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Kugler S, Hahnefeld L, Kloka JA, Ginzel S, Nürenberg-Goloub E, Zinn S, Vehreschild MJ, Zacharowski K, Lindau S, Ullrich E, Burmeister J, Kohlhammer J, Schwäble J, Gurke R, Dorochow E, Bennett A, Dauth S, Campe J, Knape T, Laux V, Kannt A, Köhm M, Geisslinger G, Resch E, Behrens F. Short-term predictor for COVID-19 severity from a longitudinal multi-omics study for practical application in intensive care units. Talanta 2024; 268:125295. [PMID: 37866305 DOI: 10.1016/j.talanta.2023.125295] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 09/29/2023] [Accepted: 10/06/2023] [Indexed: 10/24/2023]
Abstract
BACKGROUND The COVID-19 pandemic challenged the management of technical and human resources in intensive care units (ICU) across the world. Several long-term predictors for COVID-19 disease progression have been discovered. However, predictors to support short-term planning of resources and medication that can be translated to future pandemics are still missing. A workflow was established to identify a predictor for short-term COVID-19 disease progression in the acute phase of intensive care patients to support clinical decision-making. METHODS Thirty-two patients with SARS-CoV-2 infection were recruited on admission to the ICU and clinical data collected. During their hospitalization, plasma samples were acquired from each patient on multiple occasions, excepting one patient for which only one time point was possible, and the proteome (Inflammation, Immune Response and Organ Damage panels from Olink® Target 96), metabolome and lipidome (flow injection analysis and liquid chromatography-mass spectrometry) analyzed for each sample. Patient visits were grouped according to changes in disease severity based on their respiratory and organ function, and evaluated using a combination of statistical analysis and machine learning. The resulting short-term predictor from this multi-omics approach was compared to the human assessment of disease progression. Furthermore, the potential markers were compared to the baseline levels of 50 healthy subjects with no known SARS-CoV-2 or other viral infections. RESULTS A total of 124 clinical parameters, 271 proteins and 782 unique metabolites and lipids were assessed. The dimensionality of the dataset was reduced, selecting 47 from the 1177 parameters available following down-selection, to build the machine learning model. Subsequently, two proteins (C-C motif chemokine 7 (CCL7) and carbonic anhydrase 14 (CA14)) and one lipid (hexosylceramide 18:2; O2/20:0) were linked to disease progression in the studied SARS-CoV-2 infections. Thus, a predictor delivering the prognosis of an upcoming worsening of the patient's condition up to five days in advance with a reasonable accuracy (79 % three days prior to event, 84 % four to five days prior to event) was found. Interestingly, the predictor's performance was complementary to the clinicians' capabilities to foresee a worsening of a patient. CONCLUSION This study presents a workflow to identify omics-based biomarkers to support clinical decision-making and resource management in the ICU. This was successfully applied to develop a short-term predictor for aggravation of COVID-19 symptoms. The applied methods can be adapted for future small cohort studies.
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Affiliation(s)
- Sabine Kugler
- Fraunhofer Cluster of Excellence Immune Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany; Fraunhofer Institute for Intelligent Analysis and Information Systems IAIS, Schloss Birlinghoven 1, St. Augustin, Germany
| | - Lisa Hahnefeld
- Fraunhofer Cluster of Excellence Immune Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany; Goethe University Frankfurt, University Hospital, Institute of Clinical Pharmacology, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany.
| | - Jan Andreas Kloka
- Goethe University Frankfurt, University Hospital, Clinic for Anesthesiology, Intensive Care Medicine and Pain Therapy, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Sebastian Ginzel
- Fraunhofer Cluster of Excellence Immune Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany; Fraunhofer Institute for Intelligent Analysis and Information Systems IAIS, Schloss Birlinghoven 1, St. Augustin, Germany
| | - Elina Nürenberg-Goloub
- Goethe University Frankfurt, University Hospital, Clinic for Anesthesiology, Intensive Care Medicine and Pain Therapy, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Sebastian Zinn
- Goethe University Frankfurt, University Hospital, Clinic for Anesthesiology, Intensive Care Medicine and Pain Therapy, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany; Fraunhofer Leistungszentrum TheraNova, Theodor-Stern-Kai 6, 60596, Frankfurt am Main, Germany
| | - Maria Jgt Vehreschild
- Goethe University Frankfurt, University Hospital, Department of Internal Medicine, Infectious Diseases, 60590, Frankfurt am Main, Germany
| | - Kai Zacharowski
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany; Goethe University Frankfurt, University Hospital, Clinic for Anesthesiology, Intensive Care Medicine and Pain Therapy, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Simone Lindau
- Goethe University Frankfurt, University Hospital, Clinic for Anesthesiology, Intensive Care Medicine and Pain Therapy, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Evelyn Ullrich
- University Cancer Center Frankfurt (UCT), University Hospital, Goethe University Frankfurt, Frankfurt, Germany; Frankfurt Cancer Institute (FCI), Frankfurt am Main, Germany; Goethe University Frankfurt, Department of Pediatrics, Experimental Immunology and Cell Therapy, Frankfurt, Germany
| | - Jan Burmeister
- Fraunhofer Institute for Computer Graphics Research IGD, Darmstadt, Germany
| | - Jörn Kohlhammer
- Fraunhofer Institute for Computer Graphics Research IGD, Darmstadt, Germany
| | - Joachim Schwäble
- Goethe University Frankfurt, University Hospital, Institute of Transfusion Medicine and Immunohematology, German Red Cross Blood Transfusion Service Baden-Württemberg, Frankfurt, Germany
| | - Robert Gurke
- Fraunhofer Cluster of Excellence Immune Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany; Goethe University Frankfurt, University Hospital, Institute of Clinical Pharmacology, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany
| | - Erika Dorochow
- Goethe University Frankfurt, University Hospital, Institute of Clinical Pharmacology, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Alexandre Bennett
- Fraunhofer Cluster of Excellence Immune Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany
| | - Stephanie Dauth
- Fraunhofer Cluster of Excellence Immune Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany
| | - Julia Campe
- Goethe University Frankfurt, Department of Pediatrics, Experimental Immunology and Cell Therapy, Frankfurt, Germany; Goethe University Frankfurt, Biological Sciences, Frankfurt am Main, Germany
| | - Tilo Knape
- Fraunhofer Cluster of Excellence Immune Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany
| | - Volker Laux
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany
| | - Aimo Kannt
- Fraunhofer Cluster of Excellence Immune Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany; Fraunhofer Leistungszentrum TheraNova, Theodor-Stern-Kai 6, 60596, Frankfurt am Main, Germany
| | - Michaela Köhm
- Fraunhofer Cluster of Excellence Immune Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany; Goethe University Frankfurt, University Hospital, Rheumatology, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany
| | - Gerd Geisslinger
- Fraunhofer Cluster of Excellence Immune Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany; Goethe University Frankfurt, University Hospital, Institute of Clinical Pharmacology, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany
| | - Eduard Resch
- Fraunhofer Cluster of Excellence Immune Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany
| | - Frank Behrens
- Fraunhofer Cluster of Excellence Immune Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany; Goethe University Frankfurt, University Hospital, Rheumatology, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany
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Grüne B, Kugler S, Ginzel S, Wolff A, Buess M, Kossow A, Küfer-Weiß A, Rüping S, Neuhann F. Symptom diaries as a digital tool to detect SARS-CoV-2 infections and differentiate between prevalent variants. Front Public Health 2022; 10:1030939. [PMID: 36452944 PMCID: PMC9701827 DOI: 10.3389/fpubh.2022.1030939] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 10/14/2022] [Indexed: 11/16/2022] Open
Abstract
The COVID-19 pandemic and the high numbers of infected individuals pose major challenges for public health departments. To overcome these challenges, the health department in Cologne has developed a software called DiKoMa. This software offers the possibility to track contact and index persons, but also provides a digital symptom diary. In this work, the question of whether these can also be used for diagnostic purposes will be investigated. Machine learning makes it possible to identify infections based on early symptom profiles and to distinguish between the predominant dominant variants. Focusing on the occurrence of the symptoms in the first week, a decision tree is trained for the differentiation between contact and index persons and the prevailing dominant variants (Wildtype, Alpha, Delta, and Omicron). The model is evaluated, using sex- and age-stratified cross-validation and validated by symptom profiles of the first 6 days. The variants achieve an AUC-ROC from 0.89 for Omicron and 0.6 for Alpha. No significant differences are observed for the results of the validation set (Alpha 0.63 and Omicron 0.87). The evaluation of symptom combinations using artificial intelligence can determine the individual risk for the presence of a COVID-19 infection, allows assignment to virus variants, and can contribute to the management of epidemics and pandemics on a national and international level. It can help to reduce the number of specific tests in times of low labor capacity and could help to early identify new virus variants.
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Affiliation(s)
| | - Sabine Kugler
- Department of Knowledge Discovery, Fraunhofer Institute for Intelligent Analysis and Information Systems (IAIS), Sankt Augustin, Germany,*Correspondence: Sabine Kugler
| | - Sebastian Ginzel
- Department of Knowledge Discovery, Fraunhofer Institute for Intelligent Analysis and Information Systems (IAIS), Sankt Augustin, Germany
| | - Anna Wolff
- Health Department Cologne, Cologne, Germany
| | | | - Annelene Kossow
- Health Department Cologne, Cologne, Germany,Institute for Hygiene, University Hospital Muenster, Muenster, Germany
| | | | - Stefan Rüping
- Department of Knowledge Discovery, Fraunhofer Institute for Intelligent Analysis and Information Systems (IAIS), Sankt Augustin, Germany
| | - Florian Neuhann
- Heidelberg Institute for Global Health Heidelberg University Hospital, Heidelberg, Germany,School of Medicine Lewy Mwanawasa Medical University, Lusaka, Zambia
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Gruene B, Kugler S, Kuefer-Weiß A, Wolff A, Kossow A, Nießen J, Neuhann F, Ginzel S, Buess M. Public Health benefits by implementing digital symptom diaries for COVID patients from Cologne. Eur J Public Health 2022. [PMCID: PMC9594271 DOI: 10.1093/eurpub/ckac131.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Background High rate of people infected with SARS-CoV-2 and their contacts in Cologne, Germany required innovative tools for notification, monitoring and reporting. The digital tool for COVID19 (DiKoMa) provides self-service symptom diaries allowing (a) the stratification for prioritized telephone contact by the health authority and (b) training a machine learning (ML) model that predicts infections with prevailing dominant variant (PDV) from early symptom profiles (SP). Methods Pseudononymized SP covering the first week of diary recordings were included for training (16646 index, 11582 contacts). A balanced random forest (BRF) model was trained to differentiate early predictive symptom patterns of different PDV and contact persons. Model evaluation was performed using sex and age stratified cross validation (CV), the model was validated on SP recorded from days 1 and 6. Results From 03/20 to 02/22, 90478 indeces and 75444 contact persons reported symptoms and health status, covering 46% and 42% of all reported cases, respectively. Diaries contained between 1-52 entries (566791, median 2). Daily analysis of entries, prioritized according to age, prevalent co-morbidities and detoriation of symptoms allowed risk adjusted follow up even during phases with high case notification rates. The top 5 predictive factors of the BRF were immunization, cough, dysgeusia and dysnosmia, fatigue, and sniffles to differentiate infection between wildtype, three PDV and contact persons (CV AUC 80.6%, Validation AUC 77.1%). Conclusions The use of digital symptom diary surveillance helps to provide appropriate medical support for patients on a large scale. Machine learning shows potential for symptom based risk assessment to differentiate PDV for future outbreaks and can thus become a valuable tool alongside specific laboratory diagnostics. Key messages • Digital symptom diaries are a powerful and widely accepted tool to attend COVID19 patients in isolation. They allow risk stratification for follow up and are a low-threshold service. • Machine learning supports index case identification by symptom analysis and can thus become a valuable tool alongside specific laboratory diagnostics.
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Affiliation(s)
- B Gruene
- Health Department Cologne , Cologne, Germany
| | - S Kugler
- Fraunhofer Institute for Intelligent Analysis , Sankt Augustin, Germany
| | | | - A Wolff
- Health Department Cologne , Cologne, Germany
| | - A Kossow
- Health Department Cologne , Cologne, Germany
- Institut for Hygiene, University of Muenster , Muenster, Germany
| | - J Nießen
- Health Department Cologne , Cologne, Germany
| | - F Neuhann
- Health Department Cologne , Cologne, Germany
- Institut for Global Health, University of Heidelberg , Heidelberg, Germany
| | - S Ginzel
- Fraunhofer Institute for Intelligent Analysis , Sankt Augustin, Germany
| | - M Buess
- Health Department Cologne , Cologne, Germany
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Antweiler D, Sessler D, Rossknecht M, Abb B, Ginzel S, Kohlhammer J. Uncovering chains of infections through spatio-temporal and visual analysis of COVID-19 contact traces. Comput Graph 2022; 106:1-8. [PMID: 35637696 PMCID: PMC9134768 DOI: 10.1016/j.cag.2022.05.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 05/20/2022] [Accepted: 05/24/2022] [Indexed: 05/31/2023]
Abstract
A major challenge for departments of public health (DPHs) in dealing with the ongoing COVID-19 pandemic is tracing contacts in exponentially growing SARS-CoV-2 infection clusters. Prevention of further disease spread requires a comprehensive registration of the connections between individuals and clusters. Due to the high number of infections with unknown origin, the healthcare analysts need to identify connected cases and clusters through accumulated epidemiological knowledge and the metadata of the infections in their database. Here we contribute a visual analytics dashboard to identify, assess and visualize clusters in COVID-19 contact tracing networks. Additionally, we demonstrate how graph-based machine learning methods can be used to find missing links between infection clusters and thus support the mission to get a comprehensive view on infection events. This work was developed through close collaboration with DPHs in Germany. We argue how our dashboard supports the identification of clusters by public health experts, discuss ongoing developments and possible extensions.
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Affiliation(s)
- Dario Antweiler
- Fraunhofer IAIS, Schloss Birlinghoven, Sankt Augustin, 53757, Germany
- Fraunhofer Center for Machine Learning, Schloss Birlinghoven, Sankt Augustin, 53757, Germany
| | - David Sessler
- Fraunhofer IGD, Fraunhoferstraße 5, Darmstadt, 64283, Germany
| | | | - Benjamin Abb
- Fraunhofer IGD, Fraunhoferstraße 5, Darmstadt, 64283, Germany
| | - Sebastian Ginzel
- Fraunhofer IAIS, Schloss Birlinghoven, Sankt Augustin, 53757, Germany
| | - Jörn Kohlhammer
- Fraunhofer IGD, Fraunhoferstraße 5, Darmstadt, 64283, Germany
- TU Darmstadt, Karolinenpl. 5, Darmstadt, 64289, Germany
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Kratz H, Ginzel S, Ohrndorf S, Baraliakos X, Tsiami S, Haedecke E, Doll N, Holz-Müller J, Rüping S, Behrens F, Köhm M. POS0994 DEVELOPMENT OF AN AUTOMATED ALGORITHM BASED ON METHODS OF ARTIFICIAL INTELLIGENCE TO ASSIST IN THE PREDICTION OF CORRECT REFERRALS OF PSORIATIC ARTHRITIS AND AXIAL SPONDYLOARTHRITIS BY USING PATIENT HISTORY TEXTS. Ann Rheum Dis 2022. [DOI: 10.1136/annrheumdis-2022-eular.3996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BackgroundDiagnosis and treatment of PsA and axSpA is often delayed due to missing clear diagnostic criteria and limitations in resources for referral to rheumatologist including high numbers of incorrect referrals. Primary care is usually provided by either general practitioner, dermatologists, or orthopedics. Clinical discriminators with a high specificity for rheumatic conditions include morning stiffness (MST; peripheral or axial, >30min). Artificial intelligence (AI) and natural language processing (NLP) methods offer algorithms for learning systems to recognize disease associated terms and classify clinical phenotypes using large data sets that may support early identification of patients with suspected diagnosis of PsA or axSpA.ObjectivesAI and NLP methods are used to identify patients with typical attributes for inflammation by using morning stiffness as one potential discriminating pattern, which can be detected automatically and might help to prioritize referral for rheumatologist appointments.MethodsWithin a multicentre observational study, patients with visits at the rheumatologist with a suspected diagnosis of PsA or axSpA from the referral primary care provider were recruited. All data on clinical examinations and findings were collected and evaluated by rheumatologists in focus on criteria for diagnosis of PsA/axSpA (gold standard for evaluation). Unstructured text from the patient history was used to extract diagnosis-relevant characteristics. The information extraction algorithms used NLP models to detect expert curated “morning stiffness” (MST) keywords and puts them into a contextualized framework that allows to capture possible negations.ResultsA total of 116 patients were recruited (73 female, 63%) with a median age of 42 (IQR: 34-54). 51 patients were referred as axSpA (44%) and 60 as PsA (52%) by primary care providers. After preselection for PsA and axSpA patients, we observed a 23% rate of referrals without rheumatic diagnosis. Only 7.1% of patients were admitted without signs of MST, 29% with axial MST, 35% with peripheral MST and 28% with both MST types. Average morning stiffness duration was recorded as 35 minutes; patients with a finally confirmed rheumatic diagnosis had a higher average MST duration reported (36 minutes) compared to patients without a confirmed diagnosis. Our AI assisted extraction of MST identified MST in 82.7% of patient history texts. In 75% NLP methods correctly identified the negation of MST symptoms (6 of 8), and 94% of MST was detected when both axial and peripheral joints were affected (30 of 32). Manual inspection of 20 patient history reports where MST was not detected by our automated algorithm revealed that 17 reports did not contain information about MST and three mention unspecific early morning discomfort, without mention of MST.ConclusionThe high rate of correct detection of MST from patient history text using NLP methods allowed us to assess the potential for NLP models to support automated analysis of patient reports to facilitate intelligent patient referral.AcknowledgementsWe thank the Fraunhofer Excellence Cluster for Immune-Mediated Diseases CIMD for the financial support.Disclosure of InterestsNone declared
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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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Schipp C, Schlütermann D, Hönscheid A, Nabhani S, Höll J, Oommen PT, Ginzel S, Fleckenstein B, Stork B, Borkhardt A, Stepensky P, Fischer U. EBV Negative Lymphoma and Autoimmune Lymphoproliferative Syndrome Like Phenotype Extend the Clinical Spectrum of Primary Immunodeficiency Caused by STK4 Deficiency. Front Immunol 2018; 9:2400. [PMID: 30386345 PMCID: PMC6198654 DOI: 10.3389/fimmu.2018.02400] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 09/27/2018] [Indexed: 01/17/2023] Open
Abstract
Serine/threonine kinase 4 (STK4) deficiency is an autosomal recessive genetic condition that leads to primary immunodeficiency (PID) typically characterized by lymphopenia, recurrent infections and Epstein Barr Virus (EBV) induced lymphoproliferation and -lymphoma. State-of-the-art treatment regimens consist of prevention or treatment of infections, immunoglobulin substitution (IVIG) and restoration of the immune system by hematopoietic stem cell transplantation. Here, we report on two patients from two consanguineous families of Turkish (patient P1) and Moroccan (patient P2) decent, with PID due to homozygous STK4 mutations. P1 harbored a previously reported frameshift (c.1103 delT, p.M368RfsX2) and P2 a novel splice donor site mutation (P2; c.525+2 T>G). Both patients presented in childhood with recurrent infections, CD4 lymphopenia and dysregulated immunoglobulin levels. Patient P1 developed a highly malignant B cell lymphoma at the age of 10 years and a second, independent Hodgkin lymphoma 5 years later. To our knowledge she is the first STK4 deficient case reported who developed lymphoma in the absence of detectable EBV or other common viruses. Lymphoma development may be due to the lacking tumor suppressive function of STK4 or the perturbed immune surveillance due to the lack of CD4+ T cells. Our data should raise physicians' awareness of [1] lymphoma proneness of STK4 deficient patients even in the absence of EBV infection and [2] possibly underlying STK4 deficiency in pediatric patients with a history of recurrent infections, CD4 lymphopenia and lymphoma and unknown genetic make-up. Patient P2 experienced recurrent otitis in childhood, but when she presented at the age of 14, she showed clinical and immunological characteristics similar to patients suffering from Autoimmune Lymphoproliferative Syndrome (ALPS): elevated DNT cell number, non-malignant lymphadenopathy and hepatosplenomegaly, hematolytic anemia, hypergammaglobulinemia. Also patient P1 presented with ALPS-like features (lymphadenopathy, elevated DNT cell number and increased Vitamin B12 levels) and both were initially clinically diagnosed as ALPS-like. Closer examination of P2, however, revealed active EBV infection and genetic testing identified a novel STK4 mutation. None of the patients harbored typically ALPS-associated mutations of the Fas receptor mediated apoptotic pathway and Fas-mediated apoptosis was not affected. The presented case reports extend the clinical spectrum of STK4 deficiency.
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Affiliation(s)
- Cyrill Schipp
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, University Children's Hospital, Heinrich-Heine-University, Düsseldorf, Germany
| | - David Schlütermann
- Medical Faculty, Institute of Molecular Medicine I, Heinrich-Heine-University, Düsseldorf, Germany
| | - Andrea Hönscheid
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, University Children's Hospital, Heinrich-Heine-University, Düsseldorf, Germany
| | - Schafiq Nabhani
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, University Children's Hospital, Heinrich-Heine-University, Düsseldorf, Germany
| | - Jessica Höll
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, University Children's Hospital, Heinrich-Heine-University, Düsseldorf, Germany
| | - Prasad T Oommen
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, University Children's Hospital, Heinrich-Heine-University, Düsseldorf, Germany
| | - Sebastian Ginzel
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, University Children's Hospital, Heinrich-Heine-University, Düsseldorf, Germany.,Department of Computer Science, Bonn-Rhein-Sieg University of Applied Sciences, Sankt Augustin, Germany
| | - Bernhard Fleckenstein
- Department of Clinical and Molecular Virology, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Björn Stork
- Medical Faculty, Institute of Molecular Medicine I, Heinrich-Heine-University, Düsseldorf, Germany
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, University Children's Hospital, Heinrich-Heine-University, Düsseldorf, Germany
| | - Polina Stepensky
- Department of Bone Marrow Transplantation and Cancer Immunotherapy, Hadassah University Hospital, Jerusalem, Israel
| | - Ute Fischer
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, University Children's Hospital, Heinrich-Heine-University, Düsseldorf, Germany
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Martín-Lorenzo A, Auer F, Chan LN, García-Ramírez I, González-Herrero I, Rodríguez-Hernández G, Bartenhagen C, Dugas M, Gombert M, Ginzel S, Blanco O, Orfao A, Alonso-López D, Rivas JDL, García-Cenador MB, García-Criado FJ, Müschen M, Sánchez-García I, Borkhardt A, Vicente-Dueñas C, Hauer J. Loss of Pax5 Exploits Sca1-BCR-ABL p190 Susceptibility to Confer the Metabolic Shift Essential for pB-ALL. Cancer Res 2018; 78:2669-2679. [PMID: 29490943 DOI: 10.1158/0008-5472.can-17-3262] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 01/23/2018] [Accepted: 02/23/2018] [Indexed: 12/26/2022]
Abstract
Preleukemic clones carrying BCR-ABLp190 oncogenic lesions are found in neonatal cord blood, where the majority of preleukemic carriers do not convert into precursor B-cell acute lymphoblastic leukemia (pB-ALL). However, the critical question of how these preleukemic cells transform into pB-ALL remains undefined. Here, we model a BCR-ABLp190 preleukemic state and show that limiting BCR-ABLp190 expression to hematopoietic stem/progenitor cells (HS/PC) in mice (Sca1-BCR-ABLp190) causes pB-ALL at low penetrance, which resembles the human disease. pB-ALL blast cells were BCR-ABL-negative and transcriptionally similar to pro-B/pre-B cells, suggesting disease onset upon reduced Pax5 functionality. Consistent with this, double Sca1-BCR-ABLp190+Pax5+/- mice developed pB-ALL with shorter latencies, 90% incidence, and accumulation of genomic alterations in the remaining wild-type Pax5 allele. Mechanistically, the Pax5-deficient leukemic pro-B cells exhibited a metabolic switch toward increased glucose utilization and energy metabolism. Transcriptome analysis revealed that metabolic genes (IDH1, G6PC3, GAPDH, PGK1, MYC, ENO1, ACO1) were upregulated in Pax5-deficient leukemic cells, and a similar metabolic signature could be observed in human leukemia. Our studies unveil the first in vivo evidence that the combination between Sca1-BCR-ABLp190 and metabolic reprogramming imposed by reduced Pax5 expression is sufficient for pB-ALL development. These findings might help to prevent conversion of BCR-ABLp190 preleukemic cells.Significance: Loss of Pax5 drives metabolic reprogramming, which together with Sca1-restricted BCR-ABL expression enables leukemic transformation. Cancer Res; 78(10); 2669-79. ©2018 AACR.
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Affiliation(s)
- Alberto Martín-Lorenzo
- Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, CSIC/Universidad de Salamanca, Campus M. de Unamuno s/n, Salamanca, Spain.,Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Franziska Auer
- Department of Systems Biology, Beckman Research Institute, Monrovia, California.,Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine University Dusseldorf, Medical Faculty, Dusseldorf, Germany
| | - Lai N Chan
- Department of Systems Biology, Beckman Research Institute, Monrovia, California
| | - Idoia García-Ramírez
- Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, CSIC/Universidad de Salamanca, Campus M. de Unamuno s/n, Salamanca, Spain.,Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Inés González-Herrero
- Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, CSIC/Universidad de Salamanca, Campus M. de Unamuno s/n, Salamanca, Spain.,Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Guillermo Rodríguez-Hernández
- Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, CSIC/Universidad de Salamanca, Campus M. de Unamuno s/n, Salamanca, Spain.,Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | | | - Martin Dugas
- Institute of Medical Informatics, University of Muenster, Muenster, Germany
| | - Michael Gombert
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine University Dusseldorf, Medical Faculty, Dusseldorf, Germany
| | - Sebastian Ginzel
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine University Dusseldorf, Medical Faculty, Dusseldorf, Germany
| | - Oscar Blanco
- Departamento de Anatomía Patológica, Universidad de Salamanca, Salamanca, Spain
| | - Alberto Orfao
- Servicio de Citometría and Departamento de Medicina, Universidad de Salamanca, Salamanca, Spain
| | - Diego Alonso-López
- Bioinformatics Unit, Cancer Research Center (CSIC-USAL) Salamanca, Spain
| | - Javier De Las Rivas
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain.,Bioinformatics and Functional Genomics Research Group, Cancer Research Center (CSIC-USAL), Salamanca, Spain
| | | | | | - Markus Müschen
- Department of Systems Biology, Beckman Research Institute, Monrovia, California.
| | - Isidro Sánchez-García
- Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, CSIC/Universidad de Salamanca, Campus M. de Unamuno s/n, Salamanca, Spain.,Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Arndt Borkhardt
- Institute of Medical Informatics, University of Muenster, Muenster, Germany.
| | - Carolina Vicente-Dueñas
- Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, CSIC/Universidad de Salamanca, Campus M. de Unamuno s/n, Salamanca, Spain. .,Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Julia Hauer
- Institute of Medical Informatics, University of Muenster, Muenster, Germany.
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9
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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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10
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Taeubner J, Brozou T, Qin N, Bartl J, Ginzel S, Schaper J, Felsberg J, Fulda S, Vokuhl C, Borkhardt A, Kuhlen M. Congenital embryonal rhabdomyosarcoma caused by heterozygous concomitant PTCH1 and PTCH2 germline mutations. Eur J Hum Genet 2018; 26:137-142. [PMID: 29230040 PMCID: PMC5839031 DOI: 10.1038/s41431-017-0048-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Revised: 10/12/2017] [Accepted: 10/31/2017] [Indexed: 11/09/2022] Open
Abstract
The sonic hedgehog (SHH) signaling pathway has been shown to play important roles in embryogenesis, cell proliferation as well as in cell differentiation. It is aberrantly activated in various common cancers in adults, but also in pediatric neoplasms, such as rhabdomyosarcoma (RMS) and atypical teratoid/rhabdoid tumors (AT/RTs). Dysregulation and germline mutation in PATCHED1 (PTCH1), a receptor for SHH, is responsible for the Gorlin Syndrome, a familial cancer predisposing syndrome including RMS. Here, we report a newborn diagnosed with congenital embryonal RMS. Whole-exome sequencing (WES) identified the presence of two heterozygous germline mutations in two target genes of the SHH signaling pathway. The PTCH1 mutation p.(Gly38Glu) is inherited from the mother, whereas the PTCH2 p.(His622Tyr) mutation is transmitted from the father. Quantitative RT-PCR expression analysis of GLI and SMO, key players of the SHH pathway, showed significantly increase in the tumor tissue of the patient and also enrichment in the germline sample in comparison to the parents indicating activation of the SHH pathway in the patient. These findings demonstrate that SHH pathway activity seems to play a role in eRMS as evidenced by high expression levels of GLI1 RNA transcripts. We speculate that PTCH2 modulates tumorigenesis linked to the PTCH1 mutation and is likely associated with the congenital onset of the RMS observed in our patient.
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Affiliation(s)
- Julia Taeubner
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany
| | - Triantafyllia Brozou
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany
| | - Nan Qin
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany
| | - Jasmin Bartl
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany
| | - Sebastian Ginzel
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany
| | - Joerg Schaper
- Department of Diagnostic and Interventional Radiology, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany
| | - Joerg Felsberg
- Department of Neuropathology, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany
| | - Simone Fulda
- Institute for Experimental Cancer Research in Pediatrics, Goethe-University, Frankfurt, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt, Frankfurt, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christian Vokuhl
- Department of Pediatric Pathology, Christian-Albrechts-University, Kiel, Germany
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany
| | - Michaela Kuhlen
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany.
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11
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Nabhani S, Schipp C, Miskin H, Levin C, Postovsky S, Dujovny T, Koren A, Harlev D, Bis AM, Auer F, Keller B, Warnatz K, Gombert M, Ginzel S, Borkhardt A, Stepensky P, Fischer U. STAT3 gain-of-function mutations associated with autoimmune lymphoproliferative syndrome like disease deregulate lymphocyte apoptosis and can be targeted by BH3 mimetic compounds. Clin Immunol 2017; 181:32-42. [PMID: 28579554 DOI: 10.1016/j.clim.2017.05.021] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [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: 09/28/2016] [Revised: 05/19/2017] [Accepted: 05/31/2017] [Indexed: 01/19/2023]
Abstract
Autoimmune lymphoproliferative syndrome (ALPS) is typically caused by mutations in genes of the extrinsic FAS mediated apoptotic pathway, but for about 30% of ALPS-like patients the genetic diagnosis is lacking. We analyzed 30 children with ALPS-like disease of unknown cause and identified two dominant gain-of-function mutations of the Signal Transducer And Activator Of Transcription 3 (STAT3, p.R278H, p.M394T) leading to increased transcriptional activity. Hyperactivity of STAT3, a known repressor of FAS, was associated with decreased FAS-mediated apoptosis, mimicking ALPS caused by FAS mutations. Expression of BCL2 family proteins, further targets of STAT3 and regulators of the intrinsic apoptotic pathway, was disturbed. Cells with hyperactive STAT3 were consequently more resistant to intrinsic apoptotic stimuli and STAT3 inhibition alleviated this effect. Importantly, STAT3-mutant cells were more sensitive to death induced by the BCL2-inhibitor ABT-737 indicating a dependence on anti-apoptotic BCL2 proteins and potential novel therapeutic options.
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Affiliation(s)
- Schafiq Nabhani
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich-Heine-University Düsseldorf, Germany
| | - Cyrill Schipp
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich-Heine-University Düsseldorf, Germany
| | - Hagit Miskin
- Pediatric Hematology Unit, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Carina Levin
- Pediatric Hematology Unit, Emek Medical Center, Afula, Israel
| | - Sergey Postovsky
- Department of Pediatric Oncology/Hematology Meyer Children's Hospital Rambam Health Care, Haifa, Israel
| | - Tal Dujovny
- Pediatric Hematology Unit, Emek Medical Center, Afula, Israel
| | - Ariel Koren
- Pediatric Hematology Unit, Emek Medical Center, Afula, Israel
| | - Dan Harlev
- Pediatric Hematology Unit, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Anne-Marie Bis
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich-Heine-University Düsseldorf, Germany
| | - Franziska Auer
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich-Heine-University Düsseldorf, Germany
| | - Baerbel Keller
- Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Germany
| | - Klaus Warnatz
- Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Germany
| | - Michael Gombert
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich-Heine-University Düsseldorf, Germany
| | - Sebastian Ginzel
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich-Heine-University Düsseldorf, Germany; Department of Computer Science, Bonn-Rhine-Sieg University of Applied Sciences, Sankt Augustin, Germany
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich-Heine-University Düsseldorf, Germany
| | - Polina Stepensky
- Department of Bone Marrow Transplantation, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Ute Fischer
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich-Heine-University Düsseldorf, Germany.
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12
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Ghosh S, Hönscheid A, Dückers G, Ginzel S, Gohlke H, Gombert M, Kempkes B, Klapper W, Kuhlen M, Laws HJ, Linka RM, Meisel R, Mielke C, Niehues T, Schindler D, Schneider D, Schuster FR, Speckmann C, Borkhardt A. Human RAD52 - a novel player in DNA repair in cancer and immunodeficiency. Haematologica 2016; 102:e69-e72. [PMID: 27979922 DOI: 10.3324/haematol.2016.155838] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Affiliation(s)
- Sujal Ghosh
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Center of Child and Adolescent Health, Heinrich-Heine-University, Düsseldorf, Germany .,Infection, Immunity, Inflammation, Molecular and Cellular Immunology Section, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Andrea Hönscheid
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Center of Child and Adolescent Health, Heinrich-Heine-University, Düsseldorf, Germany
| | - Gregor Dückers
- Department of Pediatrics, Helios Hospital Krefeld, Germany
| | - Sebastian Ginzel
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Center of Child and Adolescent Health, Heinrich-Heine-University, Düsseldorf, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-University, Düsseldorf, Germany
| | - Michael Gombert
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Center of Child and Adolescent Health, Heinrich-Heine-University, Düsseldorf, Germany
| | - Bettina Kempkes
- Department of Gene Vectors, Helmholtz Center Munich, German Research Center for Environmental Health, Germany
| | - Wolfram Klapper
- Department of Pathology, Haematopathology Section and Lymph Node Registry, University Medical Centre Schleswig-Holstein, Kiel, Germany
| | - Michaela Kuhlen
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Center of Child and Adolescent Health, Heinrich-Heine-University, Düsseldorf, Germany
| | - Hans-Jürgen Laws
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Center of Child and Adolescent Health, Heinrich-Heine-University, Düsseldorf, Germany
| | - René Martin Linka
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Center of Child and Adolescent Health, Heinrich-Heine-University, Düsseldorf, Germany
| | - Roland Meisel
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Center of Child and Adolescent Health, Heinrich-Heine-University, Düsseldorf, Germany
| | - Christian Mielke
- Institute of Clinical Chemistry and Laboratory Diagnostics, Heinrich-Heine-University, Düsseldorf, GermanyMedical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Tim Niehues
- Department of Pediatrics, Helios Hospital Krefeld, Germany
| | | | | | - Friedhelm R Schuster
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Center of Child and Adolescent Health, Heinrich-Heine-University, Düsseldorf, Germany
| | - Carsten Speckmann
- Centre for Chronic Immunodeficiency (CCI) and Centre of Pediatrics, University of Freiburg, Germany
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Center of Child and Adolescent Health, Heinrich-Heine-University, Düsseldorf, Germany
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13
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Daschkey S, Bienemann K, Schuster V, Kreth HW, Linka RM, Hönscheid A, Fritz G, Johannes C, Fleckenstein B, Kempkes B, Gombert M, Ginzel S, Borkhardt A. Fatal Lymphoproliferative Disease in Two Siblings Lacking Functional FAAP24. J Clin Immunol 2016; 36:684-92. [PMID: 27473539 DOI: 10.1007/s10875-016-0317-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 07/13/2016] [Indexed: 12/30/2022]
Abstract
Hereditary defects in several genes have been shown to disturb the normal immune response to EBV and to give rise to severe EBV-induced lymphoproliferation in the recent years. Nevertheless, in many patients, the molecular basis of fatal EBV infection still remains unclear. The Fanconi anemia-associated protein 24 (FAAP24) plays a dual role in DNA repair. By association with FANCM as component of the FA core complex, it recruits the FA core complex to damaged DNA. Additionally, FAAP24 has been shown to evoke ATR-mediated checkpoint responses independently of the FA core complex. By whole exome sequencing, we identified a homozygous missense mutation in the FAAP24 gene (cC635T, pT212M) in two siblings of a consanguineous Turkish family who died from an EBV-associated lymphoproliferative disease after infection with a variant EBV strain, expressing a previously unknown EBNA2 allele.In order to analyze the functionality of the variant FAAP24 allele, we used herpes virus saimiri-transformed patient T cells to test endogenous cellular FAAP24 functions that are known to be important in DNA damage control. We saw an impaired FANCD2 monoubiquitination as well as delayed checkpoint responses, especially affecting CHK1 phosphorylation in patient samples in comparison to healthy controls. The phenotype of this FAAP24 mutation might have been further accelerated by an EBV strain that harbors an EBNA2 allele with enhanced activities compared to the prototype laboratory strain B95.8. This is the first report of an FAAP24 loss of function mutation found in human patients with EBV-associated lymphoproliferation.
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Affiliation(s)
- Svenja Daschkey
- Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University, Moorenstrasse 5, 40225, Düsseldorf, Germany
| | - Kirsten Bienemann
- Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University, Moorenstrasse 5, 40225, Düsseldorf, Germany.
| | - Volker Schuster
- Hospital for Children and Adolescents, University Leipzig, Leipzig, Germany
| | | | - René Martin Linka
- Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University, Moorenstrasse 5, 40225, Düsseldorf, Germany
| | - Andrea Hönscheid
- Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University, Moorenstrasse 5, 40225, Düsseldorf, Germany
| | - Gerhard Fritz
- Insitute of Toxicology, Heinrich Heine University, Düsseldorf, Germany
| | - Christian Johannes
- Center for Medical Biotechnology, Biological Faculty, University Duisburg-Essen, Essen, Germany
| | - Bernhard Fleckenstein
- Virological Institute, Clinical and Molecular Virology, University Clinic Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Bettina Kempkes
- Department of Gene Vectors, Helmholtz Center Munich, Munich, Germany
| | - Michael Gombert
- Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University, Moorenstrasse 5, 40225, Düsseldorf, Germany
| | - Sebastian Ginzel
- Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University, Moorenstrasse 5, 40225, Düsseldorf, Germany
| | - Arndt Borkhardt
- Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University, Moorenstrasse 5, 40225, Düsseldorf, Germany
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14
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Schipp C, Nabhani S, Bienemann K, Simanovsky N, Kfir-Erenfeld S, Assayag-Asherie N, Oommen PT, Revel-Vilk S, Hönscheid A, Gombert M, Ginzel S, Schäfer D, Laws HJ, Yefenof E, Fleckenstein B, Borkhardt A, Stepensky P, Fischer U. Specific antibody deficiency and autoinflammatory disease extend the clinical and immunological spectrum of heterozygous NFKB1 loss-of-function mutations in humans. Haematologica 2016; 101:e392-e396. [PMID: 27365489 DOI: 10.3324/haematol.2016.145136] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Cyrill Schipp
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Schafiq Nabhani
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Kirsten Bienemann
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Natalia Simanovsky
- Department of Radiology, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Shlomit Kfir-Erenfeld
- The Lautenberg Research Center, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | | | - Prasad T Oommen
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Shoshana Revel-Vilk
- Pediatric Hematology Oncology and Bone Marrow Transplantation Department, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Andrea Hönscheid
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Michael Gombert
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Sebastian Ginzel
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany Department of Computer Science, Bonn-Rhine-Sieg University of Applied Sciences, Sankt Augustin, Germany
| | - Daniel Schäfer
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Hans-Jürgen Laws
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Eitan Yefenof
- The Lautenberg Research Center, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Bernhard Fleckenstein
- Department of Clinical and Molecular Virology, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Polina Stepensky
- Pediatric Hematology Oncology and Bone Marrow Transplantation Department, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Ute Fischer
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
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15
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Joosten M, Ginzel S, Blex C, Schmidt D, Gombert M, Chen C, Linka RM, Gräbner O, Hain A, Hirsch B, Sommerfeld A, Seegebarth A, Gruber U, Maneck C, Zhang L, Stenin K, Dieks H, Sefkow M, Münk C, Baldus CD, Thiele R, Borkhardt A, Hummel M, Köster H, Fischer U, Dreger M, Seitz V. A novel approach to detect resistance mechanisms reveals FGR as a factor mediating HDAC inhibitor SAHA resistance in B-cell lymphoma. Mol Oncol 2016; 10:1232-44. [PMID: 27324824 DOI: 10.1016/j.molonc.2016.06.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 06/02/2016] [Accepted: 06/03/2016] [Indexed: 01/15/2023] Open
Abstract
Histone deacetylase (HDAC) inhibitors such as suberoylanilide hydroxamic acid (SAHA) are not commonly used in clinical practice for treatment of B-cell lymphomas, although a subset of patients with refractory or relapsed B-cell lymphoma achieved partial or complete remissions. Therefore, the purpose of this study was to identify molecular features that predict the response of B-cell lymphomas to SAHA treatment. We designed an integrative approach combining drug efficacy testing with exome and captured target analysis (DETECT). In this study, we tested SAHA sensitivity in 26 B-cell lymphoma cell lines and determined SAHA-interacting proteins in SAHA resistant and sensitive cell lines employing a SAHA capture compound (CC) and mass spectrometry (CCMS). In addition, we performed exome mutation analysis. Candidate validation was done by expression analysis and knock-out experiments. An integrated network analysis revealed that the Src tyrosine kinase Gardner-Rasheed feline sarcoma viral (v-fgr) oncogene homolog (FGR) is associated with SAHA resistance. FGR was specifically captured by the SAHA-CC in resistant cells. In line with this observation, we found that FGR expression was significantly higher in SAHA resistant cell lines. As functional proof, CRISPR/Cas9 mediated FGR knock-out in resistant cells increased SAHA sensitivity. In silico analysis of B-cell lymphoma samples (n = 1200) showed a wide range of FGR expression indicating that FGR expression might help to stratify patients, which clinically benefit from SAHA therapy. In conclusion, our comprehensive analysis of SAHA-interacting proteins highlights FGR as a factor involved in SAHA resistance in B-cell lymphoma.
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Affiliation(s)
- Maria Joosten
- Institute of Pathology, Charité University Medicine, Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany
| | - Sebastian Ginzel
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Center of Child and Adolescent Health, Medical Faculty, Heinrich-Heine-University, Moorenstr. 5, 40225 Düsseldorf, Germany; Department of Computer Science, Bonn-Rhine-Sieg University of Applied Sciences, Grantham-Allee 20, 53757 Sankt Augustin, Germany
| | - Christian Blex
- caprotec bioanalytics GmbH, Magnusstraße 11, 12489 Berlin, Germany
| | - Dmitri Schmidt
- caprotec bioanalytics GmbH, Magnusstraße 11, 12489 Berlin, Germany
| | - Michael Gombert
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Center of Child and Adolescent Health, Medical Faculty, Heinrich-Heine-University, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - Cai Chen
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Center of Child and Adolescent Health, Medical Faculty, Heinrich-Heine-University, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - René Martin Linka
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Center of Child and Adolescent Health, Medical Faculty, Heinrich-Heine-University, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - Olivia Gräbner
- caprotec bioanalytics GmbH, Magnusstraße 11, 12489 Berlin, Germany
| | - Anika Hain
- Clinic for Gastroenterology, Hepatology and Infectiology, Medical Faculty, Heinrich-Heine-University, Moorenstrasse 5, 40225 Düsseldorf, Germany
| | - Burkhard Hirsch
- Institute of Pathology, Charité University Medicine, Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany
| | - Anke Sommerfeld
- Institute of Pathology, Charité University Medicine, Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany
| | - Anke Seegebarth
- Institute of Pathology, Charité University Medicine, Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany
| | - Uschi Gruber
- caprotec bioanalytics GmbH, Magnusstraße 11, 12489 Berlin, Germany
| | - Corinna Maneck
- caprotec bioanalytics GmbH, Magnusstraße 11, 12489 Berlin, Germany
| | - Langhui Zhang
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Center of Child and Adolescent Health, Medical Faculty, Heinrich-Heine-University, Moorenstr. 5, 40225 Düsseldorf, Germany; Department of Hematology, Union Hospital, Fujian Medical University, NO.29,Xinquan Road, Fuzhou City, Fujian Province, China
| | - Katharina Stenin
- caprotec bioanalytics GmbH, Magnusstraße 11, 12489 Berlin, Germany
| | - Henrik Dieks
- caprotec bioanalytics GmbH, Magnusstraße 11, 12489 Berlin, Germany
| | - Michael Sefkow
- caprotec bioanalytics GmbH, Magnusstraße 11, 12489 Berlin, Germany
| | - Carsten Münk
- Clinic for Gastroenterology, Hepatology and Infectiology, Medical Faculty, Heinrich-Heine-University, Moorenstrasse 5, 40225 Düsseldorf, Germany
| | - Claudia D Baldus
- Department of Hematology and Oncology, Charité University Medicine, Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany
| | - Ralf Thiele
- Department of Computer Science, Bonn-Rhine-Sieg University of Applied Sciences, Grantham-Allee 20, 53757 Sankt Augustin, Germany
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Center of Child and Adolescent Health, Medical Faculty, Heinrich-Heine-University, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - Michael Hummel
- Institute of Pathology, Charité University Medicine, Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany
| | - Hubert Köster
- caprotec bioanalytics GmbH, Magnusstraße 11, 12489 Berlin, Germany
| | - Ute Fischer
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Center of Child and Adolescent Health, Medical Faculty, Heinrich-Heine-University, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - Mathias Dreger
- caprotec bioanalytics GmbH, Magnusstraße 11, 12489 Berlin, Germany
| | - Volkhard Seitz
- Institute of Pathology, Charité University Medicine, Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany.
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16
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Bienemann K, Daschkey S, Sörensen J, Schwabe D, Klingebiel T, Hönscheid A, Gombert M, Ginzel S, Borkhardt A. A novel homozygous mutation in UNC13D presenting as Epstein-Barr-virus-associated lymphoproliferative disease at 9 years of age. Leuk Lymphoma 2016; 57:2949-2951. [PMID: 27123661 DOI: 10.1080/10428194.2016.1177724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Kirsten Bienemann
- a Pediatric Oncology, Hematology and Clinical Immunology , Heinrich Heine University Medical Center , Düsseldorf , Germany
| | - Svenja Daschkey
- a Pediatric Oncology, Hematology and Clinical Immunology , Heinrich Heine University Medical Center , Düsseldorf , Germany
| | - Jan Sörensen
- b Clinic for Hematology/Oncology and Clinic for Stem Cell Transplantation and Immunology , University Children's Hospital , Frankfurt , Germany
| | - Dirk Schwabe
- b Clinic for Hematology/Oncology and Clinic for Stem Cell Transplantation and Immunology , University Children's Hospital , Frankfurt , Germany
| | - Thomas Klingebiel
- b Clinic for Hematology/Oncology and Clinic for Stem Cell Transplantation and Immunology , University Children's Hospital , Frankfurt , Germany
| | - Andrea Hönscheid
- a Pediatric Oncology, Hematology and Clinical Immunology , Heinrich Heine University Medical Center , Düsseldorf , Germany
| | - Michael Gombert
- a Pediatric Oncology, Hematology and Clinical Immunology , Heinrich Heine University Medical Center , Düsseldorf , Germany
| | - Sebastian Ginzel
- a Pediatric Oncology, Hematology and Clinical Immunology , Heinrich Heine University Medical Center , Düsseldorf , Germany
| | - Arndt Borkhardt
- a Pediatric Oncology, Hematology and Clinical Immunology , Heinrich Heine University Medical Center , Düsseldorf , Germany
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17
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Linka Y, Ginzel S, Borkhardt A, Landgraf P. Identification of TEL-AML1 (ETV6-RUNX1) associated DNA and its impact on mRNA and protein output using ChIP, mRNA expression arrays and SILAC. Genom Data 2015; 2:85-8. [PMID: 26484077 PMCID: PMC4536161 DOI: 10.1016/j.gdata.2014.05.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 05/15/2014] [Accepted: 05/16/2014] [Indexed: 11/30/2022]
Abstract
The contribution of the most common reciprocal translocation in childhood B-cell precursor leukemia t(12;21)(p13;q22) to leukemia development is still under debate. Direct as well as secondary indirect effects of the TEL-AML1 fusion protein are commonly recorded by using cell lines and patient samples, often bearing the TEL-AML1 fusion protein for decades. To identify direct targets of the fusion protein a short-term induction of TEL-AML1 is needed. We here describe in detail the experimental procedure, quality controls and contents of the ChIP, mRNA expression and SILAC datasets associated with the study published by Linka and colleagues in the Blood Cancer Journal [1] utilizing a short term induction of TEL-AML1 in an inducible precursor B-cell line model.
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Affiliation(s)
- Yvonne Linka
- Heinrich-Heine-University Düsseldorf, Medical Faculty, Clinic for Pediatric Oncology, Hematology and Clinical Immunology, Duesseldorf, Germany
| | - Sebastian Ginzel
- Heinrich-Heine-University Düsseldorf, Medical Faculty, Clinic for Pediatric Oncology, Hematology and Clinical Immunology, Duesseldorf, Germany ; Department of Computer Science, Bonn-Rhine-Sieg University of Applied Sciences, St. Augustin, Germany
| | - Arndt Borkhardt
- Heinrich-Heine-University Düsseldorf, Medical Faculty, Clinic for Pediatric Oncology, Hematology and Clinical Immunology, Duesseldorf, Germany
| | - Pablo Landgraf
- Heinrich-Heine-University Düsseldorf, Medical Faculty, Clinic for Pediatric Oncology, Hematology and Clinical Immunology, Duesseldorf, Germany
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18
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Martín-Lorenzo A, Hauer J, Vicente-Dueñas C, Auer F, González-Herrero I, García-Ramírez I, Ginzel S, Thiele R, Constantinescu SN, Bartenhagen C, Dugas M, Gombert M, Schäfer D, Blanco O, Mayado A, Orfao A, Alonso-López D, Rivas JDL, Cobaleda C, García-Cenador MB, García-Criado FJ, Sánchez-García I, Borkhardt A. Infection Exposure is a Causal Factor in B-cell Precursor Acute Lymphoblastic Leukemia as a Result of Pax5-Inherited Susceptibility. Cancer Discov 2015; 5:1328-43. [PMID: 26408659 DOI: 10.1158/2159-8290.cd-15-0892] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 09/17/2015] [Indexed: 11/16/2022]
Abstract
UNLABELLED Earlier in the past century, infections were regarded as the most likely cause of childhood B-cell precursor acute lymphoblastic leukemia (pB-ALL). However, there is a lack of relevant biologic evidence supporting this hypothesis. We present in vivo genetic evidence mechanistically connecting inherited susceptibility to pB-ALL and postnatal infections by showing that pB-ALL was initiated in Pax5 heterozygous mice only when they were exposed to common pathogens. Strikingly, these murine pB-ALLs closely resemble the human disease. Tumor exome sequencing revealed activating somatic, nonsynonymous mutations of Jak3 as a second hit. Transplantation experiments and deep sequencing suggest that inactivating mutations in Pax5 promote leukemogenesis by creating an aberrant progenitor compartment that is susceptible to malignant transformation through accumulation of secondary Jak3 mutations. Thus, treatment of Pax5(+/-) leukemic cells with specific JAK1/3 inhibitors resulted in increased apoptosis. These results uncover the causal role of infection in pB-ALL development. SIGNIFICANCE These results demonstrate that delayed infection exposure is a causal factor in pB-ALL. Therefore, these findings have critical implications for the understanding of the pathogenesis of leukemia and for the development of novel therapies for this disease.
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Affiliation(s)
- Alberto Martín-Lorenzo
- Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, CSIC/Universidad de Salamanca, Campus M. de Unamuno s/n, Salamanca, Spain. Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Julia Hauer
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine University Dusseldorf, Medical Faculty, Dusseldorf, Germany
| | - Carolina Vicente-Dueñas
- Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, CSIC/Universidad de Salamanca, Campus M. de Unamuno s/n, Salamanca, Spain. Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Franziska Auer
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine University Dusseldorf, Medical Faculty, Dusseldorf, Germany
| | - Inés González-Herrero
- Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, CSIC/Universidad de Salamanca, Campus M. de Unamuno s/n, Salamanca, Spain. Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Idoia García-Ramírez
- Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, CSIC/Universidad de Salamanca, Campus M. de Unamuno s/n, Salamanca, Spain. Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Sebastian Ginzel
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine University Dusseldorf, Medical Faculty, Dusseldorf, Germany. Department of Computer Science, Bonn-Rhein-Sieg University of Applied Sciences, Sankt Augustin, Germany
| | - Ralf Thiele
- Department of Computer Science, Bonn-Rhein-Sieg University of Applied Sciences, Sankt Augustin, Germany
| | - Stefan N Constantinescu
- Ludwig Institute for Cancer Research Brussels and Université catholique de Louvain, de Duve Institute, Brussels, Belgium
| | | | - Martin Dugas
- Institute of Medical Informatics, University of Muenster, Muenster, Germany
| | - Michael Gombert
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine University Dusseldorf, Medical Faculty, Dusseldorf, Germany
| | - Daniel Schäfer
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine University Dusseldorf, Medical Faculty, Dusseldorf, Germany
| | - Oscar Blanco
- Departamento de Anatomía Patológica, Universidad de Salamanca, Salamanca, Spain
| | - Andrea Mayado
- Servicio de Citometría and Departamento de Medicina, Universidad de Salamanca, Salamanca, Spain
| | - Alberto Orfao
- Servicio de Citometría and Departamento de Medicina, Universidad de Salamanca, Salamanca, Spain
| | - Diego Alonso-López
- Bioinformatics Unit, Cancer Research Center (CSIC-USAL), Salamanca, Spain
| | - Javier De Las Rivas
- Bioinformatics Unit, Cancer Research Center (CSIC-USAL), Salamanca, Spain. Bioinformatics and Functional Genomics Research Group, Cancer Research Center (CSIC-USAL), Salamanca, Spain
| | - César Cobaleda
- Centro de Biología Molecular Severo Ochoa; CSIC/Universidad Autónoma de Madrid; Campus de Cantoblanco, Madrid, Spain
| | | | | | - Isidro Sánchez-García
- Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, CSIC/Universidad de Salamanca, Campus M. de Unamuno s/n, Salamanca, Spain. Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain.
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine University Dusseldorf, Medical Faculty, Dusseldorf, Germany.
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19
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Chen C, Bartenhagen C, Gombert M, Okpanyi V, Binder V, Röttgers S, Bradtke J, Teigler-Schlegel A, Harbott J, Ginzel S, Thiele R, Husemann P, Krell PF, Borkhardt A, Dugas M, Hu J, Fischer U. Next-generation-sequencing of recurrent childhood high hyperdiploid acute lymphoblastic leukemia reveals mutations typically associated with high risk patients. Leuk Res 2015; 39:990-1001. [DOI: 10.1016/j.leukres.2015.06.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 06/08/2015] [Accepted: 06/10/2015] [Indexed: 01/07/2023]
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20
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Fischer U, Forster M, Rinaldi A, Risch T, Sungalee S, Warnatz HJ, Bornhauser B, Gombert M, Kratsch C, Stütz AM, Sultan M, Tchinda J, Worth CL, Amstislavskiy V, Badarinarayan N, Baruchel A, Bartram T, Basso G, Canpolat C, Cario G, Cavé H, Dakaj D, Delorenzi M, Dobay MP, Eckert C, Ellinghaus E, Eugster S, Frismantas V, Ginzel S, Haas OA, Heidenreich O, Hemmrich-Stanisak G, Hezaveh K, Höll JI, Hornhardt S, Husemann P, Kachroo P, Kratz CP, Te Kronnie G, Marovca B, Niggli F, McHardy AC, Moorman AV, Panzer-Grümayer R, Petersen BS, Raeder B, Ralser M, Rosenstiel P, Schäfer D, Schrappe M, Schreiber S, Schütte M, Stade B, Thiele R, von der Weid N, Vora A, Zaliova M, Zhang L, Zichner T, Zimmermann M, Lehrach H, Borkhardt A, Bourquin JP, Franke A, Korbel JO, Stanulla M, Yaspo ML. Genomics and drug profiling of fatal TCF3-HLF-positive acute lymphoblastic leukemia identifies recurrent mutation patterns and therapeutic options. Nat Genet 2015. [PMID: 26214592 PMCID: PMC4603357 DOI: 10.1038/ng.3362] [Citation(s) in RCA: 156] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
TCF3-HLF-fusion positive acute lymphoblastic leukemia (ALL) is currently incurable. Employing an integrated approach, we uncovered distinct mutation, gene expression, and drug response profiles in TCF3-HLF-positive and treatment-responsive TCF3-PBX1-positive ALL. Recurrent intragenic deletions of PAX5 or VPREB1 were identified in constellation with TCF3-HLF. Moreover somatic mutations in the non-translocated allele of TCF3 and a reduction of PAX5 gene dosage in TCF3-HLF ALL suggest cooperation within a restricted genetic context. The enrichment for stem cell and myeloid features in the TCF3-HLF signature may reflect reprogramming by TCF3-HLF of a lymphoid-committed cell of origin towards a hybrid, drug-resistant hematopoietic state. Drug response profiling of matched patient-derived xenografts revealed a distinct profile for TCF3-HLF ALL with resistance to conventional chemotherapeutics, but sensitivity towards glucocorticoids, anthracyclines and agents in clinical development. Striking on-target sensitivity was achieved with the BCL2-specific inhibitor venetoclax (ABT-199). This integrated approach thus provides alternative treatment options for this deadly disease.
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Affiliation(s)
- Ute Fischer
- Clinic for Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Michael Forster
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Anna Rinaldi
- Pediatric Oncology, Children's Research Centre, University Children's Hospital Zurich, Zurich, Switzerland
| | - Thomas Risch
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Stéphanie Sungalee
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Hans-Jörg Warnatz
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Beat Bornhauser
- Pediatric Oncology, Children's Research Centre, University Children's Hospital Zurich, Zurich, Switzerland
| | - Michael Gombert
- Clinic for Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Christina Kratsch
- Department of Algorithmic Bioinformatics, Heinrich-Heine-University, Düsseldorf, Germany
| | - Adrian M Stütz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Marc Sultan
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Joelle Tchinda
- Pediatric Oncology, Children's Research Centre, University Children's Hospital Zurich, Zurich, Switzerland
| | - Catherine L Worth
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | - Nandini Badarinarayan
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - André Baruchel
- Department of Pediatric Hemato-Immunology, Hôpital Robert Debré and Paris Diderot University, Paris, France
| | - Thies Bartram
- Department of Pediatrics, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Giuseppe Basso
- Department of Pediatrics, Laboratory of Pediatric Hematology/Oncology, University of Padova, Padova, Italy
| | - Cengiz Canpolat
- Department of Pediatrics, Acıbadem University Medical School, Ataşehir, Istanbul, Turkey
| | - Gunnar Cario
- Department of Pediatrics, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Hélène Cavé
- Department of Genetics, Hôpital Robert Debré and Paris Diderot University, Paris, France
| | - Dardane Dakaj
- Pediatric Oncology, Children's Research Centre, University Children's Hospital Zurich, Zurich, Switzerland
| | - Mauro Delorenzi
- Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland.,Swiss Institute for Bioinformatics (SIB), Lausanne, Switzerland
| | | | - Cornelia Eckert
- Pediatric Hematology and Oncology, Charité University Hospital, Berlin, Germany
| | - Eva Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Sabrina Eugster
- Pediatric Oncology, Children's Research Centre, University Children's Hospital Zurich, Zurich, Switzerland
| | - Viktoras Frismantas
- Pediatric Oncology, Children's Research Centre, University Children's Hospital Zurich, Zurich, Switzerland
| | - Sebastian Ginzel
- Clinic for Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany.,Department of Computer Science, Bonn-Rhine-Sieg University of Applied Sciences, Sankt Augustin, Germany
| | - Oskar A Haas
- Children's Cancer Research Institute, Vienna, Austria
| | - Olaf Heidenreich
- Northern Institute of Cancer Research, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Georg Hemmrich-Stanisak
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Kebria Hezaveh
- Clinic for Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Jessica I Höll
- Clinic for Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Sabine Hornhardt
- Federal Office for Radiation Protection, Oberschleissheim, Germany
| | - Peter Husemann
- Clinic for Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Priyadarshini Kachroo
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Christian P Kratz
- Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Geertruy Te Kronnie
- Department of Pediatrics, Laboratory of Pediatric Hematology/Oncology, University of Padova, Padova, Italy
| | - Blerim Marovca
- Pediatric Oncology, Children's Research Centre, University Children's Hospital Zurich, Zurich, Switzerland
| | - Felix Niggli
- Pediatric Oncology, Children's Research Centre, University Children's Hospital Zurich, Zurich, Switzerland
| | - Alice C McHardy
- Department of Algorithmic Bioinformatics, Heinrich-Heine-University, Düsseldorf, Germany
| | - Anthony V Moorman
- Northern Institute of Cancer Research, Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | - Britt S Petersen
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Benjamin Raeder
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Meryem Ralser
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Daniel Schäfer
- Clinic for Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Martin Schrappe
- Department of Pediatrics, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | | | - Björn Stade
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Ralf Thiele
- Department of Computer Science, Bonn-Rhine-Sieg University of Applied Sciences, Sankt Augustin, Germany
| | | | - Ajay Vora
- Sheffield Children's Hospital, Sheffield, United Kingdom
| | - Marketa Zaliova
- Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany.,Childhood Leukaemia Investigation Prague (CLIP), Department of Pediatric Hematology/Oncology, Second Faculty of Medicine, Charles University Prague, Prague, Czech Republic
| | - Langhui Zhang
- Clinic for Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany.,Department of Hematology, Union Hospital, Fujian Medical University, Fuzhou, China
| | - Thomas Zichner
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Martin Zimmermann
- Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Hans Lehrach
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Alacris Theranostics GmbH, Berlin, Germany.,Dahlem Centre for Genome Reseach and Medical Systems Biology, Berlin, Germany
| | - Arndt Borkhardt
- Clinic for Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Jean-Pierre Bourquin
- Pediatric Oncology, Children's Research Centre, University Children's Hospital Zurich, Zurich, Switzerland
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Jan O Korbel
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Martin Stanulla
- Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Marie-Laure Yaspo
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
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21
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Nabhani S, Ginzel S, Miskin H, Revel-Vilk S, Harlev D, Fleckenstein B, Hönscheid A, Oommen PT, Kuhlen M, Thiele R, Laws HJ, Borkhardt A, Stepensky P, Fischer U. Deregulation of Fas ligand expression as a novel cause of autoimmune lymphoproliferative syndrome-like disease. Haematologica 2015; 100:1189-98. [PMID: 26113417 DOI: 10.3324/haematol.2014.114967] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 06/19/2015] [Indexed: 12/30/2022] Open
Abstract
Autoimmune lymphoproliferative syndrome is frequently caused by mutations in genes involved in the Fas death receptor pathway, but for 20-30% of patients the genetic defect is unknown. We observed that treatment of healthy T cells with interleukin-12 induces upregulation of Fas ligand and Fas ligand-dependent apoptosis. Consistently, interleukin-12 could not induce apoptosis in Fas ligand-deficient T cells from patients with autoimmune lymphoproliferative syndrome. We hypothesized that defects in the interleukin-12 signaling pathway may cause a similar phenotype as that caused by mutations of the Fas ligand gene. To test this, we analyzed 20 patients with autoimmune lymphoproliferative syndrome of unknown cause by whole-exome sequencing. We identified a homozygous nonsense mutation (c.698G>A, p.R212*) in the interleukin-12/interleukin-23 receptor-component IL12RB1 in one of these patients. The mutation led to IL12RB1 protein truncation and loss of cell surface expression. Interleukin-12 and -23 signaling was completely abrogated as demonstrated by deficient STAT4 phosphorylation and interferon γ production. Interleukin-12-mediated expression of membrane-bound and soluble Fas ligand was lacking and basal expression was much lower than in healthy controls. The patient presented with the classical symptoms of autoimmune lymphoproliferative syndrome: chronic non-malignant, non-infectious lymphadenopathy, splenomegaly, hepatomegaly, elevated numbers of double-negative T cells, autoimmune cytopenias, and increased levels of vitamin B12 and interleukin-10. Sanger sequencing and whole-exome sequencing excluded the presence of germline or somatic mutations in genes known to be associated with the autoimmune lymphoproliferative syndrome. Our data suggest that deficient regulation of Fas ligand expression by regulators such as the interleukin-12 signaling pathway may be an alternative cause of autoimmune lymphoproliferative syndrome-like disease.
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Affiliation(s)
- Schafiq Nabhani
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Sebastian Ginzel
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany Department of Computer Science, Bonn-Rhein-Sieg University of Applied Sciences, Sankt Augustin, Germany
| | - Hagit Miskin
- Pediatric Hematology Unit, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Shoshana Revel-Vilk
- Department of Pediatric Hematology-Oncology, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Dan Harlev
- Pediatric Hematology Unit, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Bernhard Fleckenstein
- Department of Clinical and Molecular Virology, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Andrea Hönscheid
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Prasad T Oommen
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Michaela Kuhlen
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Ralf Thiele
- Department of Computer Science, Bonn-Rhein-Sieg University of Applied Sciences, Sankt Augustin, Germany
| | - Hans-Jürgen Laws
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Polina Stepensky
- Department of Pediatric Hematology-Oncology, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Ute Fischer
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
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22
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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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23
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Linka Y, Ginzel S, Krüger M, Novosel A, Gombert M, Kremmer E, Harbott J, Thiele R, Borkhardt A, Landgraf P. The impact of TEL-AML1 (ETV6-RUNX1) expression in precursor B cells and implications for leukaemia using three different genome-wide screening methods. Blood Cancer J 2013; 3:e151. [PMID: 24121163 PMCID: PMC3816209 DOI: 10.1038/bcj.2013.48] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [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: 07/01/2013] [Revised: 08/18/2013] [Accepted: 09/04/2013] [Indexed: 02/03/2023] Open
Abstract
The reciprocal translocation t(12;21)(p13;q22), the most common structural genomic alteration in B-cell precursor acute lymphoblastic leukaemia in children, results in a chimeric transcription factor TEL-AML1 (ETV6-RUNX1). We identified directly and indirectly regulated target genes utilizing an inducible TEL-AML1 system derived from the murine pro B-cell line BA/F3 and a monoclonal antibody directed against TEL-AML1. By integration of promoter binding identified with chromatin immunoprecipitation (ChIP)-on-chip, gene expression and protein output through microarray technology and stable labelling of amino acids in cell culture, we identified 217 directly and 118 indirectly regulated targets of the TEL-AML1 fusion protein. Directly, but not indirectly, regulated promoters were enriched in AML1-binding sites. The majority of promoter regions were specific for the fusion protein and not bound by native AML1 or TEL. Comparison with gene expression profiles from TEL-AML1-positive patients identified 56 concordantly misregulated genes with negative effects on proliferation and cellular transport mechanisms and positive effects on cellular migration, and stress responses including immunological responses. In summary, this work for the first time gives a comprehensive insight into how TEL-AML1 expression may directly and indirectly contribute to alter cells to become prone for leukemic transformation.
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Affiliation(s)
- Y Linka
- Heinrich-Heine University of Dusseldorf, Medical Faculty, Clinic for Pediatric Oncology, Hematology and Clinical Immunology, Dusseldorf, Germany
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24
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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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25
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Chen C, Bartenhagen C, Gombert M, Okpanyi V, Binder V, Röttgers S, Bradtke J, Teigler-Schlegel A, Harbott J, Ginzel S, Thiele R, Fischer U, Dugas M, Hu J, Borkhardt A. Next-generation-sequencing-based risk stratification and identification of new genes involved in structural and sequence variations in near haploid lymphoblastic leukemia. Genes Chromosomes Cancer 2013; 52:564-79. [DOI: 10.1002/gcc.22054] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 01/29/2013] [Indexed: 01/10/2023] Open
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26
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Salzer E, Daschkey S, Choo S, Gombert M, Santos-Valente E, Ginzel S, Schwendinger M, Haas OA, Fritsch G, Pickl WF, Förster-Waldl E, Borkhardt A, Boztug K, Bienemann K, Seidel MG. Combined immunodeficiency with life-threatening EBV-associated lymphoproliferative disorder in patients lacking functional CD27. Haematologica 2012; 98:473-8. [PMID: 22801960 DOI: 10.3324/haematol.2012.068791] [Citation(s) in RCA: 133] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
CD27, a tumor necrosis factor receptor family member, interacts with CD70 and influences T-, B- and NK-cell functions. Disturbance of this axis impairs immunity and memory generation against viruses including Epstein Barr virus (EBV), influenza, and others. CD27 is commonly used as marker of memory B cells for the classification of B-cell deficiencies including common variable immune deficiency. Flow cytometric immunophenotyping including expression analysis of CD27 on lymphoid cells was followed by capillary sequencing of CD27 in index patients, their parents, and non-affected siblings. More comprehensive genetic analysis employed single nucleotide polymorphism-based homozygosity mapping and whole exome sequencing. Analysis of exome sequencing data was performed at two centers using slightly different data analysis pipelines, each based on the Genome Analysis ToolKit Best Practice version 3 recommendations. A comprehensive clinical characterization was correlated to genotype. We report the simultaneous confirmation of human CD27 deficiency in 3 independent families (8 patients) due to a homozygous mutation (p. Cys53Tyr) revealed by whole exome sequencing, leading to disruption of an evolutionarily conserved cystein knot motif of the transmembrane receptor. Phenotypes varied from asymptomatic memory B-cell deficiency (n=3) to EBV-associated hemophagocytosis and lymphoproliferative disorder (LPD; n=3) and malignant lymphoma (n=2; +1 after LPD). Following EBV infection, hypogammaglobulinemia developed in at least 3 of the affected individuals, while specific anti-viral and anti-polysaccharide antibodies and EBV-specific T-cell responses were detectable. In severely affected patients, numbers of iNKT cells and NK-cell function were reduced. Two of 8 patients died, 2 others underwent allogeneic hematopoietic stem cell transplantation successfully, and one received anti-CD20 (rituximab) therapy repeatedly. Since homozygosity mapping and exome sequencing did not reveal additional modifying factors, our findings suggest that lack of functional CD27 predisposes towards a combined immunodeficiency associated with potentially fatal EBV-driven hemo-phagocytosis, lymphoproliferation, and lymphoma development.
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Affiliation(s)
- Elisabeth Salzer
- CeMM Research Center for Molecular Medicine, Austrian Academy of Sciences, Vienna, Austria
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27
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Herbert MK, Ginzel S, Mühlschlegel S, Weis KH. Concomitant treatment with urodilatin (ularitide) does not improve renal function in patients with acute renal failure after major abdominal surgery--a randomized controlled trial. Wien Klin Wochenschr 1999; 111:141-7. [PMID: 10192146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Acute renal failure after major abdominal surgery is a severe complication in critically ill patients in intensive care units (ICU). The aim of the study was to investigate the effect of urodilatin on the peak value and course of serum creatinine in patients with acute renal insufficiency after major abdominal surgery and the necessity of apparatus-based renal replacement treatment. Furthermore, the incidence and nature of adverse events under urodilatin was documented. In a prospective randomized double-blind placebo-controlled study, 12 critically ill patients after major abdominal surgery with acute renal failure in an intensive care unit (ICU) received 20 ng/kg b.w./min urodilatin (ularitide, INN) or placebo in addition to the standard diuretic therapy or low-dose dopamine (2.5 micrograms/kg b.w./min) and furosemide (1000 mg/24 hr) for a minimum of 96 hours. All patients received mechanical ventilation. Both groups had similar serum creatinine values on the day before the onset of urodilatin/placebo infusion (2.80 +/- 0.24 mg/dl, 2.93 +/- 0.48 mg/dl). Peak serum creatinine was lower in the urodilatin group (4.65 +/- 0.57 mg/dl) compared to vehicle treatment (5.78 +/- 1.58 mg/dl), although the difference did not reach statistical significance (P = 0.148). The total number of hemodialyses due to oligo-/anuria and/or hyperkalemia was the same in both groups during the study. In 4 patients of the placebo group, diuresis was reduced to anuria, whereas only 1 of the patients treated with urodilatin became anuric. No hemodynamic side effects or adverse events due to urodilatin were observed. This clinical study under double blind conditions revealed that the addition of urodilatin to the standard diuretic therapy of low-dose dopamine and furosemide failed to improve renal function in patients with established acute renal failure and that urodilatin did not eliminate the need for apparatus-based renal replacement treatment.
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Affiliation(s)
- M K Herbert
- Department of Anaesthesiology, University of Würzburg, Federal Republic of Germany.
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