli-Iseppi R, Defreitas T, Tos APD, Delaneau O, Demchok JA, Demeulemeester J, Demidov GM, Demircioğlu D, Dennis NM, Denroche RE, Dentro SC, Desai N, Deshpande V, Deshwar AG, Desmedt C, Deu-Pons J, Dhalla N, Dhani NC, Dhingra P, Dhir R, DiBiase A, Diamanti K, Ding L, Ding S, Dinh HQ, Dirix L, Doddapaneni H, Donmez N, Dow MT, Drapkin R, Drechsel O, Drews RM, Serge S, Dudderidge T, Dueso-Barroso A, Dunford AJ, Dunn M, Dursi LJ, Duthie FR, Dutton-Regester K, Eagles J, Easton DF, Edmonds S, Edwards PA, Edwards SE, Eeles RA, Ehinger A, Eils J, Eils R, El-Naggar A, Eldridge M, Ellrott K, Erkek S, Escaramis G, Espiritu SMG, Estivill X, Etemadmoghadam D, Eyfjord JE, Faltas BM, Fan D, Fan Y, Faquin WC, Farcas C, Fassan M, Fatima A, Favero F, Fayzullaev N, Felau I, Fereday S, Ferguson ML, Ferretti V, Feuerbach L, Field MA, Fink JL, Finocchiaro G, Fisher C, Fittall MW, Fitzgerald A, Fitzgerald RC, Flanagan AM, Fleshner NE, Flicek P, Foekens JA, Fong KM, Fonseca NA, Foster CS, Fox NS, Fraser M, Frazer S, Frenkel-Morgenstern M, Friedman W, Frigola J, Fronick CC, Fujimoto A, Fujita M, Fukayama M, Fulton LA, Fulton RS, Furuta M, Futreal PA, Füllgrabe A, Gabriel SB, Gallinger S, Gambacorti-Passerini C, Gao J, Gao S, Garraway L, Garred Ø, Garrison E, Garsed DW, Gehlenborg N, Gelpi JLL, George J, Gerhard DS, Gerhauser C, Gershenwald JE, Gerstein M, Gerstung M, Getz G, Ghori M, Ghossein R, Giama NH, Gibbs RA, Gibson B, Gill AJ, Gill P, Giri DD, Glodzik D, Gnanapragasam VJ, Goebler ME, Goldman MJ, Gomez C, Gonzalez S, Gonzalez-Perez A, Gordenin DA, Gossage J, Gotoh K, Govindan R, Grabau D, Graham JS, Grant RC, Green AR, Green E, Greger L, Grehan N, Grimaldi S, Grimmond SM, Grossman RL, Grundhoff A, Gundem G, Guo Q, Gupta M, Gupta S, Gut IG, Gut M, Göke J, Ha G, Haake A, Haan D, Haas S, Haase K, Haber JE, Habermann N, Hach F, Haider S, Hama N, Hamdy FC, Hamilton A, Hamilton MP, Han L, Hanna GB, Hansmann M, Haradhvala NJ, Harismendy O, Harliwong I, Harmanci AO, Harrington E, Hasegawa T, Haussler D, Hawkins S, Hayami S, Hayashi S, Hayes DN, Hayes SJ, Hayward NK, Hazell S, He Y, Heath AP, Heath SC, Hedley D, Hegde AM, Heiman DI, Heinold MC, Heins Z, Heisler LE, Hellstrom-Lindberg E, Helmy M, Heo SG, Hepperla AJ, Heredia-Genestar JM, Herrmann C, Hersey P, Hess JM, Hilmarsdottir H, Hinton J, Hirano S, Hiraoka N, Hoadley KA, Hobolth A, Hodzic E, Hoell JI, Hoffmann S, Hofmann O, Holbrook A, Holik AZ, Hollingsworth MA, Holmes O, Holt RA, Hong C, Hong EP, Hong JH, Hooijer GK, Hornshøj H, Hosoda F, Hou Y, Hovestadt V, Howat W, Hoyle AP, Hruban RH, Hu J, Hu T, Hua X, Huang KL, Huang M, Huang MN, Huang V, Huang Y, Huber W, Hudson TJ, Hummel M, Hung JA, Huntsman D, Hupp TR, Huse J, Huska MR, Hutter B, Hutter CM, Hübschmann D, Iacobuzio-Donahue CA, Imbusch CD, Imielinski M, Imoto S, Isaacs WB, Isaev K, Ishikawa S, Iskar M, Islam SMA, Ittmann M, Ivkovic S, Izarzugaza JMG, Jacquemier J, Jakrot V, Jamieson NB, Jang GH, Jang SJ, Jayaseelan JC, Jayasinghe R, Jefferys SR, Jegalian K, Jennings JL, Jeon SH, Jerman L, Ji Y, Jiao W, Johansson PA, Johns AL, Johns J, Johnson R, Johnson TA, Jolly C, Joly Y, Jonasson JG, Jones CD, Jones DR, Jones DTW, Jones N, Jones SJM, Jonkers J, Ju YS, Juhl H, Jung J, Juul M, Juul RI, Juul S, Jäger N, Kabbe R, Kahles A, Kahraman A, Kaiser VB, Kakavand H, Kalimuthu S, von Kalle C, Kang KJ, Karaszi K, Karlan B, Karlić R, Karsch D, Kasaian K, Kassahn KS, Katai H, Kato M, Katoh H, Kawakami Y, Kay JD, Kazakoff SH, Kazanov MD, Keays M, Kebebew E, Kefford RF, Kellis M, Kench JG, Kennedy CJ, Kerssemakers JNA, Khoo D, Khoo V, Khuntikeo N, Khurana E, Kilpinen H, Kim HK, Kim HL, Kim HY, Kim H, Kim J, Kim J, Kim JK, Kim Y, King TA, Klapper W, Kleinheinz K, Klimczak LJ, Knappskog S, Kneba M, Knoppers BM, Koh Y, Komorowski J, Komura D, Komura M, Kong G, Kool M, Korbel JO, Korchina V, Korshunov A, Koscher M, Koster R, Kote-Jarai Z, Koures A, Kovacevic M, Kremeyer B, Kretzmer H, Kreuz M, Krishnamurthy S, Kube D, Kumar K, Kumar P, Kumar S, Kumar Y, Kundra R, Kübler K, Küppers R, Lagergren J, Lai PH, Laird PW, Lakhani SR, Lalansingh CM, Lalonde E, Lamaze FC, Lambert A, Lander E, Landgraf P, Landoni L, Langerød A, Lanzós A, Larsimont D, Larsson E, Lathrop M, Lau LMS, Lawerenz C, Lawlor RT, Lawrence MS, Lazar AJ, Lazic AM, Le X, Lee D, Lee D, Lee EA, Lee HJ, Lee JJK, Lee JY, Lee J, Lee MTM, Lee-Six H, Lehmann KV, Lehrach H, Lenze D, Leonard CR, Leongamornlert DA, Leshchiner I, Letourneau L, Letunic I, Levine DA, Lewis L, Ley T, Li C, Li CH, Li HI, Li J, Li L, Li S, Li S, Li X, Li X, Li X, Li Y, Liang H, Liang SB, Lichter P, Lin P, Lin Z, Linehan WM, Lingjærde OC, Liu D, Liu EM, Liu FFF, Liu F, Liu J, Liu X, Livingstone J, Livitz D, Livni N, Lochovsky L, Loeffler M, Long GV, Lopez-Guillermo A, Lou S, Louis DN, Lovat LB, Lu Y, Lu YJ, Lu Y, Luchini C, Lungu I, Luo X, Luxton HJ, Lynch AG, Lype L, López C, López-Otín C, Ma EZ, Ma Y, MacGrogan G, MacRae S, Macintyre G, Madsen T, Maejima K, Mafficini A, Maglinte DT, Maitra A, Majumder PP, Malcovati L, Malikic S, Malleo G, Mann GJ, Mantovani-Löffler L, Marchal K, Marchegiani G, Mardis ER, Margolin AA, Marin MG, Markowetz F, Markowski J, Marks J, Marques-Bonet T, Marra MA, Marsden L, Martens JWM, Martin S, Martin-Subero JI, Martincorena I, Martinez-Fundichely A, Maruvka YE, Mashl RJ, Massie CE, Matthew TJ, Matthews L, Mayer E, Mayes S, Mayo M, Mbabaali F, McCune K, McDermott U, McGillivray PD, McLellan MD, McPherson JD, McPherson JR, McPherson TA, Meier SR, Meng A, Meng S, Menzies A, Merrett ND, Merson S, Meyerson M, Meyerson W, Mieczkowski PA, Mihaiescu GL, Mijalkovic S, Mikkelsen T, Milella M, Mileshkin L, Miller CA, Miller DK, Miller JK, Mills GB, Milovanovic A, Minner S, Miotto M, Arnau GM, Mirabello L, Mitchell C, Mitchell TJ, Miyano S, Miyoshi N, Mizuno S, Molnár-Gábor F, Moore MJ, Moore RA, Morganella S, Morris QD, Morrison C, Mose LE, Moser CD, Muiños F, Mularoni L, Mungall AJ, Mungall K, Musgrove EA, Mustonen V, Mutch D, Muyas F, Muzny DM, Muñoz A, Myers J, Myklebost O, Möller P, Nagae G, Nagrial AM, Nahal-Bose HK, Nakagama H, Nakagawa H, Nakamura H, Nakamura T, Nakano K, Nandi T, Nangalia J, Nastic M, Navarro A, Navarro FCP, Neal DE, Nettekoven G, Newell F, Newhouse SJ, Newton Y, Ng AWT, Ng A, Nicholson J, Nicol D, Nie Y, Nielsen GP, Nielsen MM, Nik-Zainal S, Noble MS, Nones K, Northcott PA, Notta F, O’Connor BD, O’Donnell P, O’Donovan M, O’Meara S, O’Neill BP, O’Neill JR, Ocana D, Ochoa A, Oesper L, Ogden C, Ohdan H, Ohi K, Ohno-Machado L, Oien KA, Ojesina AI, Ojima H, Okusaka T, Omberg L, Ong CK, Ossowski S, Ott G, Ouellette BFF, P’ng C, Paczkowska M, Paiella S, Pairojkul C, Pajic M, Pan-Hammarström Q, Papaemmanuil E, Papatheodorou I, Paramasivam N, Park JW, Park JW, Park K, Park K, Park PJ, Parker JS, Parsons SL, Pass H, Pasternack D, Pastore A, Patch AM, Pauporté I, Pea A, Pearson JV. Author Correction: Genomic basis for RNA alterations in cancer. Nature 2023; 614:E37. [PMID: 36697831 PMCID: PMC9931574 DOI: 10.1038/s41586-022-05596-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
| | - Claudia Calabrese
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Natalie R. Davidson
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.5386.8000000041936877XWeill Cornell Medical College, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Deniz Demircioğlu
- grid.4280.e0000 0001 2180 6431National University of Singapore, Singapore, Singapore ,grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore
| | - Nuno A. Fonseca
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Yao He
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - André Kahles
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Kjong-Van Lehmann
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Fenglin Liu
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - Yuichi Shiraishi
- grid.26999.3d0000 0001 2151 536XThe University of Tokyo, Minato-ku, Japan
| | - Cameron M. Soulette
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA
| | - Lara Urban
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Liliana Greger
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Siliang Li
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Dongbing Liu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Marc D. Perry
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada ,grid.266102.10000 0001 2297 6811University of California, San Francisco, San Francisco, CA USA
| | - Qian Xiang
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Fan Zhang
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - Junjun Zhang
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Peter Bailey
- grid.8756.c0000 0001 2193 314XUniversity of Glasgow, Glasgow, UK
| | - Serap Erkek
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Katherine A. Hoadley
- grid.10698.360000000122483208The University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Yong Hou
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Matthew R. Huska
- grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | - Helena Kilpinen
- grid.83440.3b0000000121901201University College London, London, UK
| | - Jan O. Korbel
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Maximillian G. Marin
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA
| | - Julia Markowski
- grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | - Tannistha Nandi
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore
| | - Qiang Pan-Hammarström
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.4714.60000 0004 1937 0626Karolinska Institutet, Stockholm, Sweden
| | - Chandra Sekhar Pedamallu
- grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Reiner Siebert
- grid.410712.10000 0004 0473 882XUlm University and Ulm University Medical Center, Ulm, Germany
| | - Stefan G. Stark
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Hong Su
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Patrick Tan
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore ,grid.428397.30000 0004 0385 0924Duke-NUS Medical School, Singapore, Singapore
| | - Sebastian M. Waszak
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Christina Yung
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Shida Zhu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Philip Awadalla
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada ,grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada
| | - Chad J. Creighton
- grid.39382.330000 0001 2160 926XBaylor College of Medicine, Houston, TX USA
| | - Matthew Meyerson
- grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | | | - Kui Wu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Huanming Yang
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China
| | | | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.
| | - Angela N. Brooks
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA ,grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA
| | - Jonathan Göke
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore ,grid.410724.40000 0004 0620 9745National Cancer Centre Singapore, Singapore, Singapore
| | - Gunnar Rätsch
- ETH Zurich, Zurich, Switzerland. .,Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Weill Cornell Medical College, New York, NY, USA. .,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland. .,University Hospital Zurich, Zurich, Switzerland.
| | - Roland F. Schwarz
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK ,grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), partner site Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Oliver Stegle
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK ,grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Zemin Zhang
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
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Kloetgen A, Duggimpudi S, Schuschel K, Hezaveh K, Picard D, Schaal H, Remke M, Klusmann JH, Borkhardt A, McHardy AC, Hoell JI. YBX1 Indirectly Targets Heterochromatin-Repressed Inflammatory Response-Related Apoptosis Genes through Regulating CBX5 mRNA. Int J Mol Sci 2020; 21:ijms21124453. [PMID: 32585856 PMCID: PMC7352269 DOI: 10.3390/ijms21124453] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 06/18/2020] [Accepted: 06/20/2020] [Indexed: 12/18/2022] Open
Abstract
Medulloblastomas arise from undifferentiated precursor cells in the cerebellum and account for about 20% of all solid brain tumors during childhood; standard therapies include radiation and chemotherapy, which oftentimes come with severe impairment of the cognitive development of the young patients. Here, we show that the posttranscriptional regulator Y-box binding protein 1 (YBX1), a DNA- and RNA-binding protein, acts as an oncogene in medulloblastomas by regulating cellular survival and apoptosis. We observed different cellular responses upon YBX1 knockdown in several medulloblastoma cell lines, with significantly altered transcription and subsequent apoptosis rates. Mechanistically, PAR-CLIP for YBX1 and integration with RNA-Seq data uncovered direct posttranscriptional control of the heterochromatin-associated gene CBX5; upon YBX1 knockdown and subsequent CBX5 mRNA instability, heterochromatin-regulated genes involved in inflammatory response, apoptosis and death receptor signaling were de-repressed. Thus, YBX1 acts as an oncogene in medulloblastoma through indirect transcriptional regulation of inflammatory genes regulating apoptosis and represents a promising novel therapeutic target in this tumor entity.
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Affiliation(s)
- Andreas Kloetgen
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany;
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany; (S.D.); (K.H.); (D.P.); (M.R.); (A.B.); (J.I.H.)
- Correspondence:
| | - Sujitha Duggimpudi
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany; (S.D.); (K.H.); (D.P.); (M.R.); (A.B.); (J.I.H.)
| | - Konstantin Schuschel
- Department of Pediatrics 1, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany; (K.S.); (J.-H.K.)
| | - Kebria Hezaveh
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany; (S.D.); (K.H.); (D.P.); (M.R.); (A.B.); (J.I.H.)
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Daniel Picard
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany; (S.D.); (K.H.); (D.P.); (M.R.); (A.B.); (J.I.H.)
| | - Heiner Schaal
- Institute of Virology, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany;
| | - Marc Remke
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany; (S.D.); (K.H.); (D.P.); (M.R.); (A.B.); (J.I.H.)
| | - Jan-Henning Klusmann
- Department of Pediatrics 1, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany; (K.S.); (J.-H.K.)
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany; (S.D.); (K.H.); (D.P.); (M.R.); (A.B.); (J.I.H.)
| | - Alice C. McHardy
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany;
| | - Jessica I. Hoell
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany; (S.D.); (K.H.); (D.P.); (M.R.); (A.B.); (J.I.H.)
- Department of Pediatrics 1, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany; (K.S.); (J.-H.K.)
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Aaltonen LA, Abascal F, Abeshouse A, Aburatani H, Adams DJ, Agrawal N, Ahn KS, Ahn SM, Aikata H, Akbani R, Akdemir KC, Al-Ahmadie H, Al-Sedairy ST, Al-Shahrour F, Alawi M, Albert M, Aldape K, Alexandrov LB, Ally A, Alsop K, Alvarez EG, Amary F, Amin SB, Aminou B, Ammerpohl O, Anderson MJ, Ang Y, Antonello D, Anur P, Aparicio S, Appelbaum EL, Arai Y, Aretz A, Arihiro K, Ariizumi SI, Armenia J, Arnould L, Asa S, Assenov Y, Atwal G, Aukema S, Auman JT, Aure MRR, Awadalla P, Aymerich M, Bader GD, Baez-Ortega A, Bailey MH, Bailey PJ, Balasundaram M, Balu S, Bandopadhayay P, Banks RE, Barbi S, Barbour AP, Barenboim J, Barnholtz-Sloan J, Barr H, Barrera E, Bartlett J, Bartolome J, Bassi C, Bathe OF, Baumhoer D, Bavi P, Baylin SB, Bazant W, Beardsmore D, Beck TA, Behjati S, Behren A, Niu B, Bell C, Beltran S, Benz C, Berchuck A, Bergmann AK, Bergstrom EN, Berman BP, Berney DM, Bernhart SH, Beroukhim R, Berrios M, Bersani S, Bertl J, Betancourt M, Bhandari V, Bhosle SG, Biankin AV, Bieg M, Bigner D, Binder H, Birney E, Birrer M, Biswas NK, Bjerkehagen B, Bodenheimer T, Boice L, Bonizzato G, De Bono JS, Boot A, Bootwalla MS, Borg A, Borkhardt A, Boroevich KA, Borozan I, Borst C, Bosenberg M, Bosio M, Boultwood J, Bourque G, Boutros PC, Bova GS, Bowen DT, Bowlby R, Bowtell DDL, Boyault S, Boyce R, Boyd J, Brazma A, Brennan P, Brewer DS, Brinkman AB, Bristow RG, Broaddus RR, Brock JE, Brock M, Broeks A, Brooks AN, Brooks D, Brors B, Brunak S, Bruxner TJC, Bruzos AL, Buchanan A, Buchhalter I, Buchholz C, Bullman S, Burke H, Burkhardt B, Burns KH, Busanovich J, Bustamante CD, Butler AP, Butte AJ, Byrne NJ, Børresen-Dale AL, Caesar-Johnson SJ, Cafferkey A, Cahill D, Calabrese C, Caldas C, Calvo F, Camacho N, Campbell PJ, Campo E, Cantù C, Cao S, Carey TE, Carlevaro-Fita J, Carlsen R, Cataldo I, Cazzola M, Cebon J, Cerfolio R, Chadwick DE, Chakravarty D, Chalmers D, Chan CWY, Chan K, Chan-Seng-Yue M, Chandan VS, Chang DK, Chanock SJ, Chantrill LA, Chateigner A, Chatterjee N, Chayama K, Chen HW, Chen J, Chen K, Chen Y, Chen Z, Cherniack AD, Chien J, Chiew YE, Chin SF, Cho J, Cho S, Choi JK, Choi W, Chomienne C, Chong Z, Choo SP, Chou A, Christ AN, Christie EL, Chuah E, Cibulskis C, Cibulskis K, Cingarlini S, Clapham P, Claviez A, Cleary S, Cloonan N, Cmero M, Collins CC, Connor AA, Cooke SL, Cooper CS, Cope L, Corbo V, Cordes MG, Cordner SM, Cortés-Ciriano I, Covington K, Cowin PA, Craft B, Craft D, Creighton CJ, Cun Y, Curley E, Cutcutache I, Czajka K, Czerniak B, Dagg RA, Danilova L, Davi MV, Davidson NR, Davies H, Davis IJ, Davis-Dusenbery BN, Dawson KJ, De La Vega FM, De Paoli-Iseppi R, Defreitas T, Tos APD, Delaneau O, Demchok JA, Demeulemeester J, Demidov GM, Demircioğlu D, Dennis NM, Denroche RE, Dentro SC, Desai N, Deshpande V, Deshwar AG, Desmedt C, Deu-Pons J, Dhalla N, Dhani NC, Dhingra P, Dhir R, DiBiase A, Diamanti K, Ding L, Ding S, Dinh HQ, Dirix L, Doddapaneni H, Donmez N, Dow MT, Drapkin R, Drechsel O, Drews RM, Serge S, Dudderidge T, Dueso-Barroso A, Dunford AJ, Dunn M, Dursi LJ, Duthie FR, Dutton-Regester K, Eagles J, Easton DF, Edmonds S, Edwards PA, Edwards SE, Eeles RA, Ehinger A, Eils J, Eils R, El-Naggar A, Eldridge M, Ellrott K, Erkek S, Escaramis G, Espiritu SMG, Estivill X, Etemadmoghadam D, Eyfjord JE, Faltas BM, Fan D, Fan Y, Faquin WC, Farcas C, Fassan M, Fatima A, Favero F, Fayzullaev N, Felau I, Fereday S, Ferguson ML, Ferretti V, Feuerbach L, Field MA, Fink JL, Finocchiaro G, Fisher C, Fittall MW, Fitzgerald A, Fitzgerald RC, Flanagan AM, Fleshner NE, Flicek P, Foekens JA, Fong KM, Fonseca NA, Foster CS, Fox NS, Fraser M, Frazer S, Frenkel-Morgenstern M, Friedman W, Frigola J, Fronick CC, Fujimoto A, Fujita M, Fukayama M, Fulton LA, Fulton RS, Furuta M, Futreal PA, Füllgrabe A, Gabriel SB, Gallinger S, Gambacorti-Passerini C, Gao J, Gao S, Garraway L, Garred Ø, Garrison E, Garsed DW, Gehlenborg N, Gelpi JLL, George J, Gerhard DS, Gerhauser C, Gershenwald JE, Gerstein M, Gerstung M, Getz G, Ghori M, Ghossein R, Giama NH, Gibbs RA, Gibson B, Gill AJ, Gill P, Giri DD, Glodzik D, Gnanapragasam VJ, Goebler ME, Goldman MJ, Gomez C, Gonzalez S, Gonzalez-Perez A, Gordenin DA, Gossage J, Gotoh K, Govindan R, Grabau D, Graham JS, Grant RC, Green AR, Green E, Greger L, Grehan N, Grimaldi S, Grimmond SM, Grossman RL, Grundhoff A, Gundem G, Guo Q, Gupta M, Gupta S, Gut IG, Gut M, Göke J, Ha G, Haake A, Haan D, Haas S, Haase K, Haber JE, Habermann N, Hach F, Haider S, Hama N, Hamdy FC, Hamilton A, Hamilton MP, Han L, Hanna GB, Hansmann M, Haradhvala NJ, Harismendy O, Harliwong I, Harmanci AO, Harrington E, Hasegawa T, Haussler D, Hawkins S, Hayami S, Hayashi S, Hayes DN, Hayes SJ, Hayward NK, Hazell S, He Y, Heath AP, Heath SC, Hedley D, Hegde AM, Heiman DI, Heinold MC, Heins Z, Heisler LE, Hellstrom-Lindberg E, Helmy M, Heo SG, Hepperla AJ, Heredia-Genestar JM, Herrmann C, Hersey P, Hess JM, Hilmarsdottir H, Hinton J, Hirano S, Hiraoka N, Hoadley KA, Hobolth A, Hodzic E, Hoell JI, Hoffmann S, Hofmann O, Holbrook A, Holik AZ, Hollingsworth MA, Holmes O, Holt RA, Hong C, Hong EP, Hong JH, Hooijer GK, Hornshøj H, Hosoda F, Hou Y, Hovestadt V, Howat W, Hoyle AP, Hruban RH, Hu J, Hu T, Hua X, Huang KL, Huang M, Huang MN, Huang V, Huang Y, Huber W, Hudson TJ, Hummel M, Hung JA, Huntsman D, Hupp TR, Huse J, Huska MR, Hutter B, Hutter CM, Hübschmann D, Iacobuzio-Donahue CA, Imbusch CD, Imielinski M, Imoto S, Isaacs WB, Isaev K, Ishikawa S, Iskar M, Islam SMA, Ittmann M, Ivkovic S, Izarzugaza JMG, Jacquemier J, Jakrot V, Jamieson NB, Jang GH, Jang SJ, Jayaseelan JC, Jayasinghe R, Jefferys SR, Jegalian K, Jennings JL, Jeon SH, Jerman L, Ji Y, Jiao W, Johansson PA, Johns AL, Johns J, Johnson R, Johnson TA, Jolly C, Joly Y, Jonasson JG, Jones CD, Jones DR, Jones DTW, Jones N, Jones SJM, Jonkers J, Ju YS, Juhl H, Jung J, Juul M, Juul RI, Juul S, Jäger N, Kabbe R, Kahles A, Kahraman A, Kaiser VB, Kakavand H, Kalimuthu S, von Kalle C, Kang KJ, Karaszi K, Karlan B, Karlić R, Karsch D, Kasaian K, Kassahn KS, Katai H, Kato M, Katoh H, Kawakami Y, Kay JD, Kazakoff SH, Kazanov MD, Keays M, Kebebew E, Kefford RF, Kellis M, Kench JG, Kennedy CJ, Kerssemakers JNA, Khoo D, Khoo V, Khuntikeo N, Khurana E, Kilpinen H, Kim HK, Kim HL, Kim HY, Kim H, Kim J, Kim J, Kim JK, Kim Y, King TA, Klapper W, Kleinheinz K, Klimczak LJ, Knappskog S, Kneba M, Knoppers BM, Koh Y, Komorowski J, Komura D, Komura M, Kong G, Kool M, Korbel JO, Korchina V, Korshunov A, Koscher M, Koster R, Kote-Jarai Z, Koures A, Kovacevic M, Kremeyer B, Kretzmer H, Kreuz M, Krishnamurthy S, Kube D, Kumar K, Kumar P, Kumar S, Kumar Y, Kundra R, Kübler K, Küppers R, Lagergren J, Lai PH, Laird PW, Lakhani SR, Lalansingh CM, Lalonde E, Lamaze FC, Lambert A, Lander E, Landgraf P, Landoni L, Langerød A, Lanzós A, Larsimont D, Larsson E, Lathrop M, Lau LMS, Lawerenz C, Lawlor RT, Lawrence MS, Lazar AJ, Lazic AM, Le X, Lee D, Lee D, Lee EA, Lee HJ, Lee JJK, Lee JY, Lee J, Lee MTM, Lee-Six H, Lehmann KV, Lehrach H, Lenze D, Leonard CR, Leongamornlert DA, Leshchiner I, Letourneau L, Letunic I, Levine DA, Lewis L, Ley T, Li C, Li CH, Li HI, Li J, Li L, Li S, Li S, Li X, Li X, Li X, Li Y, Liang H, Liang SB, Lichter P, Lin P, Lin Z, Linehan WM, Lingjærde OC, Liu D, Liu EM, Liu FFF, Liu F, Liu J, Liu X, Livingstone J, Livitz D, Livni N, Lochovsky L, Loeffler M, Long GV, Lopez-Guillermo A, Lou S, Louis DN, Lovat LB, Lu Y, Lu YJ, Lu Y, Luchini C, Lungu I, Luo X, Luxton HJ, Lynch AG, Lype L, López C, López-Otín C, Ma EZ, Ma Y, MacGrogan G, MacRae S, Macintyre G, Madsen T, Maejima K, Mafficini A, Maglinte DT, Maitra A, Majumder PP, Malcovati L, Malikic S, Malleo G, Mann GJ, Mantovani-Löffler L, Marchal K, Marchegiani G, Mardis ER, Margolin AA, Marin MG, Markowetz F, Markowski J, Marks J, Marques-Bonet T, Marra MA, Marsden L, Martens JWM, Martin S, Martin-Subero JI, Martincorena I, Martinez-Fundichely A, Maruvka YE, Mashl RJ, Massie CE, Matthew TJ, Matthews L, Mayer E, Mayes S, Mayo M, Mbabaali F, McCune K, McDermott U, McGillivray PD, McLellan MD, McPherson JD, McPherson JR, McPherson TA, Meier SR, Meng A, Meng S, Menzies A, Merrett ND, Merson S, Meyerson M, Meyerson W, Mieczkowski PA, Mihaiescu GL, Mijalkovic S, Mikkelsen T, Milella M, Mileshkin L, Miller CA, Miller DK, Miller JK, Mills GB, Milovanovic A, Minner S, Miotto M, Arnau GM, Mirabello L, Mitchell C, Mitchell TJ, Miyano S, Miyoshi N, Mizuno S, Molnár-Gábor F, Moore MJ, Moore RA, Morganella S, Morris QD, Morrison C, Mose LE, Moser CD, Muiños F, Mularoni L, Mungall AJ, Mungall K, Musgrove EA, Mustonen V, Mutch D, Muyas F, Muzny DM, Muñoz A, Myers J, Myklebost O, Möller P, Nagae G, Nagrial AM, Nahal-Bose HK, Nakagama H, Nakagawa H, Nakamura H, Nakamura T, Nakano K, Nandi T, Nangalia J, Nastic M, Navarro A, Navarro FCP, Neal DE, Nettekoven G, Newell F, Newhouse SJ, Newton Y, Ng AWT, Ng A, Nicholson J, Nicol D, Nie Y, Nielsen GP, Nielsen MM, Nik-Zainal S, Noble MS, Nones K, Northcott PA, Notta F, O’Connor BD, O’Donnell P, O’Donovan M, O’Meara S, O’Neill BP, O’Neill JR, Ocana D, Ochoa A, Oesper L, Ogden C, Ohdan H, Ohi K, Ohno-Machado L, Oien KA, Ojesina AI, Ojima H, Okusaka T, Omberg L, Ong CK, Ossowski S, Ott G, Ouellette BFF, P’ng C, Paczkowska M, Paiella S, Pairojkul C, Pajic M, Pan-Hammarström Q, Papaemmanuil E, Papatheodorou I, Paramasivam N, Park JW, Park JW, Park K, Park K, Park PJ, Parker JS, Parsons SL, Pass H, Pasternack D, Pastore A, Patch AM, Pauporté I, Pea A, Pearson JV, Pedamallu CS, Pedersen JS, Pederzoli P, Peifer M, Pennell NA, Perou CM, Perry MD, Petersen GM, Peto M, Petrelli N, Petryszak R, Pfister SM, Phillips M, Pich O, Pickett HA, Pihl TD, Pillay N, Pinder S, Pinese M, Pinho AV, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Shorser SI, Short C, Shrestha R, Shringarpure SS, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts AM, Sieverling L, Signoretti S, Sikora KO, Simbolo M, Simon R, Simons JV, Simpson JT, Simpson PT, Singer S, Sinnott-Armstrong N, Sipahimalani P, Skelly TJ, Smid M, Smith J, Smith-McCune K, Socci ND, Sofia HJ, Soloway MG, Song L, Sood AK, Sothi S, Sotiriou C, Soulette CM, Span PN, Spellman PT, Sperandio N, Spillane AJ, Spiro O, Spring J, Staaf J, Stadler PF, Staib P, Stark SG, Stebbings L, Stefánsson ÓA, Stegle O, Stein LD, Stenhouse A, Stewart C, Stilgenbauer S, Stobbe MD, Stratton MR, Stretch JR, Struck AJ, Stuart JM, Stunnenberg HG, Su H, Su X, Sun RX, Sungalee S, Susak H, Suzuki A, Sweep F, Szczepanowski M, Sültmann H, Yugawa T, Tam A, Tamborero D, Tan BKT, Tan D, Tan P, Tanaka H, Taniguchi H, Tanskanen TJ, Tarabichi M, Tarnuzzer R, Tarpey P, Taschuk ML, Tatsuno K, Tavaré S, Taylor DF, Taylor-Weiner A, Teague JW, Teh BT, Tembe V, Temes J, Thai K, Thayer SP, Thiessen N, Thomas G, Thomas S, Thompson A, Thompson AM, Thompson JFF, Thompson RH, Thorne H, Thorne LB, Thorogood A, Tiao G, Tijanic N, Timms LE, Tirabosco R, Tojo M, Tommasi S, Toon CW, Toprak UH, Torrents D, Tortora G, Tost J, Totoki Y, Townend D, Traficante N, Treilleux I, Trotta JR, Trümper LHP, Tsao M, Tsunoda T, Tubio JMC, Tucker O, Turkington R, Turner DJ, Tutt A, Ueno M, Ueno NT, Umbricht C, Umer HM, Underwood TJ, Urban L, Urushidate T, Ushiku T, Uusküla-Reimand L, Valencia A, Van Den Berg DJ, Van Laere S, Van Loo P, Van Meir EG, Van den Eynden GG, Van der Kwast T, Vasudev N, Vazquez M, Vedururu R, Veluvolu U, Vembu S, Verbeke LPC, Vermeulen P, Verrill C, Viari A, Vicente D, Vicentini C, VijayRaghavan K, Viksna J, Vilain RE, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell NM, Waddell N, Wadelius C, Wadi L, Wagener R, Wala JA, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Waring PM, Warnatz HJ, Warrell J, Warren AY, Waszak SM, Wedge DC, Weichenhan D, Weinberger P, Weinstein JN, Weischenfeldt J, Weisenberger DJ, Welch I, Wendl MC, Werner J, Whalley JP, Wheeler DA, Whitaker HC, Wigle D, Wilkerson MD, Williams A, Wilmott JS, Wilson GW, Wilson JM, Wilson RK, Winterhoff B, Wintersinger JA, Wiznerowicz M, Wolf S, Wong BH, Wong T, Wong W, Woo Y, Wood S, Wouters BG, Wright AJ, Wright DW, Wright MH, Wu CL, Wu DY, Wu G, Wu J, Wu K, Wu Y, Wu Z, Xi L, Xia T, Xiang Q, Xiao X, Xing R, Xiong H, Xu Q, Xu Y, Xue H, Yachida S, Yakneen S, Yamaguchi R, Yamaguchi TN, Yamamoto M, Yamamoto S, Yamaue H, Yang F, Yang H, Yang JY, Yang L, Yang L, Yang S, Yang TP, Yang Y, Yao X, Yaspo ML, Yates L, Yau C, Ye C, Ye K, Yellapantula VD, Yoon CJ, Yoon SS, Yousif F, Yu J, Yu K, Yu W, Yu Y, Yuan K, Yuan Y, Yuen D, Yung CK, Zaikova O, Zamora J, Zapatka M, Zenklusen JC, Zenz T, Zeps N, Zhang CZ, Zhang F, Zhang H, Zhang H, Zhang H, Zhang J, Zhang J, Zhang J, Zhang X, Zhang X, Zhang Y, Zhang Z, Zhao Z, Zheng L, Zheng X, Zhou W, Zhou Y, Zhu B, Zhu H, Zhu J, Zhu S, Zou L, Zou X, deFazio A, van As N, van Deurzen CHM, van de Vijver MJ, van’t Veer L, von Mering C. Pan-cancer analysis of whole genomes. Nature 2020; 578:82-93. [PMID: 32025007 PMCID: PMC7025898 DOI: 10.1038/s41586-020-1969-6] [Citation(s) in RCA: 1435] [Impact Index Per Article: 358.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 12/11/2019] [Indexed: 02/07/2023]
Abstract
Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10-18.
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11
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Zhuang Y, Xu HC, Shinde PV, Warfsmann J, Vasilevska J, Sundaram B, Behnke K, Huang J, Hoell JI, Borkhardt A, Pfeffer K, Taha MS, Herebian D, Mayatepek E, Brenner D, Ahmadian MR, Keitel V, Wieczorek D, Häussinger D, Pandyra AA, Lang KS, Lang PA. Fragile X mental retardation protein protects against tumour necrosis factor-mediated cell death and liver injury. Gut 2020; 69:133-145. [PMID: 31409605 PMCID: PMC6943250 DOI: 10.1136/gutjnl-2019-318215] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 07/22/2019] [Accepted: 07/24/2019] [Indexed: 12/08/2022]
Abstract
OBJECTIVE The Fragile X mental retardation (FMR) syndrome is a frequently inherited intellectual disability caused by decreased or absent expression of the FMR protein (FMRP). Lack of FMRP is associated with neuronal degradation and cognitive dysfunction but its role outside the central nervous system is insufficiently studied. Here, we identify a role of FMRP in liver disease. DESIGN Mice lacking Fmr1 gene expression were used to study the role of FMRP during tumour necrosis factor (TNF)-induced liver damage in disease model systems. Liver damage and mechanistic studies were performed using real-time PCR, Western Blot, staining of tissue sections and clinical chemistry. RESULTS Fmr1null mice exhibited increased liver damage during virus-mediated hepatitis following infection with the lymphocytic choriomeningitis virus. Exposure to TNF resulted in severe liver damage due to increased hepatocyte cell death. Consistently, we found increased caspase-8 and caspase-3 activation following TNF stimulation. Furthermore, we demonstrate FMRP to be critically important for regulating key molecules in TNF receptor 1 (TNFR1)-dependent apoptosis and necroptosis including CYLD, c-FLIPS and JNK, which contribute to prolonged RIPK1 expression. Accordingly, the RIPK1 inhibitor Necrostatin-1s could reduce liver cell death and alleviate liver damage in Fmr1null mice following TNF exposure. Consistently, FMRP-deficient mice developed increased pathology during acute cholestasis following bile duct ligation, which coincided with increased hepatic expression of RIPK1, RIPK3 and phosphorylation of MLKL. CONCLUSIONS We show that FMRP plays a central role in the inhibition of TNF-mediated cell death during infection and liver disease.
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Affiliation(s)
- Yuan Zhuang
- Department of Molecular Medicine II, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Haifeng C Xu
- Department of Molecular Medicine II, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Prashant V Shinde
- Department of Molecular Medicine II, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Jens Warfsmann
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Center for Child and Adolescent Health, Heinrich Heine University, Medical Faculty, Düsseldorf, Germany
| | - Jelena Vasilevska
- Department of Molecular Medicine II, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Balamurugan Sundaram
- Department of Molecular Medicine II, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Kristina Behnke
- Department of Molecular Medicine II, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Jun Huang
- Department of Molecular Medicine II, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Jessica I Hoell
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Center for Child and Adolescent Health, Heinrich Heine University, Medical Faculty, Düsseldorf, Germany
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Center for Child and Adolescent Health, Heinrich Heine University, Medical Faculty, Düsseldorf, Germany
| | - Klaus Pfeffer
- Institute of Medical Microbiology and Hospital Hygiene, University Hospital, Heinrich-Heine-University, Düsseldorf, Germany
| | - Mohamed S Taha
- Research on Children with Special Needs Department, Medical research Branch, National Research Centre, Cairo, Egypt,Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Diran Herebian
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Ertan Mayatepek
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Dirk Brenner
- Department of Infection and Immunity, Experimental & Molecular Immunology, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg,Department of Dermatology and Allergy Center, Odense Research Center for Anaphylaxis (ORCA), Odense University Hospital, University of Southern Denmark, Odense, Denmark,Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Mohammad Reza Ahmadian
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Verena Keitel
- Department of Gastroenterology, Hepatology, and Infectious Diseases, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Dagmar Wieczorek
- Institute of Human Genetics, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Dieter Häussinger
- Department of Gastroenterology, Hepatology, and Infectious Diseases, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Aleksandra A Pandyra
- Department of Molecular Medicine II, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany,Department of Gastroenterology, Hepatology, and Infectious Diseases, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Karl S Lang
- Institute of Immunology, Medical Faculty, University of Duisburg-Essen, Essen, Germany
| | - Philipp A Lang
- Department of Molecular Medicine II, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
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Chiu C, Loth S, Kuhlen M, Ginzel S, Schaper J, Rosenbaum T, Pietsch T, Borkhardt A, Hoell JI. Mutated SON putatively causes a cancer syndrome comprising high-risk medulloblastoma combined with café-au-lait spots. Fam Cancer 2019; 18:353-358. [PMID: 30680470 DOI: 10.1007/s10689-019-00121-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Medulloblastoma is the most frequent malignant brain tumor in childhood. This highly malignant neoplasm occurs usually before 10 years of age and more frequently in boys. The 5-year event-free survival rate for high-risk medulloblastoma is low at 62% despite a multimodal therapy including surgical resection, radiation therapy and chemotherapy. We report the case of a boy, who was born to consanguineous parents. Prominently, he had multiple café-au-lait spots. At the age of 3 years he was diagnosed with a high-risk metastatic medulloblastoma. The patient died only 11 months after diagnosis of a fulminant relapse presenting as meningeal and spinal dissemination. Whole-exome sequencing of germline DNA was employed to detect the underlying mutation for this putative cancer syndrome presenting with the combination of medulloblastoma and skin alterations. After screening all possible homozygous gene SNVs, we identified a mutation of SON, an essential protein in cell cycle regulation and cell proliferation, as the most likely genetic cause.
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Affiliation(s)
- Celine Chiu
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, University Children's Hospital, Heinrich-Heine University, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Stefanie Loth
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, University Children's Hospital, Heinrich-Heine University, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Michaela Kuhlen
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, University Children's Hospital, Heinrich-Heine University, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Sebastian Ginzel
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, University Children's Hospital, Heinrich-Heine University, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Jörg Schaper
- Department of Diagnostic and Interventional Radiology, Medical Faculty, University of Duesseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Thorsten Rosenbaum
- Department of Pediatrics, Sana Kliniken Duisburg, Zu den Rehwiesen 9, 47055, Duisburg, Germany
| | - Torsten Pietsch
- Institute of Neuropathology, DGNN Brain Tumor Reference Center, University of Bonn, DZNE German Center for Neurodegenerative Diseases, Sigmund-Freud-Str. 25, 53127, Bonn, Germany
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, University Children's Hospital, Heinrich-Heine University, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Jessica I Hoell
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, University Children's Hospital, Heinrich-Heine University, Moorenstr. 5, 40225, Düsseldorf, Germany.
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13
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Kloetgen A, Münch PC, Borkhardt A, Hoell JI, McHardy AC. Corrigendum to: Biochemical and bioinformatic methods for elucidating the role of RNA-protein interactions in posttranscriptional regulation. Brief Funct Genomics 2019; 18:433. [PMID: 31169895 PMCID: PMC6920523 DOI: 10.1093/bfgp/elz014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Affiliation(s)
| | | | | | | | - Alice C McHardy
- Corresponding author: Alice C. McHardy, Heinrich-Heine University, Department of Algorithmic Bioinformatics, Universitaetsstrasse
1, 40225 Duesseldorf, Germany. Tel.: +49-211-8110427; Fax: +49-211-8113464; E-mail:
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14
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Mukherjee N, Wessels HH, Lebedeva S, Sajek M, Ghanbari M, Garzia A, Munteanu A, Yusuf D, Farazi T, Hoell JI, Akat KM, Akalin A, Tuschl T, Ohler U. Deciphering human ribonucleoprotein regulatory networks. Nucleic Acids Res 2019; 47:570-581. [PMID: 30517751 PMCID: PMC6344852 DOI: 10.1093/nar/gky1185] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 11/26/2018] [Indexed: 01/04/2023] Open
Abstract
RNA-binding proteins (RBPs) control and coordinate each stage in the life cycle of RNAs. Although in vivo binding sites of RBPs can now be determined genome-wide, most studies typically focused on individual RBPs. Here, we examined a large compendium of 114 high-quality transcriptome-wide in vivo RBP-RNA cross-linking interaction datasets generated by the same protocol in the same cell line and representing 64 distinct RBPs. Comparative analysis of categories of target RNA binding preference, sequence preference, and transcript region specificity was performed, and identified potential posttranscriptional regulatory modules, i.e. specific combinations of RBPs that bind to specific sets of RNAs and targeted regions. These regulatory modules represented functionally related proteins and exhibited distinct differences in RNA metabolism, expression variance, as well as subcellular localization. This integrative investigation of experimental RBP-RNA interaction evidence and RBP regulatory function in a human cell line will be a valuable resource for understanding the complexity of post-transcriptional regulation.
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Affiliation(s)
- Neelanjan Mukherjee
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO 80045, USA.,Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Hans-Hermann Wessels
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.,Institute of Biology, Humboldt University, 10099 Berlin, Germany
| | - Svetlana Lebedeva
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Marcin Sajek
- lnstitute of Human Genetics, Polish Academy of Sciences, Poznan, Poland.,Howard Hughes Medical Institute and Laboratory for RNA Molecular Biology, The Rockefeller University, 1230 York Ave, Box 186, New York, NY 10065, USA
| | - Mahsa Ghanbari
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Aitor Garzia
- Howard Hughes Medical Institute and Laboratory for RNA Molecular Biology, The Rockefeller University, 1230 York Ave, Box 186, New York, NY 10065, USA
| | - Alina Munteanu
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.,Institute of Computer Science, Humboldt University, 10099 Berlin, Germany
| | - Dilmurat Yusuf
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Thalia Farazi
- Howard Hughes Medical Institute and Laboratory for RNA Molecular Biology, The Rockefeller University, 1230 York Ave, Box 186, New York, NY 10065, USA
| | - Jessica I Hoell
- Howard Hughes Medical Institute and Laboratory for RNA Molecular Biology, The Rockefeller University, 1230 York Ave, Box 186, New York, NY 10065, USA.,Department of Pediatric Oncology, Hematology and Clinical Immunology, Center for Child and Adolescent Health, Medical Faculty, Heinrich Heine University of Dusseldorf, Dusseldorf, Germany
| | - Kemal M Akat
- Howard Hughes Medical Institute and Laboratory for RNA Molecular Biology, The Rockefeller University, 1230 York Ave, Box 186, New York, NY 10065, USA
| | - Altuna Akalin
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Thomas Tuschl
- Howard Hughes Medical Institute and Laboratory for RNA Molecular Biology, The Rockefeller University, 1230 York Ave, Box 186, New York, NY 10065, USA
| | - Uwe Ohler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.,Institute of Biology, Humboldt University, 10099 Berlin, Germany.,Institute of Computer Science, Humboldt University, 10099 Berlin, Germany
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15
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Abstract
Over the past decades, striking progress has been made in the treatment of pediatric leukemia, approaching 90% overall survival in children with acute lymphoblastic leukemia (ALL) and 75% in children with acute myeloid leukemia (AML). This has mainly been achieved through multiagent chemotherapy including CNS prophylaxis and risk-adapted therapy within collaborative clinical trials. However, prognosis in children with refractory or relapsed leukemia remains poor and has not significantly improved despite great efforts. Hence, more effective and less toxic therapies are urgently needed. Our understanding of disease biology, molecular drivers, drug resistance and, thus, the possibility to identify children at high-risk for treatment failure has significantly improved in recent years. Moreover, several new drugs targeting key molecular pathways involved in leukemia development, cell growth, and proliferation have been developed and approved. These striking achievements are linked to the great hope to further improve survival in children with refractory and relapsed leukemia. This review gives an overview on current molecularly targeted therapies in children with leukemia, including kinase, and proteasome inhibitors, epigenetic and enzyme targeting, as well as apoptosis regulators among others.
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Affiliation(s)
- Michaela Kuhlen
- Swabian Children's Cancer Center, University Children's Hospital Augsburg, Augsburg, Germany
| | - Jan-Henning Klusmann
- Department of Pediatric Hematology and Oncology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Jessica I Hoell
- Department of Pediatric Hematology and Oncology, Martin Luther University Halle-Wittenberg, Halle, Germany
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16
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Duggimpudi S, Kloetgen A, Maney SK, Münch PC, Hezaveh K, Shaykhalishahi H, Hoyer W, McHardy AC, Lang PA, Borkhardt A, Hoell JI. Transcriptome-wide analysis uncovers the targets of the RNA-binding protein MSI2 and effects of MSI2's RNA-binding activity on IL-6 signaling. J Biol Chem 2018; 293:15359-15369. [PMID: 30126842 DOI: 10.1074/jbc.ra118.002243] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 07/23/2018] [Indexed: 12/14/2022] Open
Abstract
The RNA-binding protein Musashi 2 (MSI2) has emerged as an important regulator in cancer initiation, progression, and drug resistance. Translocations and deregulation of the MSI2 gene are diagnostic of certain cancers, including chronic myeloid leukemia (CML) with translocation t(7;17), acute myeloid leukemia (AML) with translocation t(10;17), and some cases of B-precursor acute lymphoblastic leukemia (pB-ALL). To better understand the function of MSI2 in leukemia, the mRNA targets that are bound and regulated by MSI2 and their MSI2-binding motifs need to be identified. To this end, using photoactivatable ribonucleoside cross-linking and immunoprecipitation (PAR-CLIP) and the multiple EM for motif elicitation (MEME) analysis tool, here we identified MSI2's mRNA targets and the consensus RNA-recognition element (RRE) motif recognized by MSI2 (UUAG). Of note, MSI2 knockdown altered the expression of several genes with roles in eukaryotic initiation factor 2 (eIF2), hepatocyte growth factor (HGF), and epidermal growth factor (EGF) signaling pathways. We also show that MSI2 regulates classic interleukin-6 (IL-6) signaling by promoting the degradation of the mRNA of IL-6 signal transducer (IL6ST or GP130), which, in turn, affected the phosphorylation statuses of signal transducer and activator of transcription 3 (STAT3) and the mitogen-activated protein kinase ERK. In summary, we have identified multiple MSI2-regulated mRNAs and provided evidence that MSI2 controls IL6ST activity that control oncogenic signaling networks. Our findings may help inform strategies for unraveling the role of MSI2 in leukemia to pave the way for the development of targeted therapies.
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Affiliation(s)
- Sujitha Duggimpudi
- From the Department of Pediatric Oncology, Hematology and Clinical Immunology, Center for Child and Adolescent Health, Medical Faculty, Heinrich Heine University, Moorenstrasse 5, 40225 Düsseldorf, Germany
| | - Andreas Kloetgen
- From the Department of Pediatric Oncology, Hematology and Clinical Immunology, Center for Child and Adolescent Health, Medical Faculty, Heinrich Heine University, Moorenstrasse 5, 40225 Düsseldorf, Germany.,Department of Algorithmic Bioinformatics, Heinrich Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany.,Computational Biology of Infection Research, Helmholtz Center for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany, and
| | - Sathish Kumar Maney
- Department of Molecular Medicine II, Heinrich Heine University, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Philipp C Münch
- Department of Algorithmic Bioinformatics, Heinrich Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany.,Computational Biology of Infection Research, Helmholtz Center for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany, and
| | - Kebria Hezaveh
- From the Department of Pediatric Oncology, Hematology and Clinical Immunology, Center for Child and Adolescent Health, Medical Faculty, Heinrich Heine University, Moorenstrasse 5, 40225 Düsseldorf, Germany
| | - Hamed Shaykhalishahi
- Institute of Physical Biology, Heinrich Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Wolfgang Hoyer
- Institute of Physical Biology, Heinrich Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Alice C McHardy
- Department of Algorithmic Bioinformatics, Heinrich Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany.,Computational Biology of Infection Research, Helmholtz Center for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany, and
| | - Philipp A Lang
- Department of Molecular Medicine II, Heinrich Heine University, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Arndt Borkhardt
- From the Department of Pediatric Oncology, Hematology and Clinical Immunology, Center for Child and Adolescent Health, Medical Faculty, Heinrich Heine University, Moorenstrasse 5, 40225 Düsseldorf, Germany
| | - Jessica I Hoell
- From the Department of Pediatric Oncology, Hematology and Clinical Immunology, Center for Child and Adolescent Health, Medical Faculty, Heinrich Heine University, Moorenstrasse 5, 40225 Düsseldorf, Germany,
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17
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Ingenhag D, Reister S, Auer F, Bhatia S, Wildenhain S, Picard D, Remke M, Hoell JI, Kloetgen A, Sohn D, Jänicke RU, Koegler G, Borkhardt A, Hauer J. The homeobox transcription factor HB9 induces senescence and blocks differentiation in hematopoietic stem and progenitor cells. Haematologica 2018; 104:35-46. [PMID: 30093397 PMCID: PMC6312034 DOI: 10.3324/haematol.2018.189407] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 07/30/2018] [Indexed: 01/09/2023] Open
Abstract
The homeobox gene HLXB9 encodes for the transcription factor HB9, which is essential for pancreatic as well as motor neuronal development. Beside its physiological expression pattern, aberrant HB9 expression has been observed in several neoplasias. Especially in infant translocation t(7;12) acute myeloid leukemia, aberrant HB9 expression is the only known molecular hallmark and is assumed to be a key factor in leukemic transformation. However, so far, only poor functional data exist addressing the oncogenic potential of HB9 or its influence on hematopoiesis. We investigated the influence of HB9 on cell proliferation and cell cycle in vitro, as well as on hematopoietic stem cell differentiation in vivo using murine and human model systems. In vitro, HB9 expression led to premature senescence in human HT1080 and murine NIH3T3 cells, providing for the first time evidence for an oncogenic potential of HB9. Onset of senescence was characterized by induction of the p53–p21 tumor suppressor network, resulting in growth arrest, accompanied by morphological transformation and expression of senescence-associated β-galactosidase. In vivo, HB9-transduced primary murine hematopoietic stem and progenitor cells underwent a profound differentiation arrest and accumulated at the megakaryocyte/erythrocyte progenitor stage. In line, gene expression analyses revealed de novo expression of erythropoiesis-related genes in human CD34+hematopoietic stem and progenitor cells upon HB9 expression. In summary, the novel findings of HB9-dependent premature senescence and myeloid-biased perturbed hematopoietic differentiation, for the first time shed light on the oncogenic properties of HB9 in translocation t(7;12) acute myeloid leukemia.
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Affiliation(s)
- Deborah Ingenhag
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty of Heinrich-Heine-University, Düsseldorf
| | - Sven Reister
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty of Heinrich-Heine-University, Düsseldorf
| | - Franziska Auer
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty of Heinrich-Heine-University, Düsseldorf
| | - Sanil Bhatia
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty of Heinrich-Heine-University, Düsseldorf
| | - Sarah Wildenhain
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty of Heinrich-Heine-University, Düsseldorf
| | - Daniel Picard
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty of Heinrich-Heine-University, Düsseldorf.,Department of Pediatric Neuro-Oncogenomics, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg
| | - Marc Remke
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty of Heinrich-Heine-University, Düsseldorf.,Department of Pediatric Neuro-Oncogenomics, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg
| | - Jessica I Hoell
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty of Heinrich-Heine-University, Düsseldorf
| | - Andreas Kloetgen
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty of Heinrich-Heine-University, Düsseldorf.,Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig
| | - Dennis Sohn
- Laboratory of Molecular Radiooncology, Clinic and Policlinic for Radiation Therapy and Radiooncology, Medical Faculty of Heinrich-Heine-University, Düsseldorf
| | - Reiner U Jänicke
- Laboratory of Molecular Radiooncology, Clinic and Policlinic for Radiation Therapy and Radiooncology, Medical Faculty of Heinrich-Heine-University, Düsseldorf
| | - Gesine Koegler
- Institute for Transplantation Diagnostics and Cell Therapeutics, Medical Faculty of Heinrich-Heine-University, Düsseldorf, Germany
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty of Heinrich-Heine-University, Düsseldorf
| | - Julia Hauer
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty of Heinrich-Heine-University, Düsseldorf
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18
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Hoell JI, Warfsmann J, Distelmaier F, Borkhardt A, Janßen G, Kuhlen M. Challenges of palliative care in children with inborn metabolic diseases. Orphanet J Rare Dis 2018; 13:112. [PMID: 29986738 PMCID: PMC6038293 DOI: 10.1186/s13023-018-0868-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 07/03/2018] [Indexed: 11/10/2022] Open
Abstract
Background Our objective was to evaluate children with metabolic diseases in paediatric palliative home care (PPC) and the process of decision-making. This study was conducted as single-centre retrospective cohort study of patients in the care of a large specialized PPC team. Results Between 01/2013 and 09/2016, 198 children, adolescents and young adults were in the care of our PPC team. Twenty-nine (14.6%) of these patients had metabolic conditions. Median age at referral was 2.6 years (0–24), median duration of care 352 days (3–2248) and median number of home visits 13 (1–80). Most patients are still alive (16; 55.2%). Median number of drugs administered was 5 (range 0–12), antiepileptics were given most frequently. Symptom burden was high in all children with metabolic disorders at referral and remained high throughout care. Predominant symptoms were gastrointestinal, respiratory and neurologic symptoms. Children with metabolic conditions, who were referred to PPC younger than 1 year of age had a shorter period of care and died earlier compared to those children, who were referred to PPC later in their lives (older than 10 years of age). Eleven (37.9%) of the children initially had no resuscitation restrictions and 7 (53.8%) of those who died, did so on ICU. Conclusions About 15% of children with life-limiting conditions in PPC present with metabolic diseases. Symptom burden is high with neurologic, respiratory and gastrointestinal symptoms being the most frequent and most of those being difficult to treat. In these children, particular attention needs to be addressed to advance care planning. Electronic supplementary material The online version of this article (10.1186/s13023-018-0868-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jessica I Hoell
- Medical Faculty, Department of Paediatric Oncology, Haematology and Clinical Immunology, Centre for Child and Adolescent Health, University of Duesseldorf, Moorenstr. 5, 40225, Duesseldorf, Germany
| | - Jens Warfsmann
- Medical Faculty, Department of Paediatric Oncology, Haematology and Clinical Immunology, Centre for Child and Adolescent Health, University of Duesseldorf, Moorenstr. 5, 40225, Duesseldorf, Germany
| | - Felix Distelmaier
- Medical Faculty, Department of General Paediatrics, Neonatology and Paediatric Cardiology, Centre for Child and Adolescent Health, University of Duesseldorf, Moorenstr. 5, 40225 Duesseldorf, Germany
| | - Arndt Borkhardt
- Medical Faculty, Department of Paediatric Oncology, Haematology and Clinical Immunology, Centre for Child and Adolescent Health, University of Duesseldorf, Moorenstr. 5, 40225, Duesseldorf, Germany
| | - Gisela Janßen
- Medical Faculty, Department of Paediatric Oncology, Haematology and Clinical Immunology, Centre for Child and Adolescent Health, University of Duesseldorf, Moorenstr. 5, 40225, Duesseldorf, Germany
| | - Michaela Kuhlen
- Medical Faculty, Department of Paediatric Oncology, Haematology and Clinical Immunology, Centre for Child and Adolescent Health, University of Duesseldorf, Moorenstr. 5, 40225, Duesseldorf, Germany.
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19
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Hoell JI, Weber HL, Balzer S, Danneberg M, Gagnon G, Trocan L, Borkhardt A, Janßen G, Kuhlen M. Advance care planning and outcome in pediatric palliative home care. Oncotarget 2018; 9:17867-17875. [PMID: 29707152 PMCID: PMC5915160 DOI: 10.18632/oncotarget.24929] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 03/08/2018] [Indexed: 11/25/2022] Open
Abstract
Pediatric advance care planning seeks to ensure end-of-life care conforming to the patients/their families' preferences. To expand our knowledge of advance care planning and "medical orders for life-sustaining treatment" (MOLST) in pediatric palliative home care, we determined the number of patients with MOLST, compared MOLST between the four "Together for Short Lives" (TfSL) groups and analyzed, whether there was a relationship between the content of the MOLST and the patients' places of death. The study was conducted as a single-center retrospective analysis of all patients of a large specialized pediatric palliative home care team (01/2013-09/2016). MOLST were available in 179/198 children (90.4%). Most parents decided fast on MOLST, 99 (55.3%) at initiation of pediatric palliative home care, 150 (83.4%) within the first 100 days. MOLST were only changed in 7.8%. Eighty/179 (44.7%) patients decided on a Do Not Attempt Cardio-Pulmonary Resuscitation (DNACPR) order, 58 (32.4%) on treatment limitations of some kind and 41 (22.9%) wished for the entire spectrum of life-sustaining measures (Full Code). Most TfSL group 1 families wanted DNACPR and most TfSL group 3/4 parents Full Code. The majority (84.9%) of all DNACPR patients died at home/hospice. Conversely, all Full Code patients died in hospital (80% in an intensive care setting). The circumstances of the childrens' deaths can therefore be predicted considering the content of the MOLST. Regular advance care planning discussions are thus a very important aspect of pediatric palliative home care.
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Affiliation(s)
- Jessica I. Hoell
- University of Duesseldorf, Medical Faculty, Department of Pediatric Oncology, Hematology and Clinical Immunology, Center for Child and Adolescent Health, Duesseldorf, Germany
| | - Hannah L. Weber
- University of Duesseldorf, Medical Faculty, Department of Pediatric Oncology, Hematology and Clinical Immunology, Center for Child and Adolescent Health, Duesseldorf, Germany
| | - Stefan Balzer
- University of Duesseldorf, Medical Faculty, Department of Pediatric Oncology, Hematology and Clinical Immunology, Center for Child and Adolescent Health, Duesseldorf, Germany
| | - Mareike Danneberg
- University of Duesseldorf, Medical Faculty, Department of Pediatric Oncology, Hematology and Clinical Immunology, Center for Child and Adolescent Health, Duesseldorf, Germany
| | - Gabriele Gagnon
- University of Duesseldorf, Medical Faculty, Department of Pediatric Oncology, Hematology and Clinical Immunology, Center for Child and Adolescent Health, Duesseldorf, Germany
| | - Laura Trocan
- University of Duesseldorf, Medical Faculty, Department of Pediatric Oncology, Hematology and Clinical Immunology, Center for Child and Adolescent Health, Duesseldorf, Germany
| | - Arndt Borkhardt
- University of Duesseldorf, Medical Faculty, Department of Pediatric Oncology, Hematology and Clinical Immunology, Center for Child and Adolescent Health, Duesseldorf, Germany
| | - Gisela Janßen
- University of Duesseldorf, Medical Faculty, Department of Pediatric Oncology, Hematology and Clinical Immunology, Center for Child and Adolescent Health, Duesseldorf, Germany
| | - Michaela Kuhlen
- University of Duesseldorf, Medical Faculty, Department of Pediatric Oncology, Hematology and Clinical Immunology, Center for Child and Adolescent Health, Duesseldorf, Germany
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20
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Taeubner J, Wimmer K, Muleris M, Lascols O, Colas C, Fauth C, Brozou T, Felsberg J, Riemer J, Gombert M, Ginzel S, Hoell JI, Borkhardt A, Kuhlen M. Diagnostic challenges in a child with early onset desmoplastic medulloblastoma and homozygous variants in MSH2 and MSH6. Eur J Hum Genet 2018; 26:440-444. [PMID: 29302048 DOI: 10.1038/s41431-017-0071-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 10/29/2017] [Accepted: 11/23/2017] [Indexed: 12/23/2022] Open
Abstract
Constitutional mismatch repair deficiency (CMMRD) is an autosomal recessively inherited childhood cancer susceptibility syndrome caused by biallelic germline mutations in one of the mismatch repair (MMR) genes. The spectrum of CMMRD-associated tumours is very broad and many CMMRD patients additionally display signposting non-neoplastic features, most frequently café-au-lait macules and other pigmentation alterations. We report on a 13-month-old girl suspected of having CMMRD due to a desmoplastic medulloblastoma and a striking skin pigmentation that included multiple café-au-lait macules, hypopigmented areas and Mongolian spots. Whole-exome sequencing revealed homozygosity for MSH2 variant p.(Leu92Val) and MSH6 variant p.(Val809del), both variants of uncertain significance (VUS). Immunohistochemical analysis of the tumour tissue showed expression of all four MMR proteins and gMSI testing was negative. However, functional assays demonstrated that the cells of the patient displayed methylation tolerance and ex vivo microsatellite instability, which unequivocally confirmed the diagnosis of CMMRD. Taken together, the results render the MSH2 variant unlikely to be responsible for the phenotype, while they are compatible with MSH6-associated CMMRD. This case illustrates the diagnostic strategy of confirming CMMRD syndrome in patients with VUS.
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Affiliation(s)
- Julia Taeubner
- Department of Paediatric Oncology, Haematology and Clinical Immunology, University Children´s Hospital, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany
| | - Katharina Wimmer
- Division of Human Genetics, Medical University Innsbruck, Innsbruck, Austria
| | - Martine Muleris
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Centre de Recherche Saint-Antoine (CRSA), F75012, Paris, France
| | - Olivier Lascols
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Centre de Recherche Saint-Antoine (CRSA), F75012, Paris, France.,Department of molecular biology and genetics, AP-HP, Saint-Antoine Hospital, Paris, France
| | - Chrystelle Colas
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Centre de Recherche Saint-Antoine (CRSA), F75012, Paris, France.,Department of genetics, AP-HP, Pitié Salpétrière Hospital, Paris, France
| | - Christine Fauth
- Division of Human Genetics, Medical University Innsbruck, Innsbruck, Austria
| | - Triantafyllia Brozou
- Department of Paediatric Oncology, Haematology and Clinical Immunology, University Children´s Hospital, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany
| | - Joerg Felsberg
- Department of Neuropathology, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany
| | - Jasmin Riemer
- Institute of Pathology, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany
| | - Michael Gombert
- Department of Paediatric Oncology, Haematology and Clinical Immunology, University Children´s Hospital, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany
| | - Sebastian Ginzel
- Department of Paediatric Oncology, Haematology and Clinical Immunology, University Children´s Hospital, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany
| | - Jessica I Hoell
- Department of Paediatric Oncology, Haematology and Clinical Immunology, University Children´s Hospital, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany
| | - Arndt Borkhardt
- Department of Paediatric Oncology, Haematology and Clinical Immunology, University Children´s Hospital, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany
| | - Michaela Kuhlen
- Department of Paediatric Oncology, Haematology and Clinical Immunology, University Children´s Hospital, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany.
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21
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Kuhlen M, Willasch AM, Dalle JH, Wachowiak J, Yaniv I, Ifversen M, Sedlacek P, Guengoer T, Lang P, Bader P, Sufliarska S, Balduzzi A, Strahm B, von Luettichau I, Hoell JI, Borkhardt A, Klingebiel T, Schrappe M, von Stackelberg A, Glogova E, Poetschger U, Meisel R, Peters C. Outcome of relapse after allogeneic HSCT in children with ALL enrolled in the ALL-SCT 2003/2007 trial. Br J Haematol 2017; 180:82-89. [DOI: 10.1111/bjh.14965] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 08/14/2017] [Indexed: 02/01/2023]
Affiliation(s)
- Michaela Kuhlen
- Department of Paediatric Oncology, Haematology and Clinical Immunology; Medical Faculty; University Children's Hospital; Heinrich Heine University; Duesseldorf Germany
| | - Andre M. Willasch
- Department for Children and Adolescents; Division for Stem Cell Transplantation and Immunology; University Hospital Frankfurt; Goethe University; Frankfurt Germany
| | - Jean-Hugues Dalle
- Paediatric Haematology Department; Robert Debré Hospital and Paris Diderot University; Paris France
| | | | - Isaac Yaniv
- Ezer Mizion Bone Marrow Donor Registry; Petach Tikva Israel
- Bone Marrow Transplant Unit; Schneider Children's Medical Centre of Israel; Petach Tikva Israel
| | - Marianne Ifversen
- Department for Children and Adolescents; Rigahospitalet; Copenhagen University Hospital; Copenhagen Denmark
| | - Petr Sedlacek
- Department of Paediatric Haematology and Oncology; Teaching Hospital Motol; Prague Czech Republic
| | - Tayfun Guengoer
- Division of Stem Cell Transplantation; University Children's Hospital Zürich; Zürich Switzerland
| | - Peter Lang
- University Hospital Tuebingen; Tuebingen Germany
| | - Peter Bader
- Department for Children and Adolescents; Division for Stem Cell Transplantation and Immunology; University Hospital Frankfurt; Goethe University; Frankfurt Germany
| | - Sabina Sufliarska
- Department of Paediatric Haematology and Oncology; Haematopoietic Stem Cell Transplantation Unit; Comenius University Children's Hospital Bratislava; Bratislava Slovakia
| | - Adriana Balduzzi
- Clinica Pediatrica Università degli Studi di Milano Bicocca; Ospedale San Gerardo; Monza Italy
| | - Brigitte Strahm
- Department of Paediatrics and Adolescent Medicine; Division of Paediatric Haematology and Oncology; Medical Centre; Faculty of Medicine; University of Freiburg; Freiburg Germany
| | - Irene von Luettichau
- Department of Paediatrics; Klinikum rechts der Isar; Technische Universität München; Munich Germany
- Comprehensive Cancer Centre Munich (CCCM); Munich Germany
| | - Jessica I. Hoell
- Department of Paediatric Oncology, Haematology and Clinical Immunology; Medical Faculty; University Children's Hospital; Heinrich Heine University; Duesseldorf Germany
| | - Arndt Borkhardt
- Department of Paediatric Oncology, Haematology and Clinical Immunology; Medical Faculty; University Children's Hospital; Heinrich Heine University; Duesseldorf Germany
| | - Thomas Klingebiel
- Department for Children and Adolescents; Division for Stem Cell Transplantation and Immunology; University Hospital Frankfurt; Goethe University; Frankfurt Germany
| | - Martin Schrappe
- Department of Paediatrics; University Medical Centre Schleswig-Holstein; Kiel Germany
| | - Arend von Stackelberg
- Department of Paediatric Oncology/Haematology; Charité Universitätsmedizin Berlin; Charité Campus Virchow; Berlin Germany
| | | | | | - Roland Meisel
- Department of Paediatric Oncology, Haematology and Clinical Immunology; Medical Faculty; University Children's Hospital; Heinrich Heine University; Duesseldorf Germany
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Hoell JI, Warfsmann J, Gagnon G, Trocan L, Balzer S, Oommen PT, Borkhardt A, Janßen G, Kuhlen M. Palliative care for children with a yet undiagnosed syndrome. Eur J Pediatr 2017; 176:1319-1327. [PMID: 28808789 DOI: 10.1007/s00431-017-2991-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 08/03/2017] [Accepted: 08/04/2017] [Indexed: 10/19/2022]
Abstract
UNLABELLED The number of children without a diagnosis in pediatric palliative home care and the process of decision-making in these children are widely unknown. The study was conducted as single-center retrospective cohort study. Between January 2013 and September 2016, 198 children and young adults were cared for; 27 (13.6%) of these were without a clear diagnosis at the start of pediatric palliative home care. A definite diagnosis was ultimately achieved in three children. Median age was 7 years (0-25), duration of care 569 days (2-2638), and number of home visits 7.5 (2-46). Most patients are still alive (19; 70.4%). Median number of drugs administered was eight (range 2-19); antiepileptics were given most frequently. Despite the lack of a clear diagnosis (and thus prognosis), 13 (48.1%) parents faced with their critically ill and clinically deteriorating children decided in favor of a DNAR order. Comparing this with 15 brain-injured children, signs, symptoms, and supportive needs were similar in both groups. CONCLUSION Children without a clear diagnosis are relatively common in pediatric palliative care and have-like all other patients-the right to receive optimized and symptom-adapted palliative care. Parents are less likely to choose treatment limitation for children who lack a definitive diagnosis. What is Known: • A clear diagnosis is usually considered important for best-practice pediatric palliative care (PPC) including advanced care planning (ACP). • Timely initiation of pediatric palliative care (PPC) is highly recommended in children with life-limiting conditions. What is New: • SWAN (syndrome without a name) children show similar signs and symptoms (mostly neurological) and have similar supportive needs as brain-injured children. • Defining treatment limitations in advance care planning is more difficult for parents of SWAN compared to brain-injured children.
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Affiliation(s)
- Jessica I Hoell
- Medical Faculty, Department of Paediatric Oncology, Haematology and Clinical Immunology, Centre for Child and Adolescent Health, University of Duesseldorf, Moorenstr. 5, 40225, Duesseldorf, Germany
| | - Jens Warfsmann
- Medical Faculty, Department of Paediatric Oncology, Haematology and Clinical Immunology, Centre for Child and Adolescent Health, University of Duesseldorf, Moorenstr. 5, 40225, Duesseldorf, Germany
| | - Gabriele Gagnon
- Medical Faculty, Department of Paediatric Oncology, Haematology and Clinical Immunology, Centre for Child and Adolescent Health, University of Duesseldorf, Moorenstr. 5, 40225, Duesseldorf, Germany
| | - Laura Trocan
- Medical Faculty, Department of Paediatric Oncology, Haematology and Clinical Immunology, Centre for Child and Adolescent Health, University of Duesseldorf, Moorenstr. 5, 40225, Duesseldorf, Germany
| | - Stefan Balzer
- Medical Faculty, Department of Paediatric Oncology, Haematology and Clinical Immunology, Centre for Child and Adolescent Health, University of Duesseldorf, Moorenstr. 5, 40225, Duesseldorf, Germany
| | - Prasad T Oommen
- Medical Faculty, Department of Paediatric Oncology, Haematology and Clinical Immunology, Centre for Child and Adolescent Health, University of Duesseldorf, Moorenstr. 5, 40225, Duesseldorf, Germany
| | - Arndt Borkhardt
- Medical Faculty, Department of Paediatric Oncology, Haematology and Clinical Immunology, Centre for Child and Adolescent Health, University of Duesseldorf, Moorenstr. 5, 40225, Duesseldorf, Germany
| | - Gisela Janßen
- Medical Faculty, Department of Paediatric Oncology, Haematology and Clinical Immunology, Centre for Child and Adolescent Health, University of Duesseldorf, Moorenstr. 5, 40225, Duesseldorf, Germany
| | - Michaela Kuhlen
- Medical Faculty, Department of Paediatric Oncology, Haematology and Clinical Immunology, Centre for Child and Adolescent Health, University of Duesseldorf, Moorenstr. 5, 40225, Duesseldorf, Germany.
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Kuhlen M, Hoell JI, Gagnon G, Balzer S, Oommen PT, Borkhardt A, Janßen G. Effective treatment of spasticity using dronabinol in pediatric palliative care. Eur J Paediatr Neurol 2016; 20:898-903. [PMID: 27506815 DOI: 10.1016/j.ejpn.2016.07.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 06/15/2016] [Accepted: 07/22/2016] [Indexed: 02/07/2023]
Abstract
BACKGROUND Cannabis extracts have a wide therapeutic potential but in many countries they have not been approved for treatment in children so far. OBJECTIVE We conducted an open, uncontrolled, retrospective study on the administration of dronabinol to determine the value, efficacy, and safety of cannabis-based medicines in the treatment of refractory spasticity in pediatric palliative care. DESIGN AND PARTICIPANTS Sixteen children, adolescents and young adults having complex neurological conditions with spasticity (aged 1.3-26.6 years, median 12.7 years) were treated with dronabinol by our specialized pediatric palliative care team between 01.12.2010 and 30.04.2015 in a home-care setting. Therapeutic efficacy and side effects were closely monitored. RESULTS Drops of the 2.5% oily tetrahydrocannabinol solution (dronabinol) were administered. A promising therapeutic effect was seen, mostly due to abolishment or marked improvement of severe, treatment resistant spasticity (n = 12). In two cases the effect could not be determined, two patients did not benefit. The median duration of treatment was 181 days (range 23-1429 days). Dosages to obtain a therapeutic effect varied from 0.08 to 1.0 mg/kg/d with a median of 0.33 mg/kg/d in patients with a documented therapeutic effect. When administered as an escalating dosage scheme, side effects were rare and only consisted in vomiting and restlessness (one patient each). No serious and enduring side effects occurred even in young children and/or over a longer period of time. CONCLUSIONS In the majority of pediatric palliative patients the treatment with dronabinol showed promising effects in treatment resistant spasticity.
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Affiliation(s)
- Michaela Kuhlen
- University of Dusseldorf, Medical Faculty, Department of Pediatric Oncology, Hematology and Clinical Immunology, Center for Child and Adolescent Health, Moorenstr. 5, 40225 Dusseldorf, Germany.
| | - Jessica I Hoell
- University of Dusseldorf, Medical Faculty, Department of Pediatric Oncology, Hematology and Clinical Immunology, Center for Child and Adolescent Health, Moorenstr. 5, 40225 Dusseldorf, Germany
| | - Gabriele Gagnon
- University of Dusseldorf, Medical Faculty, Department of Pediatric Oncology, Hematology and Clinical Immunology, Center for Child and Adolescent Health, Moorenstr. 5, 40225 Dusseldorf, Germany
| | - Stefan Balzer
- University of Dusseldorf, Medical Faculty, Department of Pediatric Oncology, Hematology and Clinical Immunology, Center for Child and Adolescent Health, Moorenstr. 5, 40225 Dusseldorf, Germany
| | - Prasad T Oommen
- University of Dusseldorf, Medical Faculty, Department of Pediatric Oncology, Hematology and Clinical Immunology, Center for Child and Adolescent Health, Moorenstr. 5, 40225 Dusseldorf, Germany
| | - Arndt Borkhardt
- University of Dusseldorf, Medical Faculty, Department of Pediatric Oncology, Hematology and Clinical Immunology, Center for Child and Adolescent Health, Moorenstr. 5, 40225 Dusseldorf, Germany
| | - Gisela Janßen
- University of Dusseldorf, Medical Faculty, Department of Pediatric Oncology, Hematology and Clinical Immunology, Center for Child and Adolescent Health, Moorenstr. 5, 40225 Dusseldorf, Germany
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24
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Kloetgen A, Borkhardt A, Hoell JI, McHardy AC. The PARA-suite: PAR-CLIP specific sequence read simulation and processing. PeerJ 2016; 4:e2619. [PMID: 27812418 PMCID: PMC5088580 DOI: 10.7717/peerj.2619] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 09/27/2016] [Indexed: 01/13/2023] Open
Abstract
Background Next-generation sequencing technologies have profoundly impacted biology over recent years. Experimental protocols, such as photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation (PAR-CLIP), which identifies protein–RNA interactions on a genome-wide scale, commonly employ deep sequencing. With PAR-CLIP, the incorporation of photoactivatable nucleosides into nascent transcripts leads to high rates of specific nucleotide conversions during reverse transcription. So far, the specific properties of PAR-CLIP-derived sequencing reads have not been assessed in depth. Methods We here compared PAR-CLIP sequencing reads to regular transcriptome sequencing reads (RNA-Seq) to identify distinctive properties that are relevant for reference-based read alignment of PAR-CLIP datasets. We developed a set of freely available tools for PAR-CLIP data analysis, called the PAR-CLIP analyzer suite (PARA-suite). The PARA-suite includes error model inference, PAR-CLIP read simulation based on PAR-CLIP specific properties, a full read alignment pipeline with a modified Burrows–Wheeler Aligner algorithm and CLIP read clustering for binding site detection. Results We show that differences in the error profiles of PAR-CLIP reads relative to regular transcriptome sequencing reads (RNA-Seq) make a distinct processing advantageous. We examine the alignment accuracy of commonly applied read aligners on 10 simulated PAR-CLIP datasets using different parameter settings and identified the most accurate setup among those read aligners. We demonstrate the performance of the PARA-suite in conjunction with different binding site detection algorithms on several real PAR-CLIP and HITS-CLIP datasets. Our processing pipeline allowed the improvement of both alignment and binding site detection accuracy. Availability The PARA-suite toolkit and the PARA-suite aligner are available at https://github.com/akloetgen/PARA-suite and https://github.com/akloetgen/PARA-suite_aligner, respectively, under the GNU GPLv3 license.
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Affiliation(s)
- Andreas Kloetgen
- Department for Algorithmic Bioinformatics, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany; Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany; Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine Universität Düsseldorf , Düsseldorf , Germany
| | - Jessica I Hoell
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine Universität Düsseldorf , Düsseldorf , Germany
| | - Alice C McHardy
- Department for Algorithmic Bioinformatics, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany; Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany
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25
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Doerrenberg M, Kloetgen A, Hezaveh K, Wössmann W, Bleckmann K, Stanulla M, Schrappe M, McHardy AC, Borkhardt A, Hoell JI. T-cell acute lymphoblastic leukemia in infants has distinct genetic and epigenetic features compared to childhood cases. Genes Chromosomes Cancer 2016; 56:159-167. [DOI: 10.1002/gcc.22423] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 09/21/2016] [Accepted: 09/22/2016] [Indexed: 12/19/2022] Open
Affiliation(s)
- Mareike Doerrenberg
- Department of Pediatric Oncology, Hematology and Clinical Immunology; Heinrich-Heine-University, Medical Faculty; Düsseldorf Germany
| | - Andreas Kloetgen
- Department of Pediatric Oncology, Hematology and Clinical Immunology; Heinrich-Heine-University, Medical Faculty; Düsseldorf Germany
- Computational Biology of Infection Research, Helmholtz Center for Infection Research; Braunschweig Germany
| | - Kebria Hezaveh
- Department of Pediatric Oncology, Hematology and Clinical Immunology; Heinrich-Heine-University, Medical Faculty; Düsseldorf Germany
| | - Wilhelm Wössmann
- Department of Pediatric Hematology and Oncology; University Hospital Gießen and Marburg; Gießen Germany
| | - Kirsten Bleckmann
- ALL BFM Trial Center; University Hospital Schleswig-Holstein; Kiel Germany
| | - Martin Stanulla
- Pediatric Hematology and Oncology; Hannover Medical School; Hannover Germany
| | - Martin Schrappe
- Department of Pediatrics; University Medical Center Schleswig-Holstein; Kiel Germany
| | - Alice C McHardy
- Computational Biology of Infection Research, Helmholtz Center for Infection Research; Braunschweig Germany
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology; Heinrich-Heine-University, Medical Faculty; Düsseldorf Germany
| | - Jessica I Hoell
- Department of Pediatric Oncology, Hematology and Clinical Immunology; Heinrich-Heine-University, Medical Faculty; Düsseldorf Germany
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26
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Hezaveh K, Kloetgen A, Bernhart SH, Mahapatra KD, Lenze D, Richter J, Haake A, Bergmann AK, Brors B, Burkhardt B, Claviez A, Drexler HG, Eils R, Haas S, Hoffmann S, Karsch D, Klapper W, Kleinheinz K, Korbel J, Kretzmer H, Kreuz M, Küppers R, Lawerenz C, Leich E, Loeffler M, Mantovani-Loeffler L, López C, McHardy AC, Möller P, Rohde M, Rosenstiel P, Rosenwald A, Schilhabel M, Schlesner M, Scholz I, Stadler PF, Stilgenbauer S, Sungalee S, Szczepanowski M, Trümper L, Weniger MA, Siebert R, Borkhardt A, Hummel M, Hoell JI. Alterations of microRNA and microRNA-regulated messenger RNA expression in germinal center B-cell lymphomas determined by integrative sequencing analysis. Haematologica 2016; 101:1380-1389. [PMID: 27390358 DOI: 10.3324/haematol.2016.143891] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 07/01/2016] [Indexed: 12/22/2022] Open
Abstract
MicroRNA are well-established players in post-transcriptional gene regulation. However, information on the effects of microRNA deregulation mainly relies on bioinformatic prediction of potential targets, whereas proof of the direct physical microRNA/target messenger RNA interaction is mostly lacking. Within the International Cancer Genome Consortium Project "Determining Molecular Mechanisms in Malignant Lymphoma by Sequencing", we performed miRnome sequencing from 16 Burkitt lymphomas, 19 diffuse large B-cell lymphomas, and 21 follicular lymphomas. Twenty-two miRNA separated Burkitt lymphomas from diffuse large B-cell lymphomas/follicular lymphomas, of which 13 have shown regulation by MYC. Moreover, we found expression of three hitherto unreported microRNA. Additionally, we detected recurrent mutations of hsa-miR-142 in diffuse large B-cell lymphomas and follicular lymphomas, and editing of the hsa-miR-376 cluster, providing evidence for microRNA editing in lymphomagenesis. To interrogate the direct physical interactions of microRNA with messenger RNA, we performed Argonaute-2 photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation experiments. MicroRNA directly targeted 208 messsenger RNA in the Burkitt lymphomas and 328 messenger RNA in the non-Burkitt lymphoma models. This integrative analysis discovered several regulatory pathways of relevance in lymphomagenesis including Ras, PI3K-Akt and MAPK signaling pathways, also recurrently deregulated in lymphomas by mutations. Our dataset reveals that messenger RNA deregulation through microRNA is a highly relevant mechanism in lymphomagenesis.
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Affiliation(s)
- Kebria Hezaveh
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine-University, Medical Faculty, Düsseldorf, Germany
| | - Andreas Kloetgen
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine-University, Medical Faculty, Düsseldorf, Germany.,Department of Algorithmic Bioinformatics, Heinrich-Heine University, Duesseldorf, Germany
| | - Stephan H Bernhart
- Transcriptome Bioinformatics Group, LIFE Research Center for Civilization Diseases, University of Leipzig, Germany.,Bioinformatics Group, Department of Computer Science, University of Leipzig, Germany.,Interdisciplinary Center for Bioinformatics, University of Leipzig, Germany
| | - Kunal Das Mahapatra
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine-University, Medical Faculty, Düsseldorf, Germany
| | - Dido Lenze
- Institute of Pathology, Charité - University Medicine Berlin, Germany
| | - Julia Richter
- Institute of Human Genetics, University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel, Germany
| | - Andrea Haake
- Institute of Human Genetics, University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel, Germany
| | - Anke K Bergmann
- Institute of Human Genetics, University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel, Germany
| | - Benedikt Brors
- Division Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Birgit Burkhardt
- Department of Pediatric Hematology and Oncology, University Hospital Münster, Germany
| | - Alexander Claviez
- Department of Pediatrics, University Hospital Schleswig-Holstein, Campus Kiel, Germany
| | - Hans G Drexler
- Department of Human and Animal Cell Cultures, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Roland Eils
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology and Bioquant, Heidelberg University, Germany
| | - Siegfried Haas
- Friedrich-Ebert Hospital Neumünster, Clinics for Hematology, Oncology and Nephrology, Neumünster, Germany
| | - Steve Hoffmann
- Transcriptome Bioinformatics Group, LIFE Research Center for Civilization Diseases, University of Leipzig, Germany.,Bioinformatics Group, Department of Computer Science, University of Leipzig, Germany
| | - Dennis Karsch
- Department of Internal Medicine II: Hematology and Oncology, University Medical Centre, Campus Kiel, Germany
| | - Wolfram Klapper
- Hematopathology Section, University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel, Germany
| | - Kortine Kleinheinz
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jan Korbel
- EMBL Heidelberg, Genome Biology, Heidelberg, Germany
| | - Helene Kretzmer
- Transcriptome Bioinformatics Group, LIFE Research Center for Civilization Diseases, University of Leipzig, Germany.,Bioinformatics Group, Department of Computer Science, University of Leipzig, Germany
| | - Markus Kreuz
- Institute for Medical Informatics Statistics and Epidemiology, Leipzig, Germany
| | - Ralf Küppers
- Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, Essen, Germany
| | - Chris Lawerenz
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ellen Leich
- Institute of Pathology, University of Würzburg, and Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | - Markus Loeffler
- Institute for Medical Informatics Statistics and Epidemiology, Leipzig, Germany
| | | | - Cristina López
- Institute of Human Genetics, University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel, Germany
| | - Alice C McHardy
- Department of Algorithmic Bioinformatics, Heinrich-Heine University, Duesseldorf, Germany.,Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Peter Möller
- Institute of Pathology, Medical Faculty of the Ulm University, Germany
| | - Marius Rohde
- Department of Pediatric Hematology and Oncology University Hospital Giessen, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel, Germany
| | - Andreas Rosenwald
- Institute of Pathology, University of Würzburg, and Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | - Markus Schilhabel
- Institute of Clinical Molecular Biology, University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel, Germany
| | - Matthias Schlesner
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ingrid Scholz
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Peter F Stadler
- Transcriptome Bioinformatics Group, LIFE Research Center for Civilization Diseases, University of Leipzig, Germany.,Bioinformatics Group, Department of Computer Science, University of Leipzig, Germany.,Interdisciplinary Center for Bioinformatics, University of Leipzig, Germany.,RNomics Group, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany.,Max-Planck-Institute for Mathematics in Sciences, Leipzig, Germany.,Santa Fe Institute, NM, USA
| | | | | | - Monika Szczepanowski
- Hematopathology Section, University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel, Germany
| | - Lorenz Trümper
- Department of Hematology and Oncology, Georg-August-University of Göttingen, Germany
| | - Marc A Weniger
- Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, Essen, Germany
| | - Reiner Siebert
- Institute of Human Genetics, University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel, Germany
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine-University, Medical Faculty, Düsseldorf, Germany
| | - Michael Hummel
- Institute of Pathology, Charité - University Medicine Berlin, Germany
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Duggimpudi S, Larsson E, Nabhani S, Borkhardt A, Hoell JI. The cell cycle regulator CCDC6 is a key target of RNA-binding protein EWS. PLoS One 2015; 10:e0119066. [PMID: 25751255 PMCID: PMC4353705 DOI: 10.1371/journal.pone.0119066] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 01/27/2015] [Indexed: 12/27/2022] Open
Abstract
Genetic translocation of EWSR1 to ETS transcription factor coding region is considered as primary cause for Ewing sarcoma. Previous studies focused on the biology of chimeric transcription factors formed due to this translocation. However, the physiological consequences of heterozygous EWSR1 loss in these tumors have largely remained elusive. Previously, we have identified various mRNAs bound to EWS using PAR-CLIP. In this study, we demonstrate CCDC6, a known cell cycle regulator protein, as a novel target regulated by EWS. siRNA mediated down regulation of EWS caused an elevated apoptosis in cells in a CCDC6-dependant manner. This effect was rescued upon re-expression of CCDC6. This study provides evidence for a novel functional link through which wild-type EWS operates in a target-dependant manner in Ewing sarcoma.
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Affiliation(s)
- Sujitha Duggimpudi
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Center for Child and Adolescent Health, Heinrich Heine University, Medical Faculty, Duesseldorf, Germany
| | - Erik Larsson
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Sweden
| | - Schafiq Nabhani
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Center for Child and Adolescent Health, Heinrich Heine University, Medical Faculty, Duesseldorf, Germany
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Center for Child and Adolescent Health, Heinrich Heine University, Medical Faculty, Duesseldorf, Germany
| | - Jessica I Hoell
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Center for Child and Adolescent Health, Heinrich Heine University, Medical Faculty, Duesseldorf, Germany
- * E-mail:
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28
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Hoell JI, Gombert M, Ginzel S, Loth S, Landgraf P, Käfer V, Streiter M, Prokop A, Weiss M, Thiele R, Borkhardt A. Constitutional mismatch repair-deficiency and whole-exome sequencing as the means of the rapid detection of the causative MSH6 defect. Klin Padiatr 2014; 226:357-61. [PMID: 25431869 DOI: 10.1055/s-0034-1389905] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
BACKGROUND Cases of children with more than one type of cancer either diagnosed simultaneously or successively, rarely occur in pediatric oncology. A second malignant neoplasm may be caused by mutagenic effects of the treatment of the primary malignancy and/or may point towards an underlying genetic cancer susceptibility syndrome. One example of such a syndrome is constitutional mismatch repair-deficiency, (CMMR-D) which carries an increased risk of various tumors including childhood hematologic malignancies and Lynch syndrome associated tumors. Timely diagnosis of CMMR-D is crucial, since this diagnosis has implications for the entire family. PATIENT We report the case of a 15-year-old girl who was born to consanguineous parents. At the age of 20 months she was diagnosed with a T-cell non-Hodgkin lymphoma. Treatment was given according to NHL-BFM 95. 12 years later, an invasive adenocarcinoma of the colon was surgically removed which relapsed shortly afterwards. METHODS Whole-exome sequencing of germline DNA was employed to rapidly detect the underlying mutation in this suspected CMMR-D patient. RESULTS After a short turnaround time of less than 3 weeks, the diagnosis of CMMR-D could be confirmed by the identification of a homozygous 29-bp deletion in MSH6 (exon 6), which was confirmed by independent methods. CONCLUSIONS We demonstrate that "bed-side" whole-exome sequencing is both feasible and cost-effective and may be the method of choice to rapidly uncover the genetical basis of (inherited) diseases.
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Affiliation(s)
- J I Hoell
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany
| | - M Gombert
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany
| | - S Ginzel
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany
| | - S Loth
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany
| | - P Landgraf
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany
| | - V Käfer
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany
| | - M Streiter
- Department of Pediatrics, Division of Pediatric Oncology and Hematology, Municipal Clinics of Cologne, Cologne, Germany
| | - A Prokop
- Department of Pediatrics, Division of Pediatric Oncology and Hematology, Municipal Clinics of Cologne, Cologne, Germany
| | - M Weiss
- Department of Pediatrics, Division of Pediatric Oncology and Hematology, Municipal Clinics of Cologne, Cologne, Germany
| | - R Thiele
- Department of Computer Science, Bonn-Rhine-Sieg University of Applied Sciences, Sankt-Augustin, Germany
| | - A Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany
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Rohde M, Richter J, Schlesner M, Betts MJ, Claviez A, Bonn BR, Zimmermann M, Damm-Welk C, Russell RB, Borkhardt A, Eils R, Hoell JI, Szczepanowski M, Oschlies I, Klapper W, Burkhardt B, Siebert R. RecurrentRHOAmutations in pediatric Burkitt lymphoma treated according to the NHL-BFM protocols. Genes Chromosomes Cancer 2014; 53:911-6. [DOI: 10.1002/gcc.22202] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 06/13/2014] [Accepted: 06/15/2014] [Indexed: 02/03/2023] Open
Affiliation(s)
- Marius Rohde
- Department of Pediatric Hematology and Oncology; University Hospital Giessen; Giessen Germany
| | - Julia Richter
- Institute of Human Genetics, Christian-Albrechts-University; Kiel Germany
| | - Matthias Schlesner
- Division Theoretical Bioinformatics; Deutsches Krebsforschungszentrum Heidelberg (DKFZ); Heidelberg Germany
| | - Matthew J. Betts
- Cell Networks, Bioquant; University of Heidelberg; Heidelberg Germany
| | - Alexander Claviez
- Department of Pediatrics; University Hospital Schleswig-Holstein; Campus Kiel Kiel Germany
| | - Bettina R. Bonn
- Department of Pediatric Hematology and Oncology University Hospital Muenster; Muenster Germany
| | - Martin Zimmermann
- Department of Pediatric Hematology and Oncology; University Hospital Giessen; Giessen Germany
| | - Christine Damm-Welk
- Department of Pediatric Hematology and Oncology; University Hospital Giessen; Giessen Germany
| | - Robert B. Russell
- Cell Networks, Bioquant; University of Heidelberg; Heidelberg Germany
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology; Heinrich-Heine-University; Düsseldorf Germany
| | - Roland Eils
- Division Theoretical Bioinformatics; Deutsches Krebsforschungszentrum Heidelberg (DKFZ); Heidelberg Germany
- Department for Bioinformatics and Functional Genomics; Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University; Heidelberg Germany
| | - Jessica I. Hoell
- Department of Pediatric Oncology, Hematology and Clinical Immunology; Heinrich-Heine-University; Düsseldorf Germany
| | | | - Ilske Oschlies
- Hematopathology Section; Christian-Albrechts-University; Kiel Germany
| | - Wolfram Klapper
- Hematopathology Section; Christian-Albrechts-University; Kiel Germany
| | - Birgit Burkhardt
- Department of Pediatric Hematology and Oncology; University Hospital Giessen; Giessen Germany
- Department of Pediatric Hematology and Oncology University Hospital Muenster; Muenster Germany
| | - Reiner Siebert
- Institute of Human Genetics, Christian-Albrechts-University; Kiel Germany
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Kloetgen A, Münch PC, Borkhardt A, Hoell JI, McHardy AC. Biochemical and bioinformatic methods for elucidating the role of RNA-protein interactions in posttranscriptional regulation. Brief Funct Genomics 2014; 14:102-14. [PMID: 24951655 PMCID: PMC4471435 DOI: 10.1093/bfgp/elu020] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [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] [Indexed: 01/03/2023] Open
Abstract
Our understanding of transcriptional gene regulation has dramatically increased over the past decades, and many regulators of gene expression, such as transcription factors, have been analyzed extensively. Additionally, in recent years, deeper insights into the physiological roles of RNA have been obtained. More precisely, splicing, polyadenylation, various modifications, localization and the translation of messenger RNAs (mRNAs) are regulated by their interaction with RNA-binding proteins (RBPs). New technologies now enable the analysis of this regulation at different levels. A technique known as ultraviolet (UV) cross-linking and immunoprecipitation (CLIP) allows us to determine physical protein–RNA interactions on a genome-wide scale. UV cross-linking introduces covalent bonds between interacting RBPs and RNAs. In combination with immunoprecipitation and deep sequencing techniques, tens of millions of short reads (representing bound RNAs by an RBP of interest) are generated and are used to characterize the regulatory network mediated by an RBP. Other methods, such as mass spectrometry, can also be used for characterization of cross-linked RBPs and RNAs instead of CLIP methods. In this review, we discuss experimental and computational methods for the generation and analysis of CLIP data. The computational methods include short-read alignment, annotation and RNA-binding motif discovery. We describe the challenges of analyzing CLIP data and indicate areas where improvements are needed.
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Affiliation(s)
| | | | | | | | - Alice C McHardy
- Corresponding author. Alice C. McHardy, Heinrich-Heine University, Department of Algorithmic Bioinformatics, Universitaetsstrasse 1, 40225 Duesseldorf, Germany. Tel.: +49-211-8110427; Fax: +49-211-8113464; E-mail:
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Hoell JI, Gombert M, Bartenhagen C, Ginzel S, Husemann P, Felsberg J, Reifenberger G, Eggert A, Dugas M, Schönberger S, Borkhardt A, Fischer U. Whole-genome paired-end analysis confirms remarkable genomic stability of atypical teratoid/rhabdoid tumors. Genes Chromosomes Cancer 2013; 52:983-5. [PMID: 23929726 DOI: 10.1002/gcc.22092] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 06/25/2013] [Indexed: 01/19/2023] Open
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