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Zhou Y, Ray PS, Zhu J, Stein F, Rettel M, Sekaran T, Sahadevan S, Perez-Perri JI, Roth EK, Myklebost O, Meza-Zepeda LA, von Deimling A, Fu C, Brosig AN, Boye K, Nathrath M, Blattmann C, Lehner B, Hentze MW, Kulozik AE. Systematic analysis of RNA-binding proteins identifies targetable therapeutic vulnerabilities in osteosarcoma. Nat Commun 2024; 15:2810. [PMID: 38561347 PMCID: PMC10984982 DOI: 10.1038/s41467-024-47031-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 03/18/2024] [Indexed: 04/04/2024] Open
Abstract
Osteosarcoma is the most common primary malignant bone tumor with a strong tendency to metastasize, limiting the prognosis of affected patients. Genomic, epigenomic and transcriptomic analyses have demonstrated the exquisite molecular complexity of this tumor, but have not sufficiently defined the underlying mechanisms or identified promising therapeutic targets. To systematically explore RNA-protein interactions relevant to OS, we define the RNA interactomes together with the full proteome and the transcriptome of cells from five malignant bone tumors (four osteosarcomata and one malignant giant cell tumor of the bone) and from normal mesenchymal stem cells and osteoblasts. These analyses uncover both systematic changes of the RNA-binding activities of defined RNA-binding proteins common to all osteosarcomata and individual alterations that are observed in only a subset of tumors. Functional analyses reveal a particular vulnerability of these tumors to translation inhibition and a positive feedback loop involving the RBP IGF2BP3 and the transcription factor Myc which affects cellular translation and OS cell viability. Our results thus provide insight into potentially clinically relevant RNA-binding protein-dependent mechanisms of osteosarcoma.
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Affiliation(s)
- Yang Zhou
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University and European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Partho Sarothi Ray
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University and European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Jianguo Zhu
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Frank Stein
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Mandy Rettel
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | | | - Sudeep Sahadevan
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | | | - Eva K Roth
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University and European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Ola Myklebost
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Leonardo A Meza-Zepeda
- Genomics Core Facility, Department of Core Facilities, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
| | - Chuli Fu
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Annika N Brosig
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University and European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Kjetil Boye
- Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Michaela Nathrath
- Department of Pediatrics and Children's Cancer Research Center, Technical University of Munich, School of Medicine, Munich, Germany
- Pediatric Hematology and Oncology, Klinikum Kassel, Kassel, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Olga Hospital, Stuttgart, Germany
| | - Claudia Blattmann
- Department of Pediatric Oncology, Hematology and Immunology, Olga Hospital, Stuttgart, Germany
| | - Burkhard Lehner
- Department of Orthopaedics, Trauma Surgery and Paraplegiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Matthias W Hentze
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University and European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
| | - Andreas E Kulozik
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University and European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany.
- Clinical Cooperation Unit Pediatric Leukemia, German Cancer Research Center (DKFZ) and Heidelberg University, Heidelberg, Germany.
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2
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Wildenberg NP, Rossi C, Kulozik AE, Kunz JB. Hb Santa Juana ( β 108(G10) Asn > Ser): a low oxygen affinity hemoglobin variant in a family of Bosnian background. Hematology 2023; 28:2184120. [PMID: 36867085 DOI: 10.1080/16078454.2023.2184120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023] Open
Abstract
We present a family that carries the β-hemoglobin variant Hb Santa Juana (HBB:c.326A>G, β 108(G10) Asn>Ser), also known as Hb Serres, in three generations. All affected family members had an anomal hemoglobin fraction as detected by HPLC but normal blood count without evidence of anemia or hemolysis. Oxygen affinity (p50 (O2) = 31.9-40.4 mmHg) was decreased in all probands, compared to 24.9-28.1 mmHg in unaffected individuals. Clinical symptoms likely related to the hemoglobin variant were cyanosis during anaesthesia, while other complaints such as shortness of breath or dizziness were less clearly linked with the hemoglobin variant.
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Affiliation(s)
- N P Wildenberg
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, Heidelberg, Germany.,Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - C Rossi
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, Heidelberg, Germany.,Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - A E Kulozik
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, Heidelberg, Germany.,Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - J B Kunz
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, Heidelberg, Germany.,Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
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3
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Serjeant GR, Serjeant BE, Mason KP, Gibson F, Gardner RA, Warren L, Reid M, Happich M, Kulozik AE. The beta thalassaemia trait in Jamaica. J Community Genet 2023; 14:355-360. [PMID: 37391652 PMCID: PMC10444720 DOI: 10.1007/s12687-023-00657-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 06/25/2023] [Indexed: 07/02/2023] Open
Abstract
The objective of this study was to review the prevalence and features of the beta thalassaemia trait in Jamaican populations. Screening of 221,306 newborns over the last 46 years has given an indication of the distribution and prevalence of beta thalassaemia genes, and screening of 16,612 senior school students in Manchester parish, central Jamaica, has provided their haematological features. The prevalence of the beta thalassaemia trait predicted from double heterozygotes was 0.8% of 100,000 babies in Kingston, 0.9% of 121,306 newborns in southwest Jamaica, and 0.9% of school students in Manchester. Mild beta+ thalassaemia variants (-88 C>T, -29 A>G, -90 C>T, polyA T>C) accounted for 75% of Kingston newborns, 76% of newborns in southwest Jamaica, and 89% of Manchester students. Severe beta+ thalassaemia variants were uncommon. Betao thalassaemia variants occurred in 43 patients and resulted from 11 different variants of which the IVSII-849 A>G accounted for 25 (58%) subjects. Red cell indices in IVSII-781 C>G did not differ significantly from HbAA, and this is probably a harmless polymorphism rather than a form of beta+ thalassaemia; the removal of 6 cases in school screening had a minimal effect on the frequency of the beta thalassaemia trait. Red cell indices in the beta+ and betao thalassaemia traits followed established patterns, although both were associated with increased HbF levels. The benign nature of beta+ thalassaemia genes in Jamaica means that cases of sickle cell-beta+ thalassaemia are likely to be overlooked, and important clinical questions such as the role of pneumococcal prophylaxis remain to be answered.
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Affiliation(s)
- G R Serjeant
- Sickle Cell Trust, 14 Milverton Cres, Kingston 6, Jamaica.
| | - B E Serjeant
- Sickle Cell Trust, 14 Milverton Cres, Kingston 6, Jamaica
| | - K P Mason
- Sickle Cell Trust, 14 Milverton Cres, Kingston 6, Jamaica
| | - F Gibson
- Sickle Cell Trust, 14 Milverton Cres, Kingston 6, Jamaica
| | - R-A Gardner
- Sickle Cell Trust, 14 Milverton Cres, Kingston 6, Jamaica
| | - L Warren
- Sickle Cell Trust, 14 Milverton Cres, Kingston 6, Jamaica
| | - M Reid
- Faculty of Medical Sciences, University of the West Indies, Mona, Kingston 7, Jamaica
| | - M Happich
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany
| | - A E Kulozik
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany
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4
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Lee OW, Rodrigues C, Lin SH, Luo W, Jones K, Brown DW, Zhou W, Karlins E, Khan SM, Baulande S, Raynal V, Surdez D, Reynaud S, Rubio RA, Zaidi S, Grossetête S, Ballet S, Lapouble E, Laurence V, Pierron G, Gaspar N, Corradini N, Marec-Bérard P, Rothman N, Dagnall CL, Burdett L, Manning M, Wyatt K, Yeager M, Chari R, Leisenring WM, Kulozik AE, Kriebel J, Meitinger T, Strauch K, Kirchner T, Dirksen U, Mirabello L, Tucker MA, Tirode F, Armstrong GT, Bhatia S, Robison LL, Yasui Y, Romero-Pérez L, Hartmann W, Metzler M, Diver WR, Lori A, Freedman ND, Hoover RN, Morton LM, Chanock SJ, Grünewald TGP, Delattre O, Machiela MJ. Targeted long-read sequencing of the Ewing sarcoma 6p25.1 susceptibility locus identifies germline-somatic interactions with EWSR1-FLI1 binding. Am J Hum Genet 2023; 110:427-441. [PMID: 36787739 PMCID: PMC10027473 DOI: 10.1016/j.ajhg.2023.01.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 01/23/2023] [Indexed: 02/16/2023] Open
Abstract
Ewing sarcoma (EwS) is a rare bone and soft tissue malignancy driven by chromosomal translocations encoding chimeric transcription factors, such as EWSR1-FLI1, that bind GGAA motifs forming novel enhancers that alter nearby expression. We propose that germline microsatellite variation at the 6p25.1 EwS susceptibility locus could impact downstream gene expression and EwS biology. We performed targeted long-read sequencing of EwS blood DNA to characterize variation and genomic features important for EWSR1-FLI1 binding. We identified 50 microsatellite alleles at 6p25.1 and observed that EwS-affected individuals had longer alleles (>135 bp) with more GGAA repeats. The 6p25.1 GGAA microsatellite showed chromatin features of an EWSR1-FLI1 enhancer and regulated expression of RREB1, a transcription factor associated with RAS/MAPK signaling. RREB1 knockdown reduced proliferation and clonogenic potential and reduced expression of cell cycle and DNA replication genes. Our integrative analysis at 6p25.1 details increased binding of longer GGAA microsatellite alleles with acquired EWSR-FLI1 to promote Ewing sarcomagenesis by RREB1-mediated proliferation.
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Affiliation(s)
- Olivia W Lee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Calvin Rodrigues
- Inserm U830, PSL Université, Research Center, Institut Curie, 75005 Paris, France; SIREDO Oncology Centre, Institut Curie, 75005 Paris, France
| | - Shu-Hong Lin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Wen Luo
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Kristine Jones
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Derek W Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Weiyin Zhou
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Eric Karlins
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Sairah M Khan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Sylvain Baulande
- ICGex Next-Generation Sequencing Platform, PSL Université, Research Center, Institut Curie, 75005 Paris, France
| | - Virginie Raynal
- ICGex Next-Generation Sequencing Platform, PSL Université, Research Center, Institut Curie, 75005 Paris, France
| | - Didier Surdez
- Inserm U830, PSL Université, Research Center, Institut Curie, 75005 Paris, France; SIREDO Oncology Centre, Institut Curie, 75005 Paris, France; Balgrist University Hospital, Faculty of Medicine, University of Zurich (UZH), Zurich, Switzerland
| | - Stephanie Reynaud
- SIREDO Oncology Centre, Institut Curie, 75005 Paris, France; Unité de Génétique Somatique, Department of Genetics, Institut Curie Hospital, 75005 Paris, France
| | - Rebeca Alba Rubio
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU, 80337 Munich, Germany
| | - Sakina Zaidi
- Inserm U830, PSL Université, Research Center, Institut Curie, 75005 Paris, France; SIREDO Oncology Centre, Institut Curie, 75005 Paris, France
| | - Sandrine Grossetête
- Inserm U830, PSL Université, Research Center, Institut Curie, 75005 Paris, France; SIREDO Oncology Centre, Institut Curie, 75005 Paris, France
| | - Stelly Ballet
- SIREDO Oncology Centre, Institut Curie, 75005 Paris, France; Unité de Génétique Somatique, Department of Genetics, Institut Curie Hospital, 75005 Paris, France
| | - Eve Lapouble
- SIREDO Oncology Centre, Institut Curie, 75005 Paris, France; Unité de Génétique Somatique, Department of Genetics, Institut Curie Hospital, 75005 Paris, France
| | | | - Gaelle Pierron
- SIREDO Oncology Centre, Institut Curie, 75005 Paris, France; Unité de Génétique Somatique, Department of Genetics, Institut Curie Hospital, 75005 Paris, France
| | - Nathalie Gaspar
- Department of Oncology for Child and Adolescent, Institut Gustave Roussy, 94800 Villejuif, France
| | - Nadège Corradini
- Institute for Paediatric Haematology and Oncology, Leon Bérard Cancer Centre, University of Lyon, 69008 Lyon, France
| | - Perrine Marec-Bérard
- Institute for Paediatric Haematology and Oncology, Leon Bérard Cancer Centre, University of Lyon, 69008 Lyon, France
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Casey L Dagnall
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Laurie Burdett
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Michelle Manning
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Kathleen Wyatt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Raj Chari
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Genome Modification Core Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Wendy M Leisenring
- Cancer Prevention and Clinical Statistics Programs, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Andreas E Kulozik
- University Children's Hospital of Heidelberg, 69120 Heidelberg, Germany
| | - Jennifer Kriebel
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 München-Neuherberg, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; Institute of Human Genetics, Technische Universität München, 80333 Munich, Germany
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU, 80539 Munich, Germany
| | - Thomas Kirchner
- Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany; Institute of Pathology, Faculty of Medicine, LMU, 80337 Munich, Germany
| | - Uta Dirksen
- University Children's Hospital of Essen, 45147 Essen, Germany
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Margaret A Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Franck Tirode
- Inserm U830, PSL Université, Research Center, Institut Curie, 75005 Paris, France; SIREDO Oncology Centre, Institut Curie, 75005 Paris, France
| | - Gregory T Armstrong
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Smita Bhatia
- Institute for Cancer Outcomes and Survivorship, University of Alabama, Birmingham, AL 35294, USA
| | - Leslie L Robison
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yutaka Yasui
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Laura Romero-Pérez
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU, 80337 Munich, Germany; Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany
| | - Wolfgang Hartmann
- Gerhard- Domagk Institute of Pathology, University Hospital of Münster, 48149 Münster, Germany
| | - Markus Metzler
- University Children's Hospital of Erlangen, 91054 Erlangen, Germany
| | - W Ryan Diver
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Adriana Lori
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Neal D Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Robert N Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Lindsay M Morton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Thomas G P Grünewald
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU, 80337 Munich, Germany; Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany; Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Olivier Delattre
- Inserm U830, PSL Université, Research Center, Institut Curie, 75005 Paris, France; SIREDO Oncology Centre, Institut Curie, 75005 Paris, France.
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA.
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5
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Olson TS, Walters MC, Kwiatkowski JL, Porter JB, Schneiderman J, Hongeng S, Kulozik AE, Cavazzana M, Sauer MG, Thrasher AJ, Thuret I, Lal A, Rasko JE, Yannaki E, Ali S, Colvin RA, Locatelli F, Thompson AA. Long-term Outcomes of 63 Patients with Transfusion-Dependent β-Thalassemia (TDT) Followed-up to 7 Years after Treatment with betibeglogene autotemcel (beti-cel) Gene Therapy (GT) and Factors Impacting Neutrophil and Platelet Engraftment. Transplant Cell Ther 2023. [DOI: 10.1016/s2666-6367(23)00454-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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6
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Jeong H, Grimes K, Rauwolf KK, Bruch PM, Rausch T, Hasenfeld P, Benito E, Roider T, Sabarinathan R, Porubsky D, Herbst SA, Erarslan-Uysal B, Jann JC, Marschall T, Nowak D, Bourquin JP, Kulozik AE, Dietrich S, Bornhauser B, Sanders AD, Korbel JO. Functional analysis of structural variants in single cells using Strand-seq. Nat Biotechnol 2022:10.1038/s41587-022-01551-4. [PMID: 36424487 DOI: 10.1038/s41587-022-01551-4] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 10/07/2022] [Indexed: 11/27/2022]
Abstract
Somatic structural variants (SVs) are widespread in cancer, but their impact on disease evolution is understudied due to a lack of methods to directly characterize their functional consequences. We present a computational method, scNOVA, which uses Strand-seq to perform haplotype-aware integration of SV discovery and molecular phenotyping in single cells by using nucleosome occupancy to infer gene expression as a readout. Application to leukemias and cell lines identifies local effects of copy-balanced rearrangements on gene deregulation, and consequences of SVs on aberrant signaling pathways in subclones. We discovered distinct SV subclones with dysregulated Wnt signaling in a chronic lymphocytic leukemia patient. We further uncovered the consequences of subclonal chromothripsis in T cell acute lymphoblastic leukemia, which revealed c-Myb activation, enrichment of a primitive cell state and informed successful targeting of the subclone in cell culture, using a Notch inhibitor. By directly linking SVs to their functional effects, scNOVA enables systematic single-cell multiomic studies of structural variation in heterogeneous cell populations.
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Affiliation(s)
- Hyobin Jeong
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Hanyang Institute of Bioscience and Biotechnology, Hanyang University, Seoul, Republic of Korea
| | - Karen Grimes
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Faculty of Biosciences, EMBL and Heidelberg University, Heidelberg, Germany
| | - Kerstin K Rauwolf
- Division of Pediatric Oncology, University Children's Hospital, Zürich, Switzerland
| | - Peter-Martin Bruch
- Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany.,Department of Hematology and Oncology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Tobias Rausch
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany
| | - Patrick Hasenfeld
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Eva Benito
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Tobias Roider
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany
| | | | - David Porubsky
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany.,Max Planck Institute for Informatics, Saarbrücken, Germany.,Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Sophie A Herbst
- Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany
| | - Büşra Erarslan-Uysal
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg and Hopp Children's Cancer Center, Heidelberg, Germany
| | - Johann-Christoph Jann
- Department of Hematology and Oncology, Medical Faculty Mannheim of the Heidelberg University, Heidelberg, Germany
| | - Tobias Marschall
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Daniel Nowak
- Department of Hematology and Oncology, Medical Faculty Mannheim of the Heidelberg University, Heidelberg, Germany
| | - Jean-Pierre Bourquin
- Division of Pediatric Oncology, University Children's Hospital, Zürich, Switzerland
| | - Andreas E Kulozik
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg and Hopp Children's Cancer Center, Heidelberg, Germany
| | - Sascha Dietrich
- Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany.,Department of Hematology and Oncology, University Hospital Düsseldorf, Düsseldorf, Germany.,Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Beat Bornhauser
- Division of Pediatric Oncology, University Children's Hospital, Zürich, Switzerland
| | - Ashley D Sanders
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany. .,Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany. .,Berlin Institute of Health (BIH), Berlin, Germany. .,Charité-Universitätsmedizin, Berlin, Germany.
| | - Jan O Korbel
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany. .,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany. .,Bridging Research Division on Mechanisms of Genomic Variation and Data Science, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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7
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Serjeant GR, Serjeant BE, Mason KP, Gibson F, Gardner RA, Warren L, Hambleton IR, Thein SL, Happich M, Kulozik AE. Newborn screening for abnormal haemoglobins in Jamaica: Practical issues in an island programme. J Med Screen 2022; 29:219-223. [PMID: 35934992 DOI: 10.1177/09691413221111209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
OBJECTIVE To report the diagnostic challenges of newborn screening for abnormal haemoglobins. SETTING Cord blood samples from 13 hospitals in southwest Jamaica taken in 2008-2019. METHODS Blood spots, collected from the umbilical cord, were analysed by high pressure liquid chromatography (HPLC) to reveal phenotypes for HbSS and HbCC, but genotype confirmation may require parental studies or gene sequencing. Such cases that were successfully traced were analysed in this follow-up study. RESULTS HPLC screening of 121,306 samples detected HbAS in 11,846 (9.8%), HbAC in 4508 (3.7%) and other electrophoretic abnormalities in 1090 babies. Among 101 previously unconfirmed cases, 34/90 (38%) with HPLC evidence of a HbSS phenotype had other genotypes, and 7/11 (64%) with a HbCC phenotype had other genotypes. Syndromes from the interaction of β thalassaemia occurred in 112 babies (85 with HbS, 27 with HbC) and of genes for hereditary persistence of fetal haemoglobin (HPFH) in 18 (12 with HbS, 6 with HbC). Variants other than HbS and HbC occurred in 270 babies, 16 in combination with either HbS or HbC, and 254 as traits. Most variants are benign even when inherited with HbS, although HbO Arab, HbD Punjab, or Hb Lepore Washington, which occurred in 6 cases, may cause sickle cell disease. CONCLUSIONS Genes for β thalassaemia and HPFH are common in western Jamaica and when associated with HbS may present diagnostic challenges in newborns, as HbF and HbA2 have not reached diagnostic levels. Family and DNA studies may be necessary for genotype confirmation.
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Affiliation(s)
| | | | | | | | | | | | - Ian R Hambleton
- Sir George Alleyne Chronic Disease Research Centre, The University of the West Indies, Cave Hill, Barbados
| | - Swee L Thein
- Sickle Cell Branch, National Heart, Lung and Blood Institutes, 2511National Institutes of Health, Bethesda, Maryland, USA
| | - Margit Happich
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany
| | - Andreas E Kulozik
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany
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8
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Muckenthaler L, Marques O, Colucci S, Kunz J, Fabrowski P, Bast T, Altamura S, Höchsmann B, Schrezenmeier H, Langlotz M, Richter-Pechanska P, Rausch T, Hofmeister-Mielke N, Gunkel N, Hentze MW, Kulozik AE, Muckenthaler MU. Constitutional PIGA mutations cause a novel subtype of hemochromatosis in patients with neurologic dysfunction. Blood 2022; 139:1418-1422. [PMID: 34875027 PMCID: PMC10652939 DOI: 10.1182/blood.2021013519] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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: 07/30/2021] [Accepted: 11/22/2021] [Indexed: 11/20/2022] Open
Abstract
Muckenthaler et al describe a novel form of hemochromatosis caused by a constitutional PIGA mutation in 3 children with associated neurologic dysfunction. Hemochromatosis results from decreased hepcidin, which is regulated by HFE, hemojuvelin (HJV), and transferrin receptor 2. HJV is a glycosylphosphatidylinositol-linked protein, so PIGA mutation leads to decreased HJV expression. Interestingly, none of the children had evidence of paroxysmal nocturnal hemoglobinuria. The cause of the novel association with central nervous system manifestations remains to be elucidated.
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Affiliation(s)
- Lena Muckenthaler
- Department of Pediatric Oncology, Hematology and Immunology and Hopp Children Cancer Center, University Hospital Heidelberg, Heidelberg, Germany
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany
| | - Oriana Marques
- Department of Pediatric Oncology, Hematology and Immunology and Hopp Children Cancer Center, University Hospital Heidelberg, Heidelberg, Germany
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany
| | - Silvia Colucci
- Department of Pediatric Oncology, Hematology and Immunology and Hopp Children Cancer Center, University Hospital Heidelberg, Heidelberg, Germany
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany
| | - Joachim Kunz
- Department of Pediatric Oncology, Hematology and Immunology and Hopp Children Cancer Center, University Hospital Heidelberg, Heidelberg, Germany
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany
| | - Piotr Fabrowski
- Cancer Drug Development Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thomas Bast
- Pediatric Epilepsy Centre, Diaconia Kork, Kehl-Kork, Germany
| | - Sandro Altamura
- Department of Pediatric Oncology, Hematology and Immunology and Hopp Children Cancer Center, University Hospital Heidelberg, Heidelberg, Germany
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany
| | - Britta Höchsmann
- Department of Transfusion Medicine and Immunogenetics, University Hospital Ulm, Ulm, Germany
| | - Hubert Schrezenmeier
- Department of Transfusion Medicine and Immunogenetics, University Hospital Ulm, Ulm, Germany
| | - Monika Langlotz
- Flow Cytometry & FACS Core Facility, Centre of Molecular Biology, University of Heidelberg, Heidelberg, Germany
| | - Paulina Richter-Pechanska
- Department of Pediatric Oncology, Hematology and Immunology and Hopp Children Cancer Center, University Hospital Heidelberg, Heidelberg, Germany
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany
| | - Tobias Rausch
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany
- Genome Biology Unit, EMBL, Heidelberg, Germany
| | | | - Nikolas Gunkel
- Cancer Drug Development Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Andreas E. Kulozik
- Department of Pediatric Oncology, Hematology and Immunology and Hopp Children Cancer Center, University Hospital Heidelberg, Heidelberg, Germany
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany
| | - Martina U. Muckenthaler
- Department of Pediatric Oncology, Hematology and Immunology and Hopp Children Cancer Center, University Hospital Heidelberg, Heidelberg, Germany
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany
- Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research, University of Heidelberg, Heidelberg, Germany; and
- German Centre for Cardiovascular Research (DZHK), Partner Site, Heidelberg/Mannheim, Germany
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9
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Kunz JB, Roth E, Mirza A, Greil J, Pavel P, Schmitt A, Schmitt M, Kunz AE, Kulozik AE. The First Real-World Experience with Betibeglogene Autotemcel (beti-cel) Gene Therapy Treatment for Transfusion-Dependent β-Thalassemia (TDT). Transplant Cell Ther 2022. [DOI: 10.1016/s2666-6367(22)00448-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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10
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Schneiderman J, Locatelli F, Thompson AA, Kwiatkowski JL, Porter JB, Hongeng S, Kulozik AE, Cavazzana M, Sauer MG, Thrasher AJ, Thuret I, Lal A, Rasko JE, Yannaki E, Schmidt M, Du L, Colvin RA, Walters MC. Efficacy and Safety of Betibeglogene Autotemcel (beti-cel) Gene Therapy in 63 Patients with Transfusion-Dependent β-Thalassemia (TDT): 7-Year Post-Infusion Follow-up of Phase 1/2 and Phase 3 Studies. Transplant Cell Ther 2022. [DOI: 10.1016/s2666-6367(22)00189-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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11
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Serjeant GR, Serjeant BE, Mason KP, Gibson F, Osmond C, Thein SL, Happich M, Kulozik AE. The haematology of Jamaicans: red cell indices in HbAA, HbAS, HbAC, and HbA-HPFH genotypes. J Community Genet 2022; 13:229-234. [PMID: 35018573 DOI: 10.1007/s12687-021-00575-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 12/22/2021] [Indexed: 11/24/2022] Open
Abstract
Based in the parish of Manchester in central Jamaica, the Manchester Project offered free detection of haemoglobin genotype to senior classes in 15 secondary schools between 2008 and 2013. Restricting the database to 15,103 students aged 15.0-19.9 years provided an opportunity to examine the red cell characteristics of the different haemoglobin genotypes, including normal (HbAA) in 85.0%, the sickle cell trait (HbAS) in 9.7%, HbC trait (HbAC) in 3.5% and hereditary persistence of foetal haemoglobin (HbA-HPFH) in 0.4%. Compared to the normal HbAA phenotype, HbAS had significantly increased mean cell haemoglobin concentration (MCHC), red cell count (RBC), and red cell distribution width (RDW) and decreased mean cell volume (MCV) and mean cell haemoglobin (MCH), these differences being even more marked in HbAC. Compared to HbAA, the HbA-HPFH had significantly increased RDW, but there were no consistent differences in other red cell indices, and there were no significant differences in haematological indices between the two common deletion HPFH variants, HPFH-1 and HPFH-2. Although these changes are unlikely to be clinically significant, they contribute to an understanding of the haematological spectrum of the common haemoglobin genotypes in peoples of African origin.
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Affiliation(s)
- G R Serjeant
- Sickle Cell Trust, 14 Milverton Cres, Kingston, Jamaica.
| | - B E Serjeant
- Sickle Cell Trust, 14 Milverton Cres, Kingston, Jamaica
| | - K P Mason
- Sickle Cell Trust, 14 Milverton Cres, Kingston, Jamaica
| | - F Gibson
- Sickle Cell Trust, 14 Milverton Cres, Kingston, Jamaica
| | - C Osmond
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, England
| | - S L Thein
- Sickle Cell Branch, National Heart, Lung and Blood Institutes National Institutes of Health, Bethesda, MD, USA
| | - M Happich
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany
| | - A E Kulozik
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany
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12
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Abstract
RNA-binding proteins are key mediators of many of the RNA-regulatory functions throughout the RNA life cycle in the nucleus and in the cytoplasm. The invention and the recent refinement of the RNA-interactome capture technology has now enabled the analysis of the global RNA-interactome in living cells in the nucleus and in the cytoplasm separately. This technology thus allows an unprecedented differential view on the function of RNA-binding proteins in these compartments. Here we describe a method combining nucleo-cytoplasmic fractionation and enhanced RNA-interactome capture (eRIC) for studying RBPs binding to polyadenylated RNAs separately in the cytoplasmic and in the nuclear compartments.
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Affiliation(s)
- Michael Backlund
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University, Heidelberg, Germany
- Hopp Children's Cancer Center, National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Andreas E Kulozik
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University, Heidelberg, Germany.
- Hopp Children's Cancer Center, National Center for Tumor Diseases (NCT), Heidelberg, Germany.
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, Heidelberg, Germany.
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
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13
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Gattermann N, Muckenthaler M, Kulozik AE, Metzgeroth G, Hastka J. The Evaluation Of Iron Deficiency And Iron Overload. Dtsch Arztebl Int 2021; 118:847-856. [PMID: 34755596 DOI: 10.3238/arztebl.m2021.0290] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 02/10/2021] [Accepted: 07/07/2021] [Indexed: 11/27/2022]
Abstract
BACKGROUND In the western world, 2-5% of women of child-bearing age suffer from irondeficiency anemia. Iron overload due to chronic treatment with blood transfusions or hereditary hemochromatosis is much rarer. METHODS This review is based on pertinent publications retrieved by a selective search on the pathophysiology, clinical features, and diagnostic evaluation of iron deficiency and iron overload. RESULTS The main causes of iron deficiency are malnutrition and blood loss. Its differential diagnosis includes iron-refractory iron deficiency anemia (IRIDA), a rare congenital disease in which the hepcidin level is pathologically elevated, as well as the more common anemia of chronic disease (anemia of chronic inflammation), in which increased amounts of hepcidin are formed under the influence of interleukin-6 and enteric iron uptake is blocked as a result. Iron overload comes about through long-term transfusion treatment or a congenital disturbance of iron metabolism (hemochromatosis). Its diagnostic evaluation is based on clinical and laboratory findings, imaging studies, and specific mutation analyses. CONCLUSION Our improving understanding of the molecular pathophysiology of iron metabolism aids in the evaluation of iron deficiency and iron overload and may in future enable treatment not just with iron supplementation or iron chelation, but also with targeted pharmacological modulation of the hepcidin regulatory system.
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14
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van Tilburg CM, Pfaff E, Pajtler KW, Langenberg KP, Fiesel P, Jones BC, Balasubramanian GP, Stark S, Johann PD, Blattner-Johnson M, Schramm K, Dikow N, Hirsch S, Sutter C, Grund K, von Stackelberg A, Kulozik AE, Lissat A, Borkhardt A, Meisel R, Reinhardt D, Klusmann JH, Fleischhack G, Tippelt S, von Schweinitz D, Schmid I, Kramm CM, von Bueren AO, Calaminus G, Vorwerk P, Graf N, Westermann F, Fischer M, Eggert A, Burkhardt B, Wößmann W, Nathrath M, Hecker-Nolting S, Frühwald MC, Schneider DT, Brecht IB, Ketteler P, Fulda S, Koscielniak E, Meister MT, Scheer M, Hettmer S, Schwab M, Tremmel R, Øra I, Hutter C, Gerber NU, Lohi O, Kazanowska B, Kattamis A, Filippidou M, Goemans B, Zwaan CM, Milde T, Jäger N, Wolf S, Reuss D, Sahm F, von Deimling A, Dirksen U, Freitag A, Witt R, Lichter P, Kopp-Schneider A, Jones DT, Molenaar JJ, Capper D, Pfister SM, Witt O. The Pediatric Precision Oncology INFORM Registry: Clinical Outcome and Benefit for Patients with Very High-Evidence Targets. Cancer Discov 2021; 11:2764-2779. [PMID: 34373263 PMCID: PMC9414287 DOI: 10.1158/2159-8290.cd-21-0094] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [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] [Received: 01/22/2021] [Revised: 05/26/2021] [Accepted: 07/28/2021] [Indexed: 01/26/2023]
Abstract
INFORM is a prospective, multinational registry gathering clinical and molecular data of relapsed, progressive, or high-risk pediatric patients with cancer. This report describes long-term follow-up of 519 patients in whom molecular alterations were evaluated according to a predefined seven-scale target prioritization algorithm. Mean turnaround time from sample receipt to report was 25.4 days. The highest target priority level was observed in 42 patients (8.1%). Of these, 20 patients received matched targeted treatment with a median progression-free survival of 204 days [95% confidence interval (CI), 99-not applicable], compared with 117 days (95% CI, 106-143; P = 0.011) in all other patients. The respective molecular targets were shown to be predictive for matched treatment response and not prognostic surrogates for improved outcome. Hereditary cancer predisposition syndromes were identified in 7.5% of patients, half of which were newly identified through the study. Integrated molecular analyses resulted in a change or refinement of diagnoses in 8.2% of cases. SIGNIFICANCE: The pediatric precision oncology INFORM registry prospectively tested a target prioritization algorithm in a real-world, multinational setting and identified subgroups of patients benefiting from matched targeted treatment with improved progression-free survival, refinement of diagnosis, and identification of hereditary cancer predisposition syndromes.See related commentary by Eggermont et al., p. 2677.This article is highlighted in the In This Issue feature, p. 2659.
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Affiliation(s)
- Cornelis M. van Tilburg
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Corresponding Author: Cornelis M. van Tilburg, Hopp Children's Cancer Center Heidelberg (KiTZ), German Cancer Research Center (DKFZ) and Heidelberg University Hospital, Im Neuenheimer Feld 430, Heidelberg 69120, Germany. Phone: 00-49-6221-56-36926; E-mail:
| | - Elke Pfaff
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kristian W. Pajtler
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Petra Fiesel
- German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Barbara C. Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Gnana Prakash Balasubramanian
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sebastian Stark
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Pascal D. Johann
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Swabian Children's Cancer Center, Paediatric and Adolescent Medicine, University Medical Center Augsburg, Augsburg, Germany
| | - Mirjam Blattner-Johnson
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kathrin Schramm
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nicola Dikow
- Institute of Human Genetics, Heidelberg University Hospital, Heidelberg, Germany
| | - Steffen Hirsch
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Institute of Human Genetics, Heidelberg University Hospital, Heidelberg, Germany
| | - Christian Sutter
- Institute of Human Genetics, Heidelberg University Hospital, Heidelberg, Germany
| | - Kerstin Grund
- Institute of Human Genetics, Heidelberg University Hospital, Heidelberg, Germany
| | - Arend von Stackelberg
- German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Pediatric Oncology and Hematology Department, Charité–Campus Virchow Klinikum, Berlin, Germany
| | - Andreas E. Kulozik
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Clinical Cooperation Unit Pediatric Leukemia, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andrej Lissat
- German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Pediatric Oncology and Hematology Department, Charité–Campus Virchow Klinikum, Berlin, Germany
| | - Arndt Borkhardt
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of Pediatric Oncology and Hematology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Roland Meisel
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Division of Pediatric Stem Cell Therapy, Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Dirk Reinhardt
- German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,West German Cancer Center, Pediatrics III, University Hospital Essen, Essen, Germany
| | - Jan-Henning Klusmann
- Department of Pediatric Hematology, Oncology and Hemostaseology, Clinic for Pediatrics, University Hospital of Frankfurt, Goethe-University Frankfurt, Frankfurt/Main, Germany
| | - Gudrun Fleischhack
- German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,West German Cancer Center, Pediatrics III, University Hospital Essen, Essen, Germany
| | - Stephan Tippelt
- German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,West German Cancer Center, Pediatrics III, University Hospital Essen, Essen, Germany
| | - Dietrich von Schweinitz
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of Pediatric Surgery, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Irene Schmid
- Department of Pediatric Oncology and Hematology, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Christof M. Kramm
- Division of Pediatric Hematology and Oncology, University Medical Center Göttingen, Göttingen, Germany
| | - André O. von Bueren
- Department of Pediatrics, Obstetrics and Gynecology, Division of Pediatric Hematology and Oncology, University Hospital Geneva, Geneva, Switzerland
| | - Gabriele Calaminus
- Department of Pediatric Oncology and Hematology, University Hospital Bonn, Bonn, Germany
| | - Peter Vorwerk
- Department of Pediatric Oncology and Hematology, University Hospital Magdeburg, Magdeburg, Germany
| | - Norbert Graf
- Department of Pediatric Oncology and Hematology, University Hospital Saarland, Saarland, Germany
| | - Frank Westermann
- German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Division of Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matthias Fischer
- National Center for Tumor Diseases (NCT) Network, Germany.,Department of Experimental Pediatric Oncology, University Hospital Köln, and Center for Molecular Medicine (CMMC), Medical Faculty, Cologne, Germany
| | - Angelika Eggert
- German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Pediatric Oncology and Hematology Department, Charité–Campus Virchow Klinikum, Berlin, Germany
| | - Birgit Burkhardt
- Clinic of Pediatric Oncology and Hematology, University Hospital Münster, Muenster, Germany
| | - Wilhelm Wößmann
- Department of Pediatric Oncology and Hematology, University Hospital Hamburg, Hamburg, Germany
| | - Michaela Nathrath
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of Pediatric Hematology and Oncology, Klinikum Kassel, Kassel, Germany.,Department of Pediatrics, Technical University Munich, Munich, Germany
| | - Stefanie Hecker-Nolting
- National Center for Tumor Diseases (NCT) Network, Germany.,Department of Pediatric Oncology, Hematology and Immunology, Klinikum Stuttgart, Olgahospital, Stuttgart, Germany
| | - Michael C. Frühwald
- National Center for Tumor Diseases (NCT) Network, Germany.,Swabian Children's Cancer Center, Paediatric and Adolescent Medicine, University Medical Center Augsburg, Augsburg, Germany
| | | | - Ines B. Brecht
- German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Department of Pediatric Oncology and Hematology, University Hospital Tübingen, Tübingen, Germany
| | - Petra Ketteler
- German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,West German Cancer Center, Pediatrics III, University Hospital Essen, Essen, Germany
| | - Simone Fulda
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Institute for Experimental Cancer Research in Pediatrics, Goethe University Frankfurt, Frankfurt, Germany
| | - Ewa Koscielniak
- National Center for Tumor Diseases (NCT) Network, Germany.,Department of Pediatric Oncology, Hematology and Immunology, Klinikum Stuttgart, Olgahospital, Stuttgart, Germany
| | - Michael T. Meister
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Monika Scheer
- German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Pediatric Oncology and Hematology Department, Charité–Campus Virchow Klinikum, Berlin, Germany
| | - Simone Hettmer
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of Pediatrics and Adolescent Medicine, Division of Pediatric Hematology and Oncology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Matthias Schwab
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,Departments of Clinical Pharmacology, Pharmacy and Biochemistry, and Cluster of Excellence iFIT (EXC 2180) “Image-Guided and Functionally Instructed Tumor Therapies,” University of Tübingen, Tübingen, Germany
| | - Roman Tremmel
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
| | - Ingrid Øra
- Department of Pediatric Oncology and Hematology, Skane University Hospital Lund, and HOPE-ITCC Unit, Pediatric Oncology, Karolinska University Hospital, Stockholm, Sweden
| | - Caroline Hutter
- St. Anna Children's Hospital, Department of Pediatrics, Medical University of Vienna, and St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Nicolas U. Gerber
- Department of Oncology, University Children's Hospital, Zurich, Switzerland
| | - Olli Lohi
- Tampere Center for Child Health Research and Tays Cancer Centre, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Bernarda Kazanowska
- Department of Pediatric Hematology/Oncology and BMT, Wroclaw Medical University, Wroclaw, Poland
| | - Antonis Kattamis
- Division of Pediatric Hematology-Oncology, First Department of Pediatrics, National and Kapodistrian University of Athens, Athens, Greece
| | - Maria Filippidou
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Division of Pediatric Hematology-Oncology, First Department of Pediatrics, National and Kapodistrian University of Athens, Athens, Greece
| | - Bianca Goemans
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - C. Michel Zwaan
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Erasmus MC-Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Till Milde
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany
| | - Natalie Jäger
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stephan Wolf
- German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David Reuss
- German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Felix Sahm
- German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Andreas von Deimling
- German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Uta Dirksen
- German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,West German Cancer Center, Pediatrics III, University Hospital Essen, Essen, Germany
| | - Angelika Freitag
- NCT Trial Center, National Center for Tumor Diseases, Heidelberg, Germany, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ruth Witt
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany
| | - Peter Lichter
- German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Annette Kopp-Schneider
- German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Department Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David T.W. Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jan J. Molenaar
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Utrecht University, Department of Pharmaceutical Sciences, Utrecht, the Netherlands
| | - David Capper
- German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Neuropathology, Berlin, Germany
| | - Stefan M. Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Olaf Witt
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany
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15
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Lobitz S, Kunz J, Cario H, Hakimeh D, Jarisch A, Kulozik AE, Oevermann L, Grosse R. Neugeborenenscreening auf Sichelzellkrankheit in Deutschland. Geburtshilfe Frauenheilkd 2021. [DOI: 10.1055/a-1487-4774] [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: 10/19/2022] Open
Affiliation(s)
- Stephan Lobitz
- Klinik für Pädiatrische Hämatologie und Onkologie, Gemeinschaftsklinikum Mittelrhein, Koblenz, Deutschland
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16
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Allard P, Alhaj N, Lobitz S, Cario H, Jarisch A, Grosse R, Oevermann L, Hakimeh D, Tagliaferri L, Kohne E, Kopp-Schneider A, Kulozik AE, Kunz JB. Genetic modifiers of fetal hemoglobin affect the course of sickle cell disease in patients treated with hydroxyurea. Haematologica 2021; 107:1577-1588. [PMID: 34706496 PMCID: PMC9244815 DOI: 10.3324/haematol.2021.278952] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 04/11/2021] [Indexed: 11/09/2022] Open
Abstract
The course of sickle cell disease (SCD) is modified by polymorphisms boosting fetal hemoglobin (HbF) synthesis. However, it has remained an open question how these polymorphisms affect patients who are treated with the HbF-inducing drug hydroxyurea/hydroxycarbamide. The German SCD registry offers the opportunity to answer this question, because >90% of patients are treated according to national guidelines recommending the use of hydroxyurea in all patients above 2 years of age. We analyzed the modifying effect of HbF-related genetic polymorphisms in 417 patients with homozygous SCD >2 years who received hydroxyurea. HbF levels were correlated with higher total hemoglobin levels, lower rates of hemolysis, a lower frequency of painful crises and of red blood cell transfusions. The minor alleles of the polymorphisms in the γ-globin promoter (rs7482144), BCL11A (rs1427407) and HMIP (rs66650371) were strongly associated with increased HbF levels. However, these associations did not translate into lower frequencies of vasoocclusive events that did not differ between patients either carrying or not carrying the HMIP and BCL11A polymorphisms. Patients on hydroxyurea carrying the γ- globin promoter polymorphism demonstrated substantially higher hemoglobin levels (p.
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Affiliation(s)
- Pierre Allard
- Department of Pediatric Oncology, Hematology and Immunology, Hopp-Children's Cancer Center (KiTZ) Heidelberg, University of Heidelberg, Heidelberg
| | - Nareen Alhaj
- Abteilung Biostatistik, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg
| | - Stephan Lobitz
- Gemeinschaftsklinikum Mittelrhein, Kemperhof, Pädiatrische Hämatologie und Onkologie, Koblenz, Germany; GPOH Konsortium Sichelzellkrankheit
| | - Holger Cario
- GPOH Konsortium Sichelzellkrankheit; Universitätsklinikum Ulm, Klinik für Kinder- und Jugendmedizin, Pädiatrische Hämatologie und Onkologie, Ulm
| | - Andreas Jarisch
- GPOH Konsortium Sichelzellkrankheit; Klinikum der Johann-Wolfgang-Goethe-Universität, Zentrum für Kinder-und Jugendmedizin, Schwerpunkt Stammzelltransplantation und Immunologie, Frankfurt am Main
| | - Regine Grosse
- GPOH Konsortium Sichelzellkrankheit; Universitätsklinikum Hamburg-Eppendorf, Zentrum für Geburtshilfe, Kinder-und Jugendmedizin, Klinik und Poliklinik für Pädiatrische Hämatologie und Onkologie, Hamburg
| | - Lena Oevermann
- GPOH Konsortium Sichelzellkrankheit; Charité - Universitätsmedizin Berlin, Campus Virchow-Klinikum, Klinik für Pädiatrie m.S. Onkologie/Hämatologie/KMT, Berlin
| | - Dani Hakimeh
- GPOH Konsortium Sichelzellkrankheit; Charité - Universitätsmedizin Berlin, Campus Virchow-Klinikum, Klinik für Pädiatrie m.S. Onkologie/Hämatologie/KMT, Berlin
| | - Laura Tagliaferri
- Department of Pediatric Oncology, Hematology and Immunology, Hopp-Children's Cancer Center (KiTZ) Heidelberg, University of Heidelberg, Heidelberg, Germany; GPOH Konsortium Sichelzellkrankheit
| | - Elisabeth Kohne
- Universitätsklinikum Ulm, Klinik für Kinder- und Jugendmedizin, Pädiatrische Hämatologie und Onkologie, Ulm
| | | | - Andreas E Kulozik
- Department of Pediatric Oncology, Hematology and Immunology, Hopp-Children's Cancer Center (KiTZ) Heidelberg, University of Heidelberg, Heidelberg, Germany; GPOH Konsortium Sichelzellkrankheit
| | - Joachim B Kunz
- Department of Pediatric Oncology, Hematology and Immunology, Hopp-Children's Cancer Center (KiTZ) Heidelberg, University of Heidelberg, Heidelberg, Germany; GPOH Konsortium Sichelzellkrankheit.
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17
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Abstract
In 1986, a paper in the Lancet was the first to collate hematology, molecular findings, and clinical features of homozygous sickle cell (SS) disease in India. The paper came from the group organized by Professor Bimal Kar in Burla Medical College, Sambalpur University, in western Odisha. Although widely quoted, few readers will be aware of the history of this work that is now attached in an informal summary.
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Affiliation(s)
| | - Andreas E. Kulozik
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany
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18
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Kulozik AE. Does the world need germline editing for ß-thalassemia? Haematologica 2021; 107:1235-1236. [PMID: 34706499 PMCID: PMC9152967 DOI: 10.3324/haematol.2021.279998] [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] [Received: 10/08/2021] [Indexed: 11/09/2022] Open
Abstract
Not available.
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Affiliation(s)
- Andreas E Kulozik
- Chairman, Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Hopp-Children Cancer Center Heidelberg (KiTZ)
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19
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Powers KT, Stevenson-Jones F, Yadav SKN, Amthor B, Bufton JC, Borucu U, Shen D, Becker JP, Lavysh D, Hentze MW, Kulozik AE, Neu-Yilik G, Schaffitzel C. Blasticidin S inhibits mammalian translation and enhances production of protein encoded by nonsense mRNA. Nucleic Acids Res 2021; 49:7665-7679. [PMID: 34157102 PMCID: PMC8287960 DOI: 10.1093/nar/gkab532] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 05/16/2021] [Accepted: 06/08/2021] [Indexed: 12/14/2022] Open
Abstract
Deciphering translation is of paramount importance for the understanding of many diseases, and antibiotics played a pivotal role in this endeavour. Blasticidin S (BlaS) targets translation by binding to the peptidyl transferase center of the large ribosomal subunit. Using biochemical, structural and cellular approaches, we show here that BlaS inhibits both translation elongation and termination in Mammalia. Bound to mammalian terminating ribosomes, BlaS distorts the 3′CCA tail of the P-site tRNA to a larger extent than previously reported for bacterial ribosomes, thus delaying both, peptide bond formation and peptidyl-tRNA hydrolysis. While BlaS does not inhibit stop codon recognition by the eukaryotic release factor 1 (eRF1), it interferes with eRF1’s accommodation into the peptidyl transferase center and subsequent peptide release. In human cells, BlaS inhibits nonsense-mediated mRNA decay and, at subinhibitory concentrations, modulates translation dynamics at premature termination codons leading to enhanced protein production.
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Affiliation(s)
- Kyle T Powers
- University of Bristol, School of Biochemistry, University Walk, Bristol BS8 1TD, UK
| | | | - Sathish K N Yadav
- University of Bristol, School of Biochemistry, University Walk, Bristol BS8 1TD, UK
| | - Beate Amthor
- Department of Pediatric Oncology, Hematology and Immunology, Hopp Children's Cancer Research Center Heidelberg (KiTZ), University of Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU) European Molecular Biology Laboratory (EMBL) and University of Heidelberg, Heidelberg, Germany
| | - Joshua C Bufton
- University of Bristol, School of Biochemistry, University Walk, Bristol BS8 1TD, UK
| | - Ufuk Borucu
- University of Bristol, School of Biochemistry, University Walk, Bristol BS8 1TD, UK
| | - Dakang Shen
- University of Bristol, School of Biochemistry, University Walk, Bristol BS8 1TD, UK
| | - Jonas P Becker
- Department of Pediatric Oncology, Hematology and Immunology, Hopp Children's Cancer Research Center Heidelberg (KiTZ), University of Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU) European Molecular Biology Laboratory (EMBL) and University of Heidelberg, Heidelberg, Germany
| | - Daria Lavysh
- Department of Pediatric Oncology, Hematology and Immunology, Hopp Children's Cancer Research Center Heidelberg (KiTZ), University of Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU) European Molecular Biology Laboratory (EMBL) and University of Heidelberg, Heidelberg, Germany
| | - Matthias W Hentze
- Molecular Medicine Partnership Unit (MMPU) European Molecular Biology Laboratory (EMBL) and University of Heidelberg, Heidelberg, Germany.,European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Andreas E Kulozik
- Department of Pediatric Oncology, Hematology and Immunology, Hopp Children's Cancer Research Center Heidelberg (KiTZ), University of Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU) European Molecular Biology Laboratory (EMBL) and University of Heidelberg, Heidelberg, Germany
| | - Gabriele Neu-Yilik
- Department of Pediatric Oncology, Hematology and Immunology, Hopp Children's Cancer Research Center Heidelberg (KiTZ), University of Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU) European Molecular Biology Laboratory (EMBL) and University of Heidelberg, Heidelberg, Germany
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20
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Lobitz S, Kunz JB, Cario H, Hakimeh D, Jarisch A, Kulozik AE, Oevermann L, Grosse R. Neugeborenenscreening auf Sichelzellkrankheit. Monatsschr Kinderheilkd 2021. [DOI: 10.1007/s00112-021-01213-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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21
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Becker JP, Helm D, Rettel M, Stein F, Hernandez-Sanchez A, Urban K, Gebert J, Kloor M, Neu-Yilik G, von Knebel Doeberitz M, Hentze MW, Kulozik AE. NMD inhibition by 5-azacytidine augments presentation of immunogenic frameshift-derived neoepitopes. iScience 2021; 24:102389. [PMID: 33981976 PMCID: PMC8082087 DOI: 10.1016/j.isci.2021.102389] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/11/2021] [Accepted: 03/30/2021] [Indexed: 12/22/2022] Open
Abstract
Frameshifted protein sequences elicit tumor-specific T cell-mediated immune responses in microsatellite-unstable (MSI) cancers if presented by HLA class I molecules. However, their expression and presentation are limited by nonsense-mediated RNA decay (NMD). We employed an unbiased immunopeptidomics workflow to analyze MSI HCT-116 cells and identified >10,000 HLA class I-presented peptides including five frameshift-derived InDel neoepitopes. Notably, pharmacological NMD inhibition with 5-azacytidine stabilizes frameshift-bearing transcripts and increases the HLA class I-mediated presentation of InDel neoepitopes. The frameshift mutation underlying one of the identified InDel neoepitopes is highly recurrent in MSI colorectal cancer cell lines and primary patient samples, and immunization with the corresponding neoepitope induces strong CD8+ T cell responses in an HLA-A∗02:01 transgenic mouse model. Our data show directly that pharmacological NMD inhibition augments HLA class I-mediated presentation of immunogenic frameshift-derived InDel neoepitopes thus highlighting the clinical potential of NMD inhibition in anti-cancer immunotherapy strategies.
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Affiliation(s)
- Jonas P. Becker
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, 69120 Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University, 69120 Heidelberg, Germany
- Hopp Children's Cancer Center, National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
| | - Dominic Helm
- Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Mandy Rettel
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Frank Stein
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Alejandro Hernandez-Sanchez
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, 69120 Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University, 69120 Heidelberg, Germany
- Collaboration Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Katharina Urban
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, 69120 Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University, 69120 Heidelberg, Germany
- Collaboration Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Johannes Gebert
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, 69120 Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University, 69120 Heidelberg, Germany
- Collaboration Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Matthias Kloor
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, 69120 Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University, 69120 Heidelberg, Germany
- Collaboration Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Gabriele Neu-Yilik
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, 69120 Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University, 69120 Heidelberg, Germany
- Hopp Children's Cancer Center, National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
| | - Magnus von Knebel Doeberitz
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, 69120 Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University, 69120 Heidelberg, Germany
- Collaboration Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Matthias W. Hentze
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, 69120 Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Andreas E. Kulozik
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, 69120 Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University, 69120 Heidelberg, Germany
- Hopp Children's Cancer Center, National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
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22
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Stockklausner C, Duffert CM, Cario H, Knöfler R, Streif W, Kulozik AE. Thrombocytosis in children and adolescents-classification, diagnostic approach, and clinical management. Ann Hematol 2021; 100:1647-1665. [PMID: 33712866 PMCID: PMC8195939 DOI: 10.1007/s00277-021-04485-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 03/02/2021] [Indexed: 11/30/2022]
Abstract
Secondary thrombocytosis is a frequent secondary finding in childhood infection and inflammation. Primary hereditary thrombocytosis may be caused by germline mutations within the genes encoding key regulators of thrombopoiesis, i.e., thrombopoietin (THPO) and its receptor c-MPL (MPL) or the receptor's effector kinase Januskinase2 (JAK2). Furthermore, somatic mutations in JAK2, MPL, and in the gene-encoding calreticulin (CALR) have been described to act as driver mutations within the so-called Philadelphia-negative myeloproliferative neoplasms (MPNs), namely essential thrombocythemia (ET), polycythemia vera (PV), and primary myelofibrosis (PMF). Increasing knowledge on the molecular mechanisms and on the clinical complications of these diseases is reflected by the WHO diagnostic criteria and European LeukemiaNet (ELN) recommendations on the management of adult MPN. However, data on childhood thrombocytosis are rare, and no consensus guidelines for pediatric thrombocytosis exist. Current literature has highlighted differences in the epidemiology and molecular pathogenesis of childhood thrombocytosis as compared to adults. Furthermore, age-dependent complications and pharmacological specificities suggest that recommendations tailored to the pediatric population are necessary in clinical practice. Here we summarize literature on classification, diagnostics, and clinical management of childhood thrombocytosis.
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Affiliation(s)
- Clemens Stockklausner
- Department of Pediatric Oncology, Hematology and Immunology and Hopp Children's Cancer Research Center (KiTZ), Heidelberg University and German Cancer Research Center (DKFZ), Heidelberg, Germany. .,Department of Pediatrics, Garmisch-Partenkirchen Hospital, Auenstraße 6, 82467, Garmisch-Partenkirchen, Germany.
| | - C M Duffert
- Department of Pediatrics, Heidelberg University, Heidelberg, Germany
| | - H Cario
- Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, Ulm, Germany
| | - R Knöfler
- Department of Pediatric Hematology and Oncology, Medical Faculty of Technical University, Dresden, Germany
| | - W Streif
- Department of Pediatrics, Medical University of Innsbruck, Innsbruck, Tirol, Austria
| | - A E Kulozik
- Department of Pediatric Oncology, Hematology and Immunology and Hopp Children's Cancer Research Center (KiTZ), Heidelberg University and German Cancer Research Center (DKFZ), Heidelberg, Germany
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23
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Walters MC, Kwiatkowski JL, Porter JB, Hongeng S, Yannaki E, Kulozik AE, Sauer MG, Thrasher AJ, Thuret I, Lal A, Guo R, Liu W, Colvin RA, Locatelli F, Thompson AA. Safety and Efficacy Outcomes in Pediatric Patients with Transfusion-Dependent β-Thalassemia (TDT) Receiving Betibeglogene Autotemcel (beti-cel; LentiGlobin for β-thalassemia) Gene Therapy in the Phase 3 Hgb-207 (Northstar-2) and Hgb-212 (Northstar-3) Studies. Transplant Cell Ther 2021. [DOI: 10.1016/s2666-6367(21)00148-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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24
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Hongeng S, Thompson AA, Kwiatkowski JL, Locatelli F, Porter JB, Rasko J, Cavazzana M, Sauer MG, Thrasher AJ, Thuret I, Lal A, Kulozik AE, Yannaki E, Schmidt M, Chen Y, Guo R, Liu W, Colvin RA, Walters MC. Efficacy and Safety of Betibeglogene Autotemcel (beti-cel; LentiGlobin for β-thalassemia) Gene Therapy in 60 Patients with Transfusion-Dependent β-Thalassemia (TDT) Followed for up to 6 Years Post-Infusion. Transplant Cell Ther 2021. [DOI: 10.1016/s2666-6367(21)00027-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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25
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Roels J, Thénoz M, Szarzyńska B, Landfors M, De Coninck S, Demoen L, Provez L, Kuchmiy A, Strubbe S, Reunes L, Pieters T, Matthijssens F, Van Loocke W, Erarslan-Uysal B, Richter-Pechańska P, Declerck K, Lammens T, De Moerloose B, Deforce D, Van Nieuwerburgh F, Cheung LC, Kotecha RS, Mansour MR, Ghesquière B, Van Camp G, Berghe WV, Kowalczyk JR, Szczepański T, Davé UP, Kulozik AE, Goossens S, Curtis DJ, Taghon T, Dawidowska M, Degerman S, Van Vlierberghe P. Aging of preleukemic thymocytes drives CpG island hypermethylation in T-cell acute lymphoblastic leukemia. Blood Cancer Discov 2020; 1:274-289. [PMID: 33179015 PMCID: PMC7116343 DOI: 10.1158/2643-3230.bcd-20-0059] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 08/06/2020] [Accepted: 09/15/2020] [Indexed: 12/20/2022] Open
Abstract
Cancer cells display DNA hypermethylation at specific CpG islands in comparison to their normal healthy counterparts, but the mechanism that drives this so-called CpG island methylator phenotype (CIMP) remains poorly understood. Here, we show that CpG island methylation in human T-cell acute lymphoblastic leukemia (T-ALL) mainly occurs at promoters of Polycomb Repressor Complex 2 (PRC2) target genes that are not expressed in normal or malignant T-cells and which display a reciprocal association with H3K27me3 binding. In addition, we revealed that this aberrant methylation profile reflects the epigenetic history of T-ALL and is established already in pre-leukemic, self-renewing thymocytes that precede T-ALL development. Finally, we unexpectedly uncover that this age-related CpG island hypermethylation signature in T-ALL is completely resistant to the FDA-approved hypomethylating agent Decitabine. Altogether, we here provide conceptual evidence for the involvement of a pre-leukemic phase characterized by self-renewing thymocytes in the pathogenesis of human T-ALL.
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Affiliation(s)
- Juliette Roels
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Morgan Thénoz
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | | | - Mattias Landfors
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
| | - Stien De Coninck
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Lisa Demoen
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Lien Provez
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Anna Kuchmiy
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Steven Strubbe
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Lindy Reunes
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Tim Pieters
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Filip Matthijssens
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Wouter Van Loocke
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Büşra Erarslan-Uysal
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, and Hopp Children's Cancer Center at NCT Heidelberg, Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany
| | - Paulina Richter-Pechańska
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, and Hopp Children's Cancer Center at NCT Heidelberg, Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany
| | - Ken Declerck
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES) and Integrated Personalized and Precision Oncology Network (IPPON), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Tim Lammens
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Barbara De Moerloose
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | | | - Laurence C Cheung
- Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, Western Australia
- School of Pharmacy and Biomedical Sciences, Curtin University, Perth, Western Australia
| | - Rishi S Kotecha
- Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, Western Australia
- School of Pharmacy and Biomedical Sciences, Curtin University, Perth, Western Australia
| | - Marc R Mansour
- Department of Haematology, University College London Cancer Institute, London, England
| | - Bart Ghesquière
- Metabolomics Expertise Center, VIB Center for Cancer Biology, Leuven, Belgium
| | - Guy Van Camp
- Center of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Wim Vanden Berghe
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES) and Integrated Personalized and Precision Oncology Network (IPPON), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Jerzy R Kowalczyk
- Department of Pediatric Hematology, Oncology and Transplantology, Medical University of Lublin, Lublin, Poland
| | - Tomasz Szczepański
- Department of Pediatric Hematology and Oncology, Zabrze, Medical University of Silesia, Katowice, Poland
| | - Utpal P Davé
- Roudebush Veterans Affairs Medical Center and Indiana University School of Medicine, Indianapolis, Indiana
| | - Andreas E Kulozik
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, and Hopp Children's Cancer Center at NCT Heidelberg, Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany
| | - Steven Goossens
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - David J Curtis
- Australian Centre for Blood Diseases (ACBD), Monash University, Melbourne, Australia
| | - Tom Taghon
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | | | - Sofie Degerman
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Pieter Van Vlierberghe
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
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26
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Backlund M, Stein F, Rettel M, Schwarzl T, Perez-Perri JI, Brosig A, Zhou Y, Neu-Yilik G, Hentze MW, Kulozik AE. Plasticity of nuclear and cytoplasmic stress responses of RNA-binding proteins. Nucleic Acids Res 2020; 48:4725-4740. [PMID: 32313943 PMCID: PMC7229827 DOI: 10.1093/nar/gkaa256] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 04/01/2020] [Accepted: 04/04/2020] [Indexed: 02/07/2023] Open
Abstract
Cellular stress causes multifaceted reactions to trigger adaptive responses to environmental cues at all levels of the gene expression pathway. RNA-binding proteins (RBP) are key contributors to stress-induced regulation of RNA fate and function. Here, we uncover the plasticity of the RNA interactome in stressed cells, differentiating between responses in the nucleus and in the cytoplasm. We applied enhanced RNA interactome capture (eRIC) analysis preceded by nucleo-cytoplasmic fractionation following arsenite-induced oxidative stress. The data reveal unexpectedly compartmentalized RNA interactomes and their responses to stress, including differential responses of RBPs in the nucleus versus the cytoplasm, which would have been missed by whole cell analyses.
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Affiliation(s)
- Michael Backlund
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, Im Neuenheimer Feld 350, 69120 Heidelberg, Germany & European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany & Hopp Children's Cancer Center, National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
- To whom correspondence should be addressed. Tel: +49 6221 564555;
| | - Frank Stein
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Mandy Rettel
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Thomas Schwarzl
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Joel I Perez-Perri
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Annika Brosig
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, Im Neuenheimer Feld 350, 69120 Heidelberg, Germany & European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany & Hopp Children's Cancer Center, National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Collaboration for joint PhD degree between EMBL and Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Yang Zhou
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, Im Neuenheimer Feld 350, 69120 Heidelberg, Germany & European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany & Hopp Children's Cancer Center, National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
| | - Gabriele Neu-Yilik
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, Im Neuenheimer Feld 350, 69120 Heidelberg, Germany & European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany & Hopp Children's Cancer Center, National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
| | - Matthias W Hentze
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, Im Neuenheimer Feld 350, 69120 Heidelberg, Germany & European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Correspondence may also be addressed to Matthias W. Hentze.
| | - Andreas E Kulozik
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, Im Neuenheimer Feld 350, 69120 Heidelberg, Germany & European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany & Hopp Children's Cancer Center, National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
- Correspondence may also be addressed to Andreas E. Kulozik.
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27
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Lin SH, Sampson JN, Grünewald TGP, Surdez D, Reynaud S, Mirabeau O, Karlins E, Rubio RA, Zaidi S, Grossetête-Lalami S, Ballet S, Lapouble E, Laurence V, Michon J, Pierron G, Kovar H, Kontny U, González-Neira A, Alonso J, Patino-Garcia A, Corradini N, Bérard PM, Miller J, Freedman ND, Rothman N, Carter BD, Dagnall CL, Burdett L, Jones K, Manning M, Wyatt K, Zhou W, Yeager M, Cox DG, Hoover RN, Khan J, Armstrong GT, Leisenring WM, Bhatia S, Robison LL, Kulozik AE, Kriebel J, Meitinger T, Metzler M, Krumbholz M, Hartmann W, Strauch K, Kirchner T, Dirksen U, Mirabello L, Tucker MA, Tirode F, Morton LM, Chanock SJ, Delattre O, Machiela MJ. Low-frequency variation near common germline susceptibility loci are associated with risk of Ewing sarcoma. PLoS One 2020; 15:e0237792. [PMID: 32881892 PMCID: PMC7470401 DOI: 10.1371/journal.pone.0237792] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 08/03/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Ewing sarcoma (EwS) is a rare, aggressive solid tumor of childhood, adolescence and young adulthood associated with pathognomonic EWSR1-ETS fusion oncoproteins altering transcriptional regulation. Genome-wide association studies (GWAS) have identified 6 common germline susceptibility loci but have not investigated low-frequency inherited variants with minor allele frequencies below 5% due to limited genotyped cases of this rare tumor. METHODS We investigated the contribution of rare and low-frequency variation to EwS susceptibility in the largest EwS genome-wide association study to date (733 EwS cases and 1,346 unaffected controls of European ancestry). RESULTS We identified two low-frequency variants, rs112837127 and rs2296730, on chromosome 20 that were associated with EwS risk (OR = 0.186 and 2.038, respectively; P-value < 5×10-8) and located near previously reported common susceptibility loci. After adjusting for the most associated common variant at the locus, only rs112837127 remained a statistically significant independent signal (OR = 0.200, P-value = 5.84×10-8). CONCLUSIONS These findings suggest rare variation residing on common haplotypes are important contributors to EwS risk. IMPACT Motivate future targeted sequencing studies for a comprehensive evaluation of low-frequency and rare variation around common EwS susceptibility loci.
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Affiliation(s)
- Shu-Hong Lin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, United States of America
| | - Joshua N Sampson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, United States of America
| | - Thomas G P Grünewald
- Max-Eder Research Group for Pediatric Sarcoma Biology, Ludwig Maximilians Universität (LMU), Munich, Germany.,Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany.,Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Didier Surdez
- Inserm U830, Équipe Labellisés LNCC, PSL Université, Institut Curie, Paris, France
| | | | - Olivier Mirabeau
- Inserm U830, Équipe Labellisés LNCC, PSL Université, Institut Curie, Paris, France.,SIREDO Oncology Centre, Institut Curie, Paris, France
| | - Eric Karlins
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, United States of America.,Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD, United States of America
| | - Rebeca Alba Rubio
- Max-Eder Research Group for Pediatric Sarcoma Biology, Ludwig Maximilians Universität (LMU), Munich, Germany
| | - Sakina Zaidi
- Inserm U830, Équipe Labellisés LNCC, PSL Université, Institut Curie, Paris, France.,SIREDO Oncology Centre, Institut Curie, Paris, France
| | - Sandrine Grossetête-Lalami
- Inserm U830, Équipe Labellisés LNCC, PSL Université, Institut Curie, Paris, France.,SIREDO Oncology Centre, Institut Curie, Paris, France
| | - Stelly Ballet
- SIREDO Oncology Centre, Institut Curie, Paris, France
| | - Eve Lapouble
- SIREDO Oncology Centre, Institut Curie, Paris, France
| | | | - Jean Michon
- SIREDO Oncology Centre, Institut Curie, Paris, France
| | | | - Heinrich Kovar
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Udo Kontny
- Division of Pediatric Hematology, Oncology and Stem Cell Transplantation, Uniklinik RWTH Aachen, Aachen, Germany
| | - Anna González-Neira
- Human Genotyping Unit-CeGen, Human Cancer Genetics Programme, Spanish National Cancer Research Centre, Madrid, Spain
| | - Javier Alonso
- Unidad de Tumores Solidos Infantiles (IIER-ISCIII) & Centro de Investigación Biomédica en Red de Enfermedades Raras (CB06/07/1009; CIBERER-ISCIII), Instituto de Salud Carlos III, Majadahonda, Spain
| | - Ana Patino-Garcia
- Laboratory of Pediatrics, University Clinic of Navarra, Program in Solid Tumors, Center for Applied Medical Research (CIMA) and Navarra's Health Research Institute (IdiSNA), Pamplona, Spain
| | - Nadège Corradini
- Institute for Paediatric Haematology and Oncology, Leon Bérard Cancer Centre, University of Lyon, Lyon, France
| | - Perrine Marec Bérard
- Institute for Paediatric Haematology and Oncology, Leon Bérard Cancer Centre, University of Lyon, Lyon, France
| | - Jeremy Miller
- Information Management Services, Inc., Calverton, MD, United States of America
| | - Neal D Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, United States of America
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, United States of America
| | - Brian D Carter
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, United States of America
| | - Casey L Dagnall
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, United States of America.,Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD, United States of America
| | - Laurie Burdett
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, United States of America.,Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD, United States of America
| | - Kristine Jones
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, United States of America.,Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD, United States of America
| | - Michelle Manning
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, United States of America.,Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD, United States of America
| | - Kathleen Wyatt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, United States of America.,Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD, United States of America
| | - Weiyin Zhou
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, United States of America.,Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD, United States of America
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, United States of America.,Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD, United States of America
| | - David G Cox
- Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France
| | - Robert N Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, United States of America
| | - Javed Khan
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States of America
| | - Gregory T Armstrong
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, United States of America
| | - Wendy M Leisenring
- Cancer Prevention and Clinical Statistics Programs, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Smita Bhatia
- Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Leslie L Robison
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, United States of America
| | - Andreas E Kulozik
- Department of Pediatric Oncology, Hematology and Immunology and Hopp Children Cancer Center, University of Heidelberg, Heidelberg, Germany
| | - Jennifer Kriebel
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,German Center for Diabetes Research (DZD), München, Neuherberg, Germany
| | - Thomas Meitinger
- German Research Center for Environmental Health, Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Markus Metzler
- Department of Paediatrics and Adolescent Medicine, University Hospital of Erlangen, Erlangen, Germany
| | - Manuela Krumbholz
- Department of Paediatrics and Adolescent Medicine, University Hospital of Erlangen, Erlangen, Germany
| | - Wolfgang Hartmann
- Division of Translational Pathology, Gerhard-Domagk Institute of Pathology, University Hospital of Münster, Münster, Germany
| | | | - Thomas Kirchner
- Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Uta Dirksen
- Pediatrics III, West German Cancer Centre, University Hospital Essen, Essen, Germany.,German Cancer Consortium (DKTK), Center Essen, Heidelberg, Germany
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, United States of America
| | - Margaret A Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, United States of America
| | - Franck Tirode
- Inserm U830, Équipe Labellisés LNCC, PSL Université, Institut Curie, Paris, France.,SIREDO Oncology Centre, Institut Curie, Paris, France
| | - Lindsay M Morton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, United States of America
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, United States of America
| | - Olivier Delattre
- Inserm U830, Équipe Labellisés LNCC, PSL Université, Institut Curie, Paris, France.,SIREDO Oncology Centre, Institut Curie, Paris, France
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, United States of America
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28
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Heidler CL, Roth EK, Thiemann M, Blattmann C, Perez RL, Huber PE, Kovac M, Amthor B, Neu‐Yilik G, Kulozik AE. Prexasertib (LY2606368) reduces clonogenic survival by inducing apoptosis in primary patient-derived osteosarcoma cells and synergizes with cisplatin and talazoparib. Int J Cancer 2020; 147:1059-1070. [PMID: 31782150 PMCID: PMC7384073 DOI: 10.1002/ijc.32814] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 08/02/2019] [Accepted: 08/13/2019] [Indexed: 12/22/2022]
Abstract
Progress in the systemic control of osteosarcoma has been limited over the past decades thus indicating the urgent clinical need for the development of novel treatment strategies. Therefore, we have recently developed new preclinical models to study promising novel agents for the treatment of pediatric osteosarcoma. The checkpoint kinase (chk) inhibitor prexasertib (LY2606368) and its salt form (LSN2940930) have recently been shown to be active in adult and pediatric malignancies, including sarcoma. We have now tested the potency of prexasertib in clonogenic survival assays in two new lines of primary patient-derived osteosarcoma cells and in two established osteosarcoma cell lines as a single agent and in combination with cisplatin and the poly ADP-ribose polymerase (PARP) inhibitor talazoparib. Prexasertib alone results in strongly reduced clonogenic survival at low nanomolar concentrations and acts by affecting cell cycle progression, induction of apoptosis and induction of double-stranded DNA breakage at concentrations that are well below clinically tolerable and safe plasma concentrations. In combination with cisplatin and talazoparib, prexasertib acts in a synergistic fashion. Chk1 inhibition by prexasertib and its combination with the DNA damaging agent cisplatin and the PARP-inhibitor talazoparib thus emerges as a potential new treatment option for pediatric osteosarcoma which will now have to be tested in preclinical primary patient derived in vivo models and clinical studies.
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Affiliation(s)
- Christopher L. Heidler
- Department of Pediatric Oncology, Hematology and Immunology, Hopp Children's Cancer Research Center Heidelberg (KiTZ)Molecular Medicine Partnership Unit (MMPU) European Molecular Biology Laboratory (EMBL) and University of HeidelbergHeidelbergGermany
| | - Eva K. Roth
- Department of Pediatric Oncology, Hematology and Immunology, Hopp Children's Cancer Research Center Heidelberg (KiTZ)Molecular Medicine Partnership Unit (MMPU) European Molecular Biology Laboratory (EMBL) and University of HeidelbergHeidelbergGermany
| | - Markus Thiemann
- Department of Pediatric Oncology, Hematology and Immunology, Hopp Children's Cancer Research Center Heidelberg (KiTZ)Molecular Medicine Partnership Unit (MMPU) European Molecular Biology Laboratory (EMBL) and University of HeidelbergHeidelbergGermany
| | - Claudia Blattmann
- Department of Pediatric Oncology, Hematology and Immunology, Hopp Children's Cancer Research Center Heidelberg (KiTZ)Molecular Medicine Partnership Unit (MMPU) European Molecular Biology Laboratory (EMBL) and University of HeidelbergHeidelbergGermany
- Pediatrics 5 (Oncology, Hematology, Immunology)Klinikum Stuttgart OlgahospitalStuttgartGermany
- German Cancer Consortium (DKTK)HeidelbergGermany
| | - Ramon L. Perez
- Department of Molecular and Radiation OncologyGerman Cancer Research Center (DKFZ)HeidelbergGermany
- Heidelberg Institute for Radiation Oncology (HIRO)National Center for Radiation Research in OncologyHeidelbergGermany
| | - Peter E. Huber
- Department of Molecular and Radiation OncologyGerman Cancer Research Center (DKFZ)HeidelbergGermany
- Heidelberg Institute for Radiation Oncology (HIRO)National Center for Radiation Research in OncologyHeidelbergGermany
- Department of Radiation OncologyHeidelberg University HospitalHeidelbergGermany
| | - Michal Kovac
- Bone Tumour Reference Center, Institute of PathologyUniversity Hospital Basel and University of BaselBaselSwitzerland
| | - Beate Amthor
- Department of Pediatric Oncology, Hematology and Immunology, Hopp Children's Cancer Research Center Heidelberg (KiTZ)Molecular Medicine Partnership Unit (MMPU) European Molecular Biology Laboratory (EMBL) and University of HeidelbergHeidelbergGermany
| | - Gabriele Neu‐Yilik
- Department of Pediatric Oncology, Hematology and Immunology, Hopp Children's Cancer Research Center Heidelberg (KiTZ)Molecular Medicine Partnership Unit (MMPU) European Molecular Biology Laboratory (EMBL) and University of HeidelbergHeidelbergGermany
| | - Andreas E. Kulozik
- Department of Pediatric Oncology, Hematology and Immunology, Hopp Children's Cancer Research Center Heidelberg (KiTZ)Molecular Medicine Partnership Unit (MMPU) European Molecular Biology Laboratory (EMBL) and University of HeidelbergHeidelbergGermany
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29
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Erarslan-Uysal B, Kunz JB, Rausch T, Richter-Pechańska P, van Belzen IA, Frismantas V, Bornhauser B, Ordoñez-Rueada D, Paulsen M, Benes V, Stanulla M, Schrappe M, Cario G, Escherich G, Bakharevich K, Kirschner-Schwabe R, Eckert C, Loukanov T, Gorenflo M, Waszak SM, Bourquin JP, Muckenthaler MU, Korbel JO, Kulozik AE. Chromatin accessibility landscape of pediatric T-lymphoblastic leukemia and human T-cell precursors. EMBO Mol Med 2020; 12:e12104. [PMID: 32755029 PMCID: PMC7507092 DOI: 10.15252/emmm.202012104] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 06/19/2020] [Accepted: 06/24/2020] [Indexed: 01/11/2023] Open
Abstract
We aimed at identifying the developmental stage at which leukemic cells of pediatric T-ALLs are arrested and at defining leukemogenic mechanisms based on ATAC-Seq. Chromatin accessibility maps of seven developmental stages of human healthy T cells revealed progressive chromatin condensation during T-cell maturation. Developmental stages were distinguished by 2,823 signature chromatin regions with 95% accuracy. Open chromatin surrounding SAE1 was identified to best distinguish thymic developmental stages suggesting a potential role of SUMOylation in T-cell development. Deconvolution using signature regions revealed that T-ALLs, including those with mature immunophenotypes, resemble the most immature populations, which was confirmed by TF-binding motif profiles. We integrated ATAC-Seq and RNA-Seq and found DAB1, a gene not related to leukemia previously, to be overexpressed, abnormally spliced and hyper-accessible in T-ALLs. DAB1-negative patients formed a distinct subgroup with particularly immature chromatin profiles and hyper-accessible binding sites for SPI1 (PU.1), a TF crucial for normal T-cell maturation. In conclusion, our analyses of chromatin accessibility and TF-binding motifs showed that pediatric T-ALL cells are most similar to immature thymic precursors, indicating an early developmental arrest.
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Affiliation(s)
- Büşra Erarslan-Uysal
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, Heidelberg, Germany.,Hopp Children's Cancer Center (KiTZ) Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Joachim B Kunz
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, Heidelberg, Germany.,Hopp Children's Cancer Center (KiTZ) Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Tobias Rausch
- Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Paulina Richter-Pechańska
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, Heidelberg, Germany.,Hopp Children's Cancer Center (KiTZ) Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Ianthe Aem van Belzen
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Viktoras Frismantas
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Beat Bornhauser
- Division of Pediatric Oncology, University Children's Hospital, Zürich, Switzerland
| | - Diana Ordoñez-Rueada
- Flow Cytometry Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Malte Paulsen
- Flow Cytometry Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Vladimir Benes
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Martin Stanulla
- Department of Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Martin Schrappe
- Department of Pediatrics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Gunnar Cario
- Department of Pediatrics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Gabriele Escherich
- Clinic of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kseniya Bakharevich
- Clinic of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Renate Kirschner-Schwabe
- Department of Pediatric Oncology/Hematology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Cornelia Eckert
- Department of Pediatric Oncology/Hematology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Tsvetomir Loukanov
- Department of Cardiac Surgery, University of Heidelberg, Heidelberg, Germany
| | - Matthias Gorenflo
- Department of Pediatric Cardiology and Congenital Heart Diseases, University of Heidelberg, Heidelberg, Germany
| | - Sebastian M Waszak
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Jean-Pierre Bourquin
- Division of Pediatric Oncology, University Children's Hospital, Zürich, Switzerland
| | - Martina U Muckenthaler
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, Heidelberg, Germany.,Hopp Children's Cancer Center (KiTZ) Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Jan O Korbel
- Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Andreas E Kulozik
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, Heidelberg, Germany.,Hopp Children's Cancer Center (KiTZ) Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
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30
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Kunz JB, Lobitz S, Grosse R, Oevermann L, Hakimeh D, Jarisch A, Cario H, Beier R, Schenk D, Schneider D, Groß-Wieltsch U, Prokop A, Heine S, Khurana C, Erlacher M, Dürken M, Linke C, Frühwald M, Corbacioglu S, Claviez A, Metzler M, Ebinger M, Full H, Wiesel T, Eberl W, Reinhard H, Tagliaferri L, Allard P, Karapanagiotou-Schenkel I, Rother LM, Beck D, Le Cornet L, Kulozik AE. Sickle cell disease in Germany: Results from a national registry. Pediatr Blood Cancer 2020; 67:e28130. [PMID: 31867835 DOI: 10.1002/pbc.28130] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 11/27/2019] [Accepted: 11/27/2019] [Indexed: 11/06/2022]
Abstract
BACKGROUND Limited data on the prevalence and medical care of sickle cell disease (SCD) in Germany are available. Here, we make use of a patient registry to characterize the burden of disease and the treatment modalities for patients with SCD in Germany. PROCEDURE A nationwide German registry for patients with SCD documents basic data on diagnosis and patient history retrospectively at the time of registration. A prospective annual documentation provides more details on complications and treatment of SCD. For the current analyses, data of 439 patients were available. RESULTS Most patients had homozygous SCD (HbSS 75.1%, HbS/β-thalassemia 13.2%, and HbSC 11.3%). The median age at diagnosis was 1.9 years (interquartile range, 0.6-4.4 years), most patients were diagnosed when characteristic symptoms occurred. Sepsis and stroke had affected 3.2% and 4.2% of patients, respectively. During the first year of observation, 48.3% of patients were admitted to a hospital and 10.1% required intensive care. Prophylactic penicillin was prescribed to 95.6% of patients with homozygous SCD or HbS/β thalassemia below the age of six and hydroxycarbamide to 90.4% of patients above the age of two years. At least one annual transcranial Doppler ultrasound was documented for 74.8% of patients between 2 and 18 years. CONCLUSION With an estimated number of at least 2000, the prevalence of SCD in Germany remains low. Prospectively, we expect that the quality of care for children with SCD will be further improved by an earlier diagnosis after the anticipated introduction of a newborn screening program for SCD.
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Affiliation(s)
- Joachim B Kunz
- Department of Pediatric Oncology, Hematology and Immunology, Hopp-Children's Cancer Center (KiTZ) Heidelberg, University of Heidelberg, Heidelberg, Germany.,GPOH Konsortium Sichelzellkrankheit, Germany
| | - Stephan Lobitz
- GPOH Konsortium Sichelzellkrankheit, Germany.,Gemeinschaftsklinikum Mittelrhein, Kemperhof, Pädiatrische Hämatologie und Onkologie, Koblenz, Germany
| | - Regine Grosse
- GPOH Konsortium Sichelzellkrankheit, Germany.,Universitätsklinikum Hamburg-Eppendorf, Zentrum für Geburtshilfe, Kinder- und Jugendmedizin, Klinik und Poliklinik für Pädiatrische Hämatologie und Onkologie, Hamburg, Germany
| | - Lena Oevermann
- GPOH Konsortium Sichelzellkrankheit, Germany.,Charité - Universitätsmedizin Berlin, Campus Virchow-Klinikum, Klinik für Pädiatrie m.S. Onkologie/Hämatologie/KMT, Berlin, Germany
| | - Dani Hakimeh
- GPOH Konsortium Sichelzellkrankheit, Germany.,Charité - Universitätsmedizin Berlin, Campus Virchow-Klinikum, Klinik für Pädiatrie m.S. Onkologie/Hämatologie/KMT, Berlin, Germany
| | - Andrea Jarisch
- GPOH Konsortium Sichelzellkrankheit, Germany.,Klinikum der Johann-Wolfgang-Goethe-Universität, Zentrum für Kinder- und Jugendmedizin, Schwerpunkt Stammzelltransplantation und Immunologie, Frankfurt am Main, Germany
| | - Holger Cario
- GPOH Konsortium Sichelzellkrankheit, Germany.,Universitätsklinikum Ulm, Klinik für Kinder- und Jugendmedizin, Pädiatrische Hämatologie und Onkologie, Ulm, Germany
| | - Rita Beier
- University Hospital Essen, Pediatric Haematology and Oncology, Essen, Germany
| | - Daniela Schenk
- Department of Pediatrics and Children's Cancer Research Center, Kinderklinik München Schwabing, Klinikum rechts der Isar, Fakultät für Medizin, Technische Universität München, Munich, Germany
| | - Dominik Schneider
- Clinic of Pediatrics, Dortmund Municipal Hospital, Dortmund, Germany
| | - Ute Groß-Wieltsch
- Pediatrics 5 (Oncology, Hematology, Immunology), Center for Pediatric, Adolescent and Women's Medicine, Klinikum Stuttgart - Olgahospital, Stuttgart, Germany
| | - Aram Prokop
- Children's Hospital Amsterdamer Straße Cologne, Clinic for Children and Youth Medicine, Paediatric Oncology/Haematology, Cologne, Germany
| | - Sabine Heine
- Department of Pediatric Hematology and Oncology, Saarland University Hospital, Homburg, Saar, Germany
| | - Claudia Khurana
- Klinik für Kinder- und Jugendmedizin, Evangelisches Klinikum Bethel, Bielefeld, Germany
| | - Miriam Erlacher
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Hematology and Oncology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Breisgau, Germany
| | - Matthias Dürken
- Department of Pediatric Hematology and Oncology, University of Mannheim, Mannheim, Germany
| | - Christina Linke
- Universitätsklinikum Münster, Klinik für Kinder- und Jugendmedizin - Pädiatrische Hämatologie und Onkologie, Münster, Germany
| | - Michael Frühwald
- University Children's Hospital Augsburg, University Hospital Augsburg, Augsburg, Germany
| | - Selim Corbacioglu
- Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, Franz-Josef-Strauss-Allee 11, University Hospital of Regensburg, Regensburg, Germany
| | - Alexander Claviez
- Klinik für Kinder- und Jugendmedizin I, Pädiatrische Onkologie, Hämatologie, Stammzelltransplantation, Universitätsklinikum Schleswig-Holstein, Kiel, Germany
| | - Markus Metzler
- Pediatric Oncology and Hematology, Department of Pediatrics and Adolescent Medicine, University Hospital Erlangen, Erlangen, Germany
| | - Martin Ebinger
- Universitätsklinikum Tübingen, Klinik für Kinder- und Jugendmedizin, Tübingen, Germany
| | | | - Thomas Wiesel
- Children's Hospital, Vestische Youth Hospital, University of Witten/Herdecke, Datteln, Germany
| | - Wolfgang Eberl
- Institute for Clinical Transfusion Medicine and Children's Hospital, Klinikum Braunschweig GmbH, Germany
| | - Harald Reinhard
- Asklepios Kinderklinik Sankt Augustin, St. Augustin, Germany
| | - Laura Tagliaferri
- Department of Pediatric Oncology, Hematology and Immunology, Hopp-Children's Cancer Center (KiTZ) Heidelberg, University of Heidelberg, Heidelberg, Germany.,GPOH Konsortium Sichelzellkrankheit, Germany
| | - Pierre Allard
- Department of Pediatric Oncology, Hematology and Immunology, Hopp-Children's Cancer Center (KiTZ) Heidelberg, University of Heidelberg, Heidelberg, Germany
| | - Irini Karapanagiotou-Schenkel
- NCT Trial Center, National Center for Tumor Diseases (NCT) Heidelberg, German Cancer Research Center (dkfz), Heidelberg, Germany
| | - Lisa-Marie Rother
- NCT Trial Center, National Center for Tumor Diseases (NCT) Heidelberg, German Cancer Research Center (dkfz), Heidelberg, Germany
| | - Dorothea Beck
- NCT Trial Center, National Center for Tumor Diseases (NCT) Heidelberg, German Cancer Research Center (dkfz), Heidelberg, Germany
| | - Lucian Le Cornet
- NCT Trial Center, National Center for Tumor Diseases (NCT) Heidelberg, German Cancer Research Center (dkfz), Heidelberg, Germany
| | - Andreas E Kulozik
- Department of Pediatric Oncology, Hematology and Immunology, Hopp-Children's Cancer Center (KiTZ) Heidelberg, University of Heidelberg, Heidelberg, Germany.,GPOH Konsortium Sichelzellkrankheit, Germany
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31
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Sanders AD, Meiers S, Ghareghani M, Porubsky D, Jeong H, van Vliet MACC, Rausch T, Richter-Pechańska P, Kunz JB, Jenni S, Bolognini D, Longo GMC, Raeder B, Kinanen V, Zimmermann J, Benes V, Schrappe M, Mardin BR, Kulozik AE, Bornhauser B, Bourquin JP, Marschall T, Korbel JO. Single-cell analysis of structural variations and complex rearrangements with tri-channel processing. Nat Biotechnol 2020; 38:343-354. [PMID: 31873213 PMCID: PMC7612647 DOI: 10.1038/s41587-019-0366-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 11/20/2019] [Indexed: 02/07/2023]
Abstract
Structural variation (SV), involving deletions, duplications, inversions and translocations of DNA segments, is a major source of genetic variability in somatic cells and can dysregulate cancer-related pathways. However, discovering somatic SVs in single cells has been challenging, with copy-number-neutral and complex variants typically escaping detection. Here we describe single-cell tri-channel processing (scTRIP), a computational framework that integrates read depth, template strand and haplotype phase to comprehensively discover SVs in individual cells. We surveyed SV landscapes of 565 single cells, including transformed epithelial cells and patient-derived leukemic samples, to discover abundant SV classes, including inversions, translocations and complex DNA rearrangements. Analysis of the leukemic samples revealed four times more somatic SVs than cytogenetic karyotyping, submicroscopic copy-number alterations, oncogenic copy-neutral rearrangements and a subclonal chromothripsis event. Advancing current methods, single-cell tri-channel processing can directly measure SV mutational processes in individual cells, such as breakage-fusion-bridge cycles, facilitating studies of clonal evolution, genetic mosaicism and SV formation mechanisms, which could improve disease classification for precision medicine.
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Affiliation(s)
- Ashley D Sanders
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Sascha Meiers
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Maryam Ghareghani
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
- Max Planck Institute for Informatics, Saarbrücken, Germany
- Graduate School of Computer Science, Saarland University, Saarbrücken, Germany
| | - David Porubsky
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
- Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Hyobin Jeong
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | | | - Tobias Rausch
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany
| | - Paulina Richter-Pechańska
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg and Hopp Children's Cancer Center, Heidelberg, Germany
| | - Joachim B Kunz
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg and Hopp Children's Cancer Center, Heidelberg, Germany
| | - Silvia Jenni
- Division of Pediatric Oncology, University Children's Hospital, Zürich, Switzerland
| | - Davide Bolognini
- European Molecular Biology Laboratory, Genomics Core Facility, Heidelberg, Germany
| | - Gabriel M C Longo
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Benjamin Raeder
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Venla Kinanen
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Jürgen Zimmermann
- European Molecular Biology Laboratory, Genomics Core Facility, Heidelberg, Germany
| | - Vladimir Benes
- European Molecular Biology Laboratory, Genomics Core Facility, Heidelberg, Germany
| | - Martin Schrappe
- Department of Pediatrics, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Balca R Mardin
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
- BioMed X Innovation Center, Heidelberg, Germany
| | - Andreas E Kulozik
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg and Hopp Children's Cancer Center, Heidelberg, Germany
| | - Beat Bornhauser
- Division of Pediatric Oncology, University Children's Hospital, Zürich, Switzerland
| | - Jean-Pierre Bourquin
- Division of Pediatric Oncology, University Children's Hospital, Zürich, Switzerland
| | - Tobias Marschall
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany.
- Max Planck Institute for Informatics, Saarbrücken, Germany.
| | - Jan O Korbel
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany.
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32
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Schneiderman J, Thompson AA, Walters MC, Kwiatkowski JL, Kulozik AE, Sauer MG, Porter JB, Thuret I, Hongeng S, Lal A, Thrasher AJ, Yannaki E, Elliot H, Tao G, Liu W, Colvin RA, Locatelli F. Interim Results from the Phase 3 Hgb-207 (Northstar-2) and Hgb-212 (Northstar-3) Studies of Betibeglogene Autotemcel Gene Therapy (LentiGlobin) for the Treatment of Transfusion-Dependent β-Thalassemia. Biol Blood Marrow Transplant 2020. [DOI: 10.1016/j.bbmt.2019.12.588] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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33
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Walters MC, Locatelli F, Thrasher AJ, Tisdale JF, Orchard PJ, Duncan CN, Kühl JS, De Oliveira SN, Sauer MG, Kulozik AE, Yannaki E, Hongeng S, Mapara MY, Krishnamurti L, Hermine O, Blanche S, Aubourg P, Smith NJ, Shi W, Colvin RA, McNeil E, Ribeil JA, Cavazzana M, Williams DA. Safety of Autologous Hematopoietic Stem Cell Transplantation with Gene Addition Therapy for Transfusion-Dependent β-Thalassemia, Sickle Cell Disease, and Cerebral Adrenoleukodystrophy. Biol Blood Marrow Transplant 2020. [DOI: 10.1016/j.bbmt.2019.12.104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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34
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Kulozik AE, Kunz J. Gentherapie von Hämoglobinkrankheiten – aktuelle Konzepte und Herausforderungen. Transfusionsmedizin 2019. [DOI: 10.1055/a-0825-9666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
ZusammenfassungDie β-Thalassämien und die Sichelzellerkrankung sind weltweit die häufigsten Einzelgendefekte, die konventionell nur durch eine lebenslang erforderliche Supportivtherapie oder kurativ mittels allogener Stammzelltransplantation behandelbar sind. Aktuell werden Gentherapiestrategien entwickelt, die nach Transduktion von hämatopoetischen Stammzellen durch lentivirale Vektoren zu einer Expression eines therapeutischen β-Globin-Gens oder zur therapeutischen Reexpression der fetalen Globinsynthese und damit des fetalen Hämoglobins (HbF) führen. Für die β-Thalassämie hat die Genadditionstherapie für eine ausgewählte Gruppe von Patientinnen und Patienten mit transfusionsbedürftiger Non-β0-Thalassaemia major nach konditionaler Zulassung durch die European Medicines Agency (EMA) im Juni 2019 einen ersten Grad klinischer Reife erreicht. In dieser Übersicht diskutieren wir darüber hinaus die Möglichkeiten und Herausforderungen von Genomeditierungsstrategien für die Hämoglobinkrankheiten, insbesondere durch Inaktivierung von BCL11A, des zentralen Inhibitors der postnatalen fetalen Hämoglobinsynthese. Insgesamt verspricht die Entwicklung der Gentherapie für die Hämoglobinkrankheiten eine relevante Chance für diese, auch in Deutschland zahlreicher werdenden Gruppe von Patientinnen und Patienten mit schweren, sowohl Lebensqualität als auch Lebenserwartung erheblich einschränkenden Erkrankungen.
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Affiliation(s)
- Andreas E. Kulozik
- Klinik für Pädiatrische Onkologie, Hämatologie und Immunologie, Hopp Kindertumorzentrum Heidelberg (KiTZ), Universität Heidelberg
| | - Joachim Kunz
- Klinik für Pädiatrische Onkologie, Hämatologie und Immunologie, Hopp Kindertumorzentrum Heidelberg (KiTZ), Universität Heidelberg
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35
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Richter-Pechańska P, Kunz JB, Bornhauser B, von Knebel Doeberitz C, Rausch T, Erarslan-Uysal B, Assenov Y, Frismantas V, Marovca B, Waszak SM, Zimmermann M, Seemann J, Happich M, Stanulla M, Schrappe M, Cario G, Escherich G, Bakharevich K, Kirschner-Schwabe R, Eckert C, Muckenthaler MU, Korbel JO, Bourquin JP, Kulozik AE. PDX models recapitulate the genetic and epigenetic landscape of pediatric T-cell leukemia. EMBO Mol Med 2019; 10:emmm.201809443. [PMID: 30389682 PMCID: PMC6284381 DOI: 10.15252/emmm.201809443] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We compared 24 primary pediatric T‐cell acute lymphoblastic leukemias (T‐ALL) collected at the time of initial diagnosis and relapse from 12 patients and 24 matched patient‐derived xenografts (PDXs). DNA methylation profile was preserved in PDX mice in 97.5% of the promoters (ρ = 0.99). Similarly, the genome‐wide chromatin accessibility (ATAC‐Seq) was preserved remarkably well (ρ = 0.96). Interestingly, both the ATAC regions, which showed a significant decrease in accessibility in PDXs and the regions hypermethylated in PDXs, were associated with immune response, which might reflect the immune deficiency of the mice and potentially the incomplete interaction between murine cytokines and human receptors. The longitudinal approach of this study allowed an observation that samples collected from patients who developed a type 1 relapse (clonal mutations maintained at relapse) preserved their genomic composition; whereas in patients who developed a type 2 relapse (subset of clonal mutations lost at relapse), the preservation of the leukemia's composition was more variable. In sum, this study underlines the remarkable genomic stability, and for the first time documents the preservation of the epigenomic landscape in T‐ALL‐derived PDX models.
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Affiliation(s)
- Paulina Richter-Pechańska
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, and Hopp Children's Cancer Center at NCT Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany
| | - Joachim B Kunz
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, and Hopp Children's Cancer Center at NCT Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany.,German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Beat Bornhauser
- Division of Pediatric Oncology, University Children's Hospital, Zürich, Switzerland
| | - Caroline von Knebel Doeberitz
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, and Hopp Children's Cancer Center at NCT Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany
| | - Tobias Rausch
- Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany.,European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Büşra Erarslan-Uysal
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, and Hopp Children's Cancer Center at NCT Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany
| | - Yassen Assenov
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Viktoras Frismantas
- Division of Pediatric Oncology, University Children's Hospital, Zürich, Switzerland
| | - Blerim Marovca
- Division of Pediatric Oncology, University Children's Hospital, Zürich, Switzerland
| | | | - Martin Zimmermann
- Department of Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Julia Seemann
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, and Hopp Children's Cancer Center at NCT Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany
| | - Margit Happich
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, and Hopp Children's Cancer Center at NCT Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany
| | - Martin Stanulla
- Department of Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Martin Schrappe
- Department of Pediatrics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Gunnar Cario
- Department of Pediatrics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Gabriele Escherich
- Clinic of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kseniya Bakharevich
- Clinic of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Renate Kirschner-Schwabe
- Department of Pediatric Oncology/Hematology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Cornelia Eckert
- Department of Pediatric Oncology/Hematology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Martina U Muckenthaler
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, and Hopp Children's Cancer Center at NCT Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany
| | - Jan O Korbel
- Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany.,European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Jean-Pierre Bourquin
- Division of Pediatric Oncology, University Children's Hospital, Zürich, Switzerland
| | - Andreas E Kulozik
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, and Hopp Children's Cancer Center at NCT Heidelberg, Heidelberg, Germany .,Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany
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El-Helou SM, Biegner AK, Bode S, Ehl SR, Heeg M, Maccari ME, Ritterbusch H, Speckmann C, Rusch S, Scheible R, Warnatz K, Atschekzei F, Beider R, Ernst D, Gerschmann S, Jablonka A, Mielke G, Schmidt RE, Schürmann G, Sogkas G, Baumann UH, Klemann C, Viemann D, von Bernuth H, Krüger R, Hanitsch LG, Scheibenbogen CM, Wittke K, Albert MH, Eichinger A, Hauck F, Klein C, Rack-Hoch A, Sollinger FM, Avila A, Borte M, Borte S, Fasshauer M, Hauenherm A, Kellner N, Müller AH, Ülzen A, Bader P, Bakhtiar S, Lee JY, Heß U, Schubert R, Wölke S, Zielen S, Ghosh S, Laws HJ, Neubert J, Oommen PT, Hönig M, Schulz A, Steinmann S, Schwarz K, Dückers G, Lamers B, Langemeyer V, Niehues T, Shai S, Graf D, Müglich C, Schmalzing MT, Schwaneck EC, Tony HP, Dirks J, Haase G, Liese JG, Morbach H, Foell D, Hellige A, Wittkowski H, Masjosthusmann K, Mohr M, Geberzahn L, Hedrich CM, Müller C, Rösen-Wolff A, Roesler J, Zimmermann A, Behrends U, Rieber N, Schauer U, Handgretinger R, Holzer U, Henes J, Kanz L, Boesecke C, Rockstroh JK, Schwarze-Zander C, Wasmuth JC, Dilloo D, Hülsmann B, Schönberger S, Schreiber S, Zeuner R, Ankermann T, von Bismarck P, Huppertz HI, Kaiser-Labusch P, Greil J, Jakoby D, Kulozik AE, Metzler M, Naumann-Bartsch N, Sobik B, Graf N, Heine S, Kobbe R, Lehmberg K, Müller I, Herrmann F, Horneff G, Klein A, Peitz J, Schmidt N, Bielack S, Groß-Wieltsch U, Classen CF, Klasen J, Deutz P, Kamitz D, Lassay L, Tenbrock K, Wagner N, Bernbeck B, Brummel B, Lara-Villacanas E, Münstermann E, Schneider DT, Tietsch N, Westkemper M, Weiß M, Kramm C, Kühnle I, Kullmann S, Girschick H, Specker C, Vinnemeier-Laubenthal E, Haenicke H, Schulz C, Schweigerer L, Müller TG, Stiefel M, Belohradsky BH, Soetedjo V, Kindle G, Grimbacher B. The German National Registry of Primary Immunodeficiencies (2012-2017). Front Immunol 2019; 10:1272. [PMID: 31379802 PMCID: PMC6659583 DOI: 10.3389/fimmu.2019.01272] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 05/20/2019] [Indexed: 12/16/2022] Open
Abstract
Introduction: The German PID-NET registry was founded in 2009, serving as the first national registry of patients with primary immunodeficiencies (PID) in Germany. It is part of the European Society for Immunodeficiencies (ESID) registry. The primary purpose of the registry is to gather data on the epidemiology, diagnostic delay, diagnosis, and treatment of PIDs. Methods: Clinical and laboratory data was collected from 2,453 patients from 36 German PID centres in an online registry. Data was analysed with the software Stata® and Excel. Results: The minimum prevalence of PID in Germany is 2.72 per 100,000 inhabitants. Among patients aged 1-25, there was a clear predominance of males. The median age of living patients ranged between 7 and 40 years, depending on the respective PID. Predominantly antibody disorders were the most prevalent group with 57% of all 2,453 PID patients (including 728 CVID patients). A gene defect was identified in 36% of patients. Familial cases were observed in 21% of patients. The age of onset for presenting symptoms ranged from birth to late adulthood (range 0-88 years). Presenting symptoms comprised infections (74%) and immune dysregulation (22%). Ninety-three patients were diagnosed without prior clinical symptoms. Regarding the general and clinical diagnostic delay, no PID had undergone a slight decrease within the last decade. However, both, SCID and hyper IgE- syndrome showed a substantial improvement in shortening the time between onset of symptoms and genetic diagnosis. Regarding treatment, 49% of all patients received immunoglobulin G (IgG) substitution (70%-subcutaneous; 29%-intravenous; 1%-unknown). Three-hundred patients underwent at least one hematopoietic stem cell transplantation (HSCT). Five patients had gene therapy. Conclusion: The German PID-NET registry is a precious tool for physicians, researchers, the pharmaceutical industry, politicians, and ultimately the patients, for whom the outcomes will eventually lead to a more timely diagnosis and better treatment.
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Affiliation(s)
- Sabine M. El-Helou
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- RESIST - Cluster of Excellence 2155 to Hanover Medical School, Satellite Center Freiburg, Freiburg, Germany
| | - Anika-Kerstin Biegner
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sebastian Bode
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Pediatrics and Adolescent Medicine, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Stephan R. Ehl
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Pediatrics and Adolescent Medicine, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Maximilian Heeg
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Pediatrics and Adolescent Medicine, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Maria E. Maccari
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Pediatrics and Adolescent Medicine, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Henrike Ritterbusch
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Pediatrics and Adolescent Medicine, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Carsten Speckmann
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Pediatrics and Adolescent Medicine, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Stephan Rusch
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Central Facility Biobanking, Medical Center and Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Raphael Scheible
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Institute for Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Klaus Warnatz
- Department of Rheumatology and Clinical Immunology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Faranaz Atschekzei
- Department of Clinical Immunology and Rheumatology, Hannover Medical School, Hannover, Germany
| | - Renata Beider
- Department of Clinical Immunology and Rheumatology, Hannover Medical School, Hannover, Germany
| | - Diana Ernst
- Department of Clinical Immunology and Rheumatology, Hannover Medical School, Hannover, Germany
| | - Stev Gerschmann
- Department of Clinical Immunology and Rheumatology, Hannover Medical School, Hannover, Germany
| | - Alexandra Jablonka
- Department of Clinical Immunology and Rheumatology, Hannover Medical School, Hannover, Germany
| | - Gudrun Mielke
- Department of Clinical Immunology and Rheumatology, Hannover Medical School, Hannover, Germany
| | - Reinhold E. Schmidt
- Department of Clinical Immunology and Rheumatology, Hannover Medical School, Hannover, Germany
| | - Gesine Schürmann
- Department of Clinical Immunology and Rheumatology, Hannover Medical School, Hannover, Germany
| | - Georgios Sogkas
- Department of Clinical Immunology and Rheumatology, Hannover Medical School, Hannover, Germany
| | - Ulrich H. Baumann
- Department of Paediatric Pulmonology, Allergy and Neonatology, Hannover Medical School, Hannover, Germany
| | - Christian Klemann
- Department of Paediatric Pulmonology, Allergy and Neonatology, Hannover Medical School, Hannover, Germany
| | - Dorothee Viemann
- Department of Paediatric Pulmonology, Allergy and Neonatology, Hannover Medical School, Hannover, Germany
| | - Horst von Bernuth
- Department of Pediatric Pneumology, Immunology and Intensive Care, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Renate Krüger
- Department of Pediatric Pneumology, Immunology and Intensive Care, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Leif G. Hanitsch
- Outpatient Clinic for Immunodeficiencies, Institute Medical Immunology, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Carmen M. Scheibenbogen
- Outpatient Clinic for Immunodeficiencies, Institute Medical Immunology, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Kirsten Wittke
- Outpatient Clinic for Immunodeficiencies, Institute Medical Immunology, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Michael H. Albert
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Anna Eichinger
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Fabian Hauck
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Christoph Klein
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Anita Rack-Hoch
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Franz M. Sollinger
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Anne Avila
- ImmunoDeficiencyCenter Leipzig (IDCL), Hospital St. Georg gGmbH Leipzig, Academic Teaching Hospital of the University of Leipzig, Leipzig, Germany
| | - Michael Borte
- ImmunoDeficiencyCenter Leipzig (IDCL), Hospital St. Georg gGmbH Leipzig, Academic Teaching Hospital of the University of Leipzig, Leipzig, Germany
| | - Stephan Borte
- ImmunoDeficiencyCenter Leipzig (IDCL), Hospital St. Georg gGmbH Leipzig, Academic Teaching Hospital of the University of Leipzig, Leipzig, Germany
| | - Maria Fasshauer
- ImmunoDeficiencyCenter Leipzig (IDCL), Hospital St. Georg gGmbH Leipzig, Academic Teaching Hospital of the University of Leipzig, Leipzig, Germany
| | - Anja Hauenherm
- ImmunoDeficiencyCenter Leipzig (IDCL), Hospital St. Georg gGmbH Leipzig, Academic Teaching Hospital of the University of Leipzig, Leipzig, Germany
| | - Nils Kellner
- ImmunoDeficiencyCenter Leipzig (IDCL), Hospital St. Georg gGmbH Leipzig, Academic Teaching Hospital of the University of Leipzig, Leipzig, Germany
| | - Anna H. Müller
- ImmunoDeficiencyCenter Leipzig (IDCL), Hospital St. Georg gGmbH Leipzig, Academic Teaching Hospital of the University of Leipzig, Leipzig, Germany
| | - Anett Ülzen
- ImmunoDeficiencyCenter Leipzig (IDCL), Hospital St. Georg gGmbH Leipzig, Academic Teaching Hospital of the University of Leipzig, Leipzig, Germany
| | - Peter Bader
- Division for Stem Cell Transplantation and Immunology, Department for Children and Adolescents, Frankfurt University Hospital, Frankfurt, Germany
| | - Shahrzad Bakhtiar
- Division for Stem Cell Transplantation and Immunology, Department for Children and Adolescents, Frankfurt University Hospital, Frankfurt, Germany
| | - Jae-Yun Lee
- Division for Stem Cell Transplantation and Immunology, Department for Children and Adolescents, Frankfurt University Hospital, Frankfurt, Germany
| | - Ursula Heß
- Department for Children and Adolescents, Division for Allergology, Pneumology and Cystic Fibrosis, University Hospital Goethe University, Frankfurt am Main, Germany
| | - Ralf Schubert
- Department for Children and Adolescents, Division for Allergology, Pneumology and Cystic Fibrosis, University Hospital Goethe University, Frankfurt am Main, Germany
| | - Sandra Wölke
- Department for Children and Adolescents, Division for Allergology, Pneumology and Cystic Fibrosis, University Hospital Goethe University, Frankfurt am Main, Germany
| | - Stefan Zielen
- Department for Children and Adolescents, Division for Allergology, Pneumology and Cystic Fibrosis, University Hospital Goethe University, Frankfurt am Main, Germany
| | - Sujal Ghosh
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, University Children's Hospital, Heinrich-Heine-University, Düsseldorf, Germany
| | - Hans-Juergen Laws
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, University Children's Hospital, Heinrich-Heine-University, Düsseldorf, Germany
| | - Jennifer Neubert
- 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
| | - Manfred Hönig
- Department of Pediatrics, University Medical Center Ulm, Ulm, Germany
| | - Ansgar Schulz
- Department of Pediatrics, University Medical Center Ulm, Ulm, Germany
| | - Sandra Steinmann
- Department of Pediatrics, University Medical Center Ulm, Ulm, Germany
| | - Klaus Schwarz
- Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Service Baden-Württemberg - Hessen and Institute for Transfusion Medicine, University Ulm, Ulm, Germany
| | - Gregor Dückers
- Centre for Child and Adolescenct Health, Helios Klinikum Krefeld, Krefeld, Germany
| | - Beate Lamers
- Centre for Child and Adolescenct Health, Helios Klinikum Krefeld, Krefeld, Germany
| | - Vanessa Langemeyer
- Centre for Child and Adolescenct Health, Helios Klinikum Krefeld, Krefeld, Germany
| | - Tim Niehues
- Centre for Child and Adolescenct Health, Helios Klinikum Krefeld, Krefeld, Germany
| | - Sonu Shai
- Centre for Child and Adolescenct Health, Helios Klinikum Krefeld, Krefeld, Germany
| | - Dagmar Graf
- MVZ Dr. Reising-Ackermann und Kollegen, Leipzig, Germany
| | - Carmen Müglich
- Rheumatology/Clinical Immunology, Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany
| | - Marc T. Schmalzing
- Rheumatology/Clinical Immunology, Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany
| | - Eva C. Schwaneck
- Rheumatology/Clinical Immunology, Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany
| | - Hans-Peter Tony
- Rheumatology/Clinical Immunology, Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany
| | - Johannes Dirks
- Pediatric Immunology, Department of Pediatrics, University Hospital Würzburg, Würzburg, Germany
| | - Gabriele Haase
- Pediatric Immunology, Department of Pediatrics, University Hospital Würzburg, Würzburg, Germany
| | - Johannes G. Liese
- Pediatric Immunology, Department of Pediatrics, University Hospital Würzburg, Würzburg, Germany
| | - Henner Morbach
- Pediatric Immunology, Department of Pediatrics, University Hospital Würzburg, Würzburg, Germany
| | - Dirk Foell
- Department of Pediatric Rheumatology and Immunology, University Children's Hospital, Muenster, Germany
| | - Antje Hellige
- Department of Pediatric Rheumatology and Immunology, University Children's Hospital, Muenster, Germany
| | - Helmut Wittkowski
- Department of Pediatric Rheumatology and Immunology, University Children's Hospital, Muenster, Germany
| | - Katja Masjosthusmann
- Department of General Pediatrics, University Children's Hospital Muenster, Muenster, Germany
| | - Michael Mohr
- Department of Hematology, Oncology and Respiratory Medicine, University Hospital Muenster, Muenster, Germany
| | - Linda Geberzahn
- Department of Pediatrics, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Christian M. Hedrich
- Department of Pediatrics, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
- Department of Women's and Children's Health, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Christiane Müller
- Department of Pediatrics, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Angela Rösen-Wolff
- Department of Pediatrics, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Joachim Roesler
- Department of Pediatrics, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Antje Zimmermann
- Department of Pediatrics, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Uta Behrends
- Department of Pediatrics, Kinderklinik München Schwabing, StKM GmbH und Klinikum Rechts der Isar, Technische Universität München, Munich, Germany
| | - Nikolaus Rieber
- Department of Pediatrics, Kinderklinik München Schwabing, StKM GmbH und Klinikum Rechts der Isar, Technische Universität München, Munich, Germany
- Department of Oncology/Haematology, University Children's Hospital Tübingen, Tuebingen, Germany
| | - Uwe Schauer
- University Children's Hospital, Ruhr University Bochum, Bochum, Germany
| | - Rupert Handgretinger
- Department of Oncology/Haematology, University Children's Hospital Tübingen, Tuebingen, Germany
| | - Ursula Holzer
- Department of Oncology/Haematology, University Children's Hospital Tübingen, Tuebingen, Germany
| | - Jörg Henes
- Department of Internal Medicine II (Oncology, Hematology, Rheumatology, Immunology), University Hospital Tübingen, Tuebingen, Germany
| | - Lothar Kanz
- Department of Internal Medicine II (Oncology, Hematology, Rheumatology, Immunology), University Hospital Tübingen, Tuebingen, Germany
| | - Christoph Boesecke
- Department of Internal Medicine I, Bonn University Hospital, Bonn, Germany
| | | | | | | | - Dagmar Dilloo
- Department of Paediatric Haematology and Oncology, Bonn University Hospital, Bonn, Germany
| | - Brigitte Hülsmann
- Department of Paediatric Haematology and Oncology, Bonn University Hospital, Bonn, Germany
| | - Stefan Schönberger
- Department of Paediatric Haematology and Oncology, Bonn University Hospital, Bonn, Germany
| | - Stefan Schreiber
- Department of General Internal Medicine, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Rainald Zeuner
- Department of General Internal Medicine, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Tobias Ankermann
- Klinik für Kinder und Jugendmedizin I, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Philipp von Bismarck
- Klinik für Kinder und Jugendmedizin I, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Hans-Iko Huppertz
- Prof.-Hess Childrens Hospital, Klinikum Bremen-Mitte, Bremen, Germany
| | | | - Johann Greil
- Department of Pediatric Oncology, Hematology and Immunology and Hopp Children's Tumor Center, University of Heidelberg, Heidelberg, Germany
| | - Donate Jakoby
- Department of Pediatric Oncology, Hematology and Immunology and Hopp Children's Tumor Center, University of Heidelberg, Heidelberg, Germany
| | - Andreas E. Kulozik
- Department of Pediatric Oncology, Hematology and Immunology and Hopp Children's Tumor Center, University of Heidelberg, Heidelberg, Germany
| | - Markus Metzler
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, University Hospital Erlangen, Erlangen, Germany
| | - Nora Naumann-Bartsch
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, University Hospital Erlangen, Erlangen, Germany
| | - Bettina Sobik
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, University Hospital Erlangen, Erlangen, Germany
| | - Norbert Graf
- Department of Paediatric Haematology and Oncology, Saarland University Homburg, Homburg, Germany
| | - Sabine Heine
- Department of Paediatric Haematology and Oncology, Saarland University Homburg, Homburg, Germany
| | - Robin Kobbe
- Division for Pediatric Stem Cell Transplantation and Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kai Lehmberg
- Division for Pediatric Stem Cell Transplantation and Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ingo Müller
- Division for Pediatric Stem Cell Transplantation and Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Friedrich Herrmann
- Department of Pediatrics, Asklepios Clinic Sankt Augustin, Sankt Augustin, Germany
| | - Gerd Horneff
- Department of Pediatrics, Asklepios Clinic Sankt Augustin, Sankt Augustin, Germany
- Department of Pediatric and Adolescents Medicine, Medical Faculty, University Hospital of Cologne, Cologne, Germany
| | - Ariane Klein
- Department of Pediatrics, Asklepios Clinic Sankt Augustin, Sankt Augustin, Germany
- Department of Pediatric and Adolescents Medicine, Medical Faculty, University Hospital of Cologne, Cologne, Germany
| | - Joachim Peitz
- Department of Pediatrics, Asklepios Clinic Sankt Augustin, Sankt Augustin, Germany
| | - Nadine Schmidt
- Department of Pediatrics, Asklepios Clinic Sankt Augustin, Sankt Augustin, Germany
| | - Stefan Bielack
- Pediatrics 5 (Oncology, Hematology, Immunology), Center for Pediatric, Adolescent and Women's Medicine, Klinikum Stuttgart - Olgahospital, Stuttgart, Germany
| | - Ute Groß-Wieltsch
- Pediatrics 5 (Oncology, Hematology, Immunology), Center for Pediatric, Adolescent and Women's Medicine, Klinikum Stuttgart - Olgahospital, Stuttgart, Germany
| | - Carl F. Classen
- Oncology Hematology Division, Department for Children and Adolescents, University Medicine Rostock, Rostock, Germany
| | - Jessica Klasen
- Oncology Hematology Division, Department for Children and Adolescents, University Medicine Rostock, Rostock, Germany
| | | | | | | | | | | | | | | | | | | | | | - Nadine Tietsch
- Clinic of Pediatrics, Klinikum Dortmund, Dortmund, Germany
| | | | - Michael Weiß
- Department of Pediatrics, Children's Hospital Amsterdamer Strasse, Cologne, Germany
| | - Christof Kramm
- Division of Pediatric Hematology and Oncology, University Medical Center Göttingen, Göttingen, Germany
| | - Ingrid Kühnle
- Division of Pediatric Hematology and Oncology, University Medical Center Göttingen, Göttingen, Germany
| | - Silke Kullmann
- Division of Pediatric Hematology and Oncology, University Medical Center Göttingen, Göttingen, Germany
| | | | - Christof Specker
- Clinic of Rheumatology and Clinical Immunology, Hospitals Essen-Mitte, Essen, Germany
| | | | - Henriette Haenicke
- Department of Pediatric and Adolescents Medicine, Helios Hospital Berlin-Buch, Berlin, Germany
| | - Claudia Schulz
- Department of Pediatric and Adolescents Medicine, Helios Hospital Berlin-Buch, Berlin, Germany
| | - Lothar Schweigerer
- Department of Pediatric and Adolescents Medicine, Helios Hospital Berlin-Buch, Berlin, Germany
| | - Thomas G. Müller
- Department for Pediatrics I, Martin Luther University Hospital, Halle, Germany
| | - Martina Stiefel
- Department for Pediatrics I, Martin Luther University Hospital, Halle, Germany
| | - Bernd H. Belohradsky
- dsai - Deutsche Selbsthilfe Angeborene Immundefekte e.V. (Patient Organization) e.V., Schnaitsee, Germany
| | - Veronika Soetedjo
- Institute for Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Gerhard Kindle
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Central Facility Biobanking, Medical Center and Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Bodo Grimbacher
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- RESIST - Cluster of Excellence 2155 to Hanover Medical School, Satellite Center Freiburg, Freiburg, Germany
- DZIF – German Center for Infection Research, Satellite Center Freiburg, Freiburg, Germany
- CIBSS – Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
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Szarzyńska‐Zawadzka B, Kunz JB, Sędek Ł, Kosmalska M, Zdon K, Biecek P, Bandapalli OR, Kraszewska‐Hamilton M, Jaksik R, Drobna M, Kowalczyk JR, Szczepański T, Van Vlierberghe P, Kulozik AE, Witt M, Dawidowska M. PTEN abnormalities predict poor outcome in children with T-cell acute lymphoblastic leukemia treated according to ALL IC-BFM protocols. Am J Hematol 2019; 94:E93-E96. [PMID: 30614545 DOI: 10.1002/ajh.25396] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 01/02/2019] [Indexed: 01/11/2023]
Affiliation(s)
| | - Joachim B. Kunz
- Department of Pediatric Oncology, Hematology, and Immunology and Hopp Children's Cancer Center (KiTZ) University of Heidelberg Heidelberg Germany
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory University of Heidelberg Heidelberg Germany
- German Consortium for Translational Cancer Research (DKTK) Heidelberg Germany
| | - Łukasz Sędek
- Department of Microbiology and Immunology Medical University of Silesia Katowice Poland
| | - Maria Kosmalska
- Institute of Human Genetics, Polish Academy of Sciences Poznań Poland
| | - Katarzyna Zdon
- Faculty of Mathematics and Information Science Warsaw University of Technology Warsaw Poland
| | - Przemysław Biecek
- Faculty of Mathematics and Information Science Warsaw University of Technology Warsaw Poland
| | - Obul R. Bandapalli
- Department of Pediatric Oncology, Hematology, and Immunology and Hopp Children's Cancer Center (KiTZ) University of Heidelberg Heidelberg Germany
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory University of Heidelberg Heidelberg Germany
- German Consortium for Translational Cancer Research (DKTK) Heidelberg Germany
| | | | - Roman Jaksik
- Silesian University of Technology Gliwice Poland
| | - Monika Drobna
- Institute of Human Genetics, Polish Academy of Sciences Poznań Poland
| | - Jerzy R. Kowalczyk
- Department of Pediatric Hematology, Oncology and Transplantology Medical University of Lublin Lublin Poland
| | - Tomasz Szczepański
- Department of Pediatric Hematology and Oncology, Zabrze Medical University of Silesia Katowice Poland
| | - Pieter Van Vlierberghe
- Department of Biomolecular Medicine Ghent University Ghent Belgium
- Cancer Research Institute Ghent (CRIG) Ghent Belgium
| | - Andreas E. Kulozik
- Department of Pediatric Oncology, Hematology, and Immunology and Hopp Children's Cancer Center (KiTZ) University of Heidelberg Heidelberg Germany
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory University of Heidelberg Heidelberg Germany
- German Consortium for Translational Cancer Research (DKTK) Heidelberg Germany
| | - Michał Witt
- Institute of Human Genetics, Polish Academy of Sciences Poznań Poland
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Erkek S, Johann PD, Finetti MA, Drosos Y, Chou HC, Zapatka M, Sturm D, Jones DTW, Korshunov A, Rhyzova M, Wolf S, Mallm JP, Beck K, Witt O, Kulozik AE, Frühwald MC, Northcott PA, Korbel JO, Lichter P, Eils R, Gajjar A, Roberts CWM, Williamson D, Hasselblatt M, Chavez L, Pfister SM, Kool M. Comprehensive Analysis of Chromatin States in Atypical Teratoid/Rhabdoid Tumor Identifies Diverging Roles for SWI/SNF and Polycomb in Gene Regulation. Cancer Cell 2019; 35:95-110.e8. [PMID: 30595504 PMCID: PMC6341227 DOI: 10.1016/j.ccell.2018.11.014] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 05/30/2018] [Accepted: 11/21/2018] [Indexed: 12/27/2022]
Abstract
Biallelic inactivation of SMARCB1, encoding a member of the SWI/SNF chromatin remodeling complex, is the hallmark genetic aberration of atypical teratoid rhabdoid tumors (ATRT). Here, we report how loss of SMARCB1 affects the epigenome in these tumors. Using chromatin immunoprecipitation sequencing (ChIP-seq) on primary tumors for a series of active and repressive histone marks, we identified the chromatin states differentially represented in ATRTs compared with other brain tumors and non-neoplastic brain. Re-expression of SMARCB1 in ATRT cell lines enabled confirmation of our genome-wide findings for the chromatin states. Additional generation of ChIP-seq data for SWI/SNF and Polycomb group proteins and the transcriptional repressor protein REST determined differential dependencies of SWI/SNF and Polycomb complexes in regulation of diverse gene sets in ATRTs.
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Affiliation(s)
- Serap Erkek
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany; Izmir Biomedicine and Genome Center, 35340 Izmir, Turkey
| | - Pascal D Johann
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Department of Pediatric Hematology and Oncology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Martina A Finetti
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, NE2 Newcastle Upon Tyne, UK
| | - Yiannis Drosos
- Department of Oncology, St Jude Children's Research Hospital, 38105 Memphis, USA
| | - Hsien-Chao Chou
- Department of Oncology, St Jude Children's Research Hospital, 38105 Memphis, USA
| | - Marc Zapatka
- Division of Molecular Genetics, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Dominik Sturm
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Department of Pediatric Hematology and Oncology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - David T W Jones
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Andrey Korshunov
- Department of Neuropathology, University Hospital Heidelberg, 69120 Heidelberg, Germany; Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Marina Rhyzova
- Department of Neuropathology, Burdenko Neurosurgical Institute, 125047 Moscow, Russia
| | - Stephan Wolf
- Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Jan-Philipp Mallm
- Genome Organization & Function Research Group, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Heidelberg Center for Personalized Oncology, DKFZ-HIPO, DKFZ, 69120 Heidelberg, Germany
| | - Katja Beck
- Heidelberg Center for Personalized Oncology, DKFZ-HIPO, DKFZ, 69120 Heidelberg, Germany
| | - Olaf Witt
- Department of Pediatric Hematology and Oncology, University Hospital Heidelberg, 69120 Heidelberg, Germany; Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Andreas E Kulozik
- Department of Pediatric Hematology and Oncology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Michael C Frühwald
- University Children's Hospital Augsburg, Swabian Children's Cancer Center, 86156 Augsburg, Germany; EU-RHAB Registry Center, 86156 Augsburg, Germany
| | - Paul A Northcott
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 38105 Memphis, TN, USA
| | - Jan O Korbel
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
| | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; Heidelberg Center for Personalized Oncology, DKFZ-HIPO, DKFZ, 69120 Heidelberg, Germany
| | - Roland Eils
- Genome Organization & Function Research Group, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Amar Gajjar
- Department of Oncology, St Jude Children's Research Hospital, 38105 Memphis, USA
| | - Charles W M Roberts
- Department of Oncology, St Jude Children's Research Hospital, 38105 Memphis, USA
| | - Daniel Williamson
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, NE2 Newcastle Upon Tyne, UK
| | - Martin Hasselblatt
- Institute of Neuropathology, University Hospital Münster, 48149 Münster, Germany
| | - Lukas Chavez
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Stefan M Pfister
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Department of Pediatric Hematology and Oncology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Marcel Kool
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
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Serjeant GR, Serjeant BE, Mason KP, Happich M, Kulozik AE. β-Thalassemia Mutations in Jamaica: Geographic Variation in Small Communities. Hemoglobin 2019; 42:294-296. [DOI: 10.1080/03630269.2018.1540354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Graham R. Serjeant
- Sickle Cell Trust (Jamaica), Southern Regional Health Authority, Mandeville, Jamaica
| | - Beryl E. Serjeant
- Sickle Cell Trust (Jamaica), Southern Regional Health Authority, Mandeville, Jamaica
| | - Karlene P. Mason
- Sickle Cell Trust (Jamaica), Southern Regional Health Authority, Mandeville, Jamaica
| | - Margit Happich
- Department of Paediatric Oncology, Haematology and Immunology, Heidelberg University, Heidelberg, Germany
| | - Andreas E. Kulozik
- Department of Paediatric Oncology, Haematology and Immunology, Heidelberg University, Heidelberg, Germany
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Machiela MJ, Grünewald TG, Surdez D, Reynaud S, Mirabeau O, Karlins E, Rubio RA, Zaidi S, Grossetete-Lalami S, Ballet S, Lapouble E, Laurence V, Michon J, Pierron G, Kovar H, Gaspar N, Kontny U, González-Neira A, Picci P, Alonso J, Patino-Garcia A, Corradini N, Freedman ND, Rothman N, Dagnall CL, Burdett L, Jones K, Manning M, Wyatt K, Zhou W, Yeager M, Cox DG, Hoover RN, Khan J, Armstrong GT, Leisenring WM, Bhatia S, Robison LL, Dirksen U, Metzler M, Hartmann W, Strauch K, Kirchner T, Kulozik AE, Morton LM, Mirabello L, Tucker MA, Tirode F, Chanock S, Delattre O. Abstract A13: Genome-wide association study identifies multiple new loci associated with Ewing sarcoma susceptibility. Cancer Res 2018. [DOI: 10.1158/1538-7445.pedca17-a13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Ewing sarcoma (EWS), a pediatric tumor predominantly occurring in children of European ancestry, is characterized by the EWSR1-FLI1 fusion oncogene. We performed a genome-wide association study (GWAS) of 749 EWS cases and 1,378 unaffected individuals of European ancestry. Our study replicated previously reported susceptibility loci at 1p36.22, 10q21.3, and 15q15.1 and identified new loci at 6p25.1, 8q24.23, 20p11.22, and 20p11.23 (P-values <5x10-8). Effect estimates exhibited odds ratios (ORs) in excess of 1.7, which is high for cancer GWAS, and striking in light of the rarity of EWS cases in familial cancer syndromes. In expression quantitative trait locus (eQTL) analyses, we observed altered expression patterns for plausible candidate genes at 6p25.1 with RREB1, a RAS-responsive element, and at 20p11.23 with KIZ, a centrosomal stabilization protein. The 20p11.22 locus is also near NKX2-2, a highly overexpressed gene in EWS. Interestingly, most loci reside near GGAA repeat sequences where binding of the EWSR1-FLI1 fusion protein occurs. The seven EWS susceptibility loci discovered in only 749 cases make EWS one of the most productive GWAS studied cancers when considering a locus-to-case discovery ratio. The substantive estimated ORs suggest a distinctive underlying genetic architecture for EWS in which moderate-risk SNPs likely constitute a significant fraction and may interact with EWSR1-FLI1 binding.
Citation Format: Mitchell J. Machiela, Thomas G.P. Grünewald, Didier Surdez, Stephanie Reynaud, Olivier Mirabeau, Eric Karlins, Rebeca Alba Rubio, Sakina Zaidi, Sandrine Grossetete-Lalami, Stelly Ballet, Eve Lapouble, Valérie Laurence, Jean Michon, Gaelle Pierron, Heinrich Kovar, Nathalie Gaspar, Udo Kontny, Anna González-Neira, Piero Picci, Javier Alonso, Ana Patino-Garcia, Nadège Corradini, Neal D. Freedman, Nathaniel Rothman, Casey L. Dagnall, Laurie Burdett, Kristine Jones, Michelle Manning, Kathleen Wyatt, Weiyin Zhou, Meredith Yeager, David G. Cox, Robert N. Hoover, Javed Khan, Gregory T. Armstrong, Wendy M. Leisenring, Smita Bhatia, Leslie L. Robison, Uta Dirksen, Markus Metzler, Wolfgang Hartmann, Konstantin Strauch, Thomas Kirchner, Andreas E. Kulozik, Lindsay M. Morton, Lisa Mirabello, Margaret A. Tucker, Franck Tirode, Stephen Chanock, Olivier Delattre. Genome-wide association study identifies multiple new loci associated with Ewing sarcoma susceptibility [abstract]. In: Proceedings of the AACR Special Conference: Pediatric Cancer Research: From Basic Science to the Clinic; 2017 Dec 3-6; Atlanta, Georgia. Philadelphia (PA): AACR; Cancer Res 2018;78(19 Suppl):Abstract nr A13.
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Affiliation(s)
- Mitchell J. Machiela
- 1Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD,
| | - Thomas G.P. Grünewald
- 2Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine,, Munich, Germany,
| | - Didier Surdez
- 3Inserm U830, Équipe Labellisés LNCC, PSL université, Institut Curie, Paris, France,
| | | | | | - Eric Karlins
- 1Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD,
| | - Rebeca Alba Rubio
- 2Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine,, Munich, Germany,
| | - Sakina Zaidi
- 4SIREDO Oncology Centre, Institut Curie, Paris, France,
| | | | - Stelly Ballet
- 4SIREDO Oncology Centre, Institut Curie, Paris, France,
| | - Eve Lapouble
- 4SIREDO Oncology Centre, Institut Curie, Paris, France,
| | | | - Jean Michon
- 4SIREDO Oncology Centre, Institut Curie, Paris, France,
| | | | - Heinrich Kovar
- 5Children’s Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria,
| | - Nathalie Gaspar
- 6Service de Pédiatrie, Institut Gustave Roussy, Villejuif, France,
| | - Udo Kontny
- 7Division of Pediatric Hematology Oncology and Stem Cell Transplantation, RWTH Aachen University, Aachen, Germany,
| | - Anna González-Neira
- 8Human Cancer Genetics Programme, Spanish National Cancer Research Centre, Madrid, Spain,
| | - Piero Picci
- 9Laboratorio di Oncologia Sperimentale, Istituto Ortopedico Rizzoli di Bologna, Bologna, Italy,
| | - Javier Alonso
- 10Instituto de Investigación de Enfermedades Raras, Instituto de Salud Carlos III, Majadahonda, Spain,
| | - Ana Patino-Garcia
- 11Laboratory of Pediatrics, University of Navarra, University Clinic of Navarra, IdiSNA, Pamplona, Spain,
| | | | - Neal D. Freedman
- 1Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD,
| | - Nathaniel Rothman
- 1Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD,
| | - Casey L. Dagnall
- 1Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD,
| | - Laurie Burdett
- 1Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD,
| | - Kristine Jones
- 1Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD,
| | - Michelle Manning
- 1Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD,
| | - Kathleen Wyatt
- 1Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD,
| | - Weiyin Zhou
- 1Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD,
| | - Meredith Yeager
- 1Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD,
| | - David G. Cox
- 13Centre Léon Bérard, INSERM U1052, Lyon, France,
| | - Robert N. Hoover
- 1Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD,
| | - Javed Khan
- 14Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD,
| | - Gregory T. Armstrong
- 15Department of Epidemiology and Cancer Control, St. Jude Children’s Research Hospital, Memphis, TN,
| | - Wendy M. Leisenring
- 16Cancer Prevention and Clinical Statistics Programs, Fred Hutchinson Cancer Research Center, Seattle, WA,
| | - Smita Bhatia
- 17Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL,
| | - Leslie L. Robison
- 15Department of Epidemiology and Cancer Control, St. Jude Children’s Research Hospital, Memphis, TN,
| | - Uta Dirksen
- 18University Children’s Hospital of Essen, Essen, Germany,
| | - Markus Metzler
- 19University Children’s Hospital of Erlangen, Erlangen, Germany,
| | - Wolfgang Hartmann
- 20Gerhard-Domagk Institute of Pathology, University Hospital of Münster, Münster, Germany,
| | | | - Thomas Kirchner
- 22Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany,
| | | | - Lindsay M. Morton
- 1Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD,
| | - Lisa Mirabello
- 1Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD,
| | - Margaret A. Tucker
- 1Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD,
| | - Franck Tirode
- 4SIREDO Oncology Centre, Institut Curie, Paris, France,
| | - Stephen Chanock
- 1Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD,
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Jones DTW, Worst BC, Pfaff E, Tilburg CMV, Balasubramanian GP, Fiesel P, Pajtler KW, Freitag A, Witt R, Kulozik AE, Sahm F, Deimling AV, Eggert A, Dirksen U, Lichter P, Capper D, Witt O, Pfister SM. Abstract IA11: Pediatric precision oncology programs in Germany and Europe. Cancer Res 2018. [DOI: 10.1158/1538-7445.pedca17-ia11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The treatment of relapses from high-risk entities remains a major clinical challenge, thus the desperate need for precision medicine approaches. To serve this need, we have developed the INFORM registry study (INdividualized therapy FOr Relapsed Malignancies in Childhood), which attempts to rapidly generate personalized tumor profiles and identify therapeutic targets in a clinical diagnostic environment for relapse patients. The INFORM study assesses the feasibility of integrating rapid molecular profiling in the clinical management of pediatric cancer patients with progressive or relapsed high-risk malignancies. Whole-exome and low-coverage whole-genome sequencing are being performed on tumor and normal DNA, complemented with matched tumor RNA sequencing (Illumina HiSeq4000), DNA methylation profiling, and gene expression profiling (for outlier gene expression). To date, more than 400 patients were enrolled from >50 centers in seven different countries (Germany, The Netherlands, Switzerland, Austria, Sweden, Finland, and Australia). The average turnaround time from tissue arrival to molecular results is 3 weeks. Actionable targets with at least “borderline” evidence (according to a prioritization score harmonized with the other major pediatric precision oncology programs across Europe) are being identified in ~50% of patients. Based on these findings, several patients were recruited onto ongoing clinical trials, or targeted therapeutics and/or patient-specific peptide vaccines were incorporated into individualized treatment regimes, with first reports of marked responses. Furthermore, we have established a systematic workflow for the reporting of hereditary predisposition, which is detected in ~7% of cases. In 2018, we will start recruiting patients onto several target-defined (entity independent) subtrials of the INFORM2 interventional trial series as well as the complementary counterpart conducted in France, the eSMART trial, which will collectively provide a portfolio of ~10 mechanism-of-action defined, investigator-initiated early phase clinical (combination) trials for pediatric patients at relapse within the European Innovative Therapies for Children with Cancer (ITCC) Consortium.
Citation Format: David T. W. Jones, Barbara C.Worst, Elke Pfaff, Cornelis M. Van Tilburg, Gnana Prakash Balasubramanian, Petra Fiesel, Kristian W. Pajtler, Angelika Freitag, Ruth Witt, Andreas E. Kulozik, Felix Sahm, Andreas von Deimling, Angelika Eggert, Uta Dirksen, Peter Lichter, David Capper, Olaf Witt, Stefan M. Pfister. Pediatric precision oncology programs in Germany and Europe [abstract]. In: Proceedings of the AACR Special Conference: Pediatric Cancer Research: From Basic Science to the Clinic; 2017 Dec 3-6; Atlanta, Georgia. Philadelphia (PA): AACR; Cancer Res 2018;78(19 Suppl):Abstract nr IA11.
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Affiliation(s)
- David T. W. Jones
- 1Hopp Children’s Cancer Center at NCT Heidelberg (KiTZ), Heidelberg, Germany,
- 2German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany,
| | - Barbara C. Worst
- 1Hopp Children’s Cancer Center at NCT Heidelberg (KiTZ), Heidelberg, Germany,
- 2German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany,
- 3Heidelberg University Hospital, Heidelberg, Germany,
| | - Elke Pfaff
- 1Hopp Children’s Cancer Center at NCT Heidelberg (KiTZ), Heidelberg, Germany,
- 2German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany,
- 3Heidelberg University Hospital, Heidelberg, Germany,
| | - Cornelis M. Van Tilburg
- 1Hopp Children’s Cancer Center at NCT Heidelberg (KiTZ), Heidelberg, Germany,
- 2German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany,
- 3Heidelberg University Hospital, Heidelberg, Germany,
| | - Gnana Prakash Balasubramanian
- 1Hopp Children’s Cancer Center at NCT Heidelberg (KiTZ), Heidelberg, Germany,
- 2German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany,
| | - Petra Fiesel
- 1Hopp Children’s Cancer Center at NCT Heidelberg (KiTZ), Heidelberg, Germany,
- 3Heidelberg University Hospital, Heidelberg, Germany,
| | - Kristian W. Pajtler
- 1Hopp Children’s Cancer Center at NCT Heidelberg (KiTZ), Heidelberg, Germany,
- 2German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany,
- 3Heidelberg University Hospital, Heidelberg, Germany,
| | - Angelika Freitag
- 1Hopp Children’s Cancer Center at NCT Heidelberg (KiTZ), Heidelberg, Germany,
- 2German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany,
| | - Ruth Witt
- 1Hopp Children’s Cancer Center at NCT Heidelberg (KiTZ), Heidelberg, Germany,
- 2German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany,
| | - Andreas E. Kulozik
- 1Hopp Children’s Cancer Center at NCT Heidelberg (KiTZ), Heidelberg, Germany,
- 3Heidelberg University Hospital, Heidelberg, Germany,
| | - Felix Sahm
- 1Hopp Children’s Cancer Center at NCT Heidelberg (KiTZ), Heidelberg, Germany,
- 3Heidelberg University Hospital, Heidelberg, Germany,
| | - Andreas von Deimling
- 1Hopp Children’s Cancer Center at NCT Heidelberg (KiTZ), Heidelberg, Germany,
- 3Heidelberg University Hospital, Heidelberg, Germany,
| | | | - Uta Dirksen
- 5University Hospital of Muenster, Muenster, Germany
| | - Peter Lichter
- 2German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany,
| | - David Capper
- 4Charité Universitätsmedizin Berlin, Berlin, Germany,
| | - Olaf Witt
- 1Hopp Children’s Cancer Center at NCT Heidelberg (KiTZ), Heidelberg, Germany,
- 2German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany,
- 3Heidelberg University Hospital, Heidelberg, Germany,
| | - Stefan M. Pfister
- 1Hopp Children’s Cancer Center at NCT Heidelberg (KiTZ), Heidelberg, Germany,
- 2German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany,
- 3Heidelberg University Hospital, Heidelberg, Germany,
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Vanden Bempt M, Demeyer S, Broux M, De Bie J, Bornschein S, Mentens N, Vandepoel R, Geerdens E, Radaelli E, Bornhauser BC, Kulozik AE, Meijerink JP, Bourquin JP, de Bock CE, Cools J. Cooperative Enhancer Activation by TLX1 and STAT5 Drives Development of NUP214-ABL1/TLX1-Positive T Cell Acute Lymphoblastic Leukemia. Cancer Cell 2018; 34:271-285.e7. [PMID: 30107177 PMCID: PMC6097876 DOI: 10.1016/j.ccell.2018.07.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 05/04/2018] [Accepted: 07/18/2018] [Indexed: 01/01/2023]
Abstract
The NUP214-ABL1 fusion is a constitutively activated tyrosine kinase that is significantly associated with overexpression of the TLX1 and TLX3 transcription factors in T cell acute lymphoblastic leukemia (T-ALL). Here we show that NUP214-ABL1 cooperates with TLX1 in driving T-ALL development using a transgenic mouse model and human T-ALL cells. Using integrated ChIP-sequencing, ATAC-sequencing, and RNA-sequencing data, we demonstrate that TLX1 and STAT5, the downstream effector of NUP214-ABL1, co-bind poised enhancer regions, and cooperatively activate the expression of key proto-oncogenes such as MYC and BCL2. Inhibition of STAT5, downregulation of TLX1 or MYC, or interference with enhancer function through BET-inhibitor treatment leads to reduction of target gene expression and induction of leukemia cell death.
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Affiliation(s)
- Marlies Vanden Bempt
- KU Leuven Center for Human Genetics, KU Leuven, Leuven, Belgium; VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Sofie Demeyer
- KU Leuven Center for Human Genetics, KU Leuven, Leuven, Belgium; VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Michaël Broux
- KU Leuven Center for Human Genetics, KU Leuven, Leuven, Belgium; VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Jolien De Bie
- KU Leuven Center for Human Genetics, KU Leuven, Leuven, Belgium; VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Simon Bornschein
- KU Leuven Center for Human Genetics, KU Leuven, Leuven, Belgium; VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Nicole Mentens
- KU Leuven Center for Human Genetics, KU Leuven, Leuven, Belgium; VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Roel Vandepoel
- KU Leuven Center for Human Genetics, KU Leuven, Leuven, Belgium; VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Ellen Geerdens
- KU Leuven Center for Human Genetics, KU Leuven, Leuven, Belgium; VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Enrico Radaelli
- KU Leuven Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Beat C Bornhauser
- Department of Oncology and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Andreas E Kulozik
- Department of Pediatric Hematology and Oncology, Heidelberg University Children's Hospital, Heidelberg, Germany; Hopp Children's Cancer Center at the NCT Heidelberg, Heidelberg, Germany
| | - Jules P Meijerink
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Jean-Pierre Bourquin
- Department of Oncology and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Charles E de Bock
- KU Leuven Center for Human Genetics, KU Leuven, Leuven, Belgium; VIB Center for Cancer Biology, VIB, Leuven, Belgium.
| | - Jan Cools
- KU Leuven Center for Human Genetics, KU Leuven, Leuven, Belgium; VIB Center for Cancer Biology, VIB, Leuven, Belgium.
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43
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Fuhrmann S, Schabath R, Möricke A, Zimmermann M, Kunz JB, Kulozik AE, Ludwig WD, Schrappe M, Karawajew L, Ratei R. Expression of CD56 defines a distinct subgroup in childhood T-ALL with inferior outcome. Results of the ALL-BFM 2000 trial. Br J Haematol 2018; 183:96-103. [PMID: 30028023 DOI: 10.1111/bjh.15503] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 06/07/2018] [Indexed: 12/15/2022]
Abstract
This study reports the prognostic impact of the expression of the natural killer cell marker CD56 in a large series of risk-adapted paediatric patients with T cell acute lymphoblastic leukaemia (T-ALL; n = 493) treated within the ALL-Berlin-Frankfurt-Münster (BFM) 2000 protocol. The immunophenotype was analysed centrally at diagnosis using flow cytometry and correlated with clinical parameters and outcome. CD56 expression was detected in 7·1% and early T-cell precursor (ETP) phenotype in 6·7% of all T-ALL patients. The percentage of ETP in the CD56+ T-ALL cohort was 4-fold higher than in the whole cohort. CD56+ T-ALL frequently expressed the progenitor marker CD34 and myeloid antigens CD13 and CD33. The 5-year event-free survival (EFS) rates for the European Group for the Immunological classification of Leukaemias/World Health Organization subgroups and the ETP phenotype were not statistically different. By contrast, patients with CD56 expression had a significantly reduced EFS (60 ± 8%) and overall survival (60 ± 8%) at 5 years, with a hazard ratio of 2·46 (P = 0·002) and 2·99 (P < 0·001), respectively. Moreover, CD56 expression in combination with the minimal residual disease (MRD)-based high risk assignment defined a population with a 'very-high' risk probability of relapse in the ALL-BFM 2000 trial. The CD56 marker has the potential to augment MRD-based risk stratification and may serve as a molecular target for antibody-based treatment strategies in childhood T-ALL.
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Affiliation(s)
- Stephan Fuhrmann
- Department of Haematology and Stem Cell Transplantation, Helios Klinikum Berlin Buch, Berlin, Germany
| | - Richard Schabath
- Department of Haematology and Stem Cell Transplantation, Helios Klinikum Berlin Buch, Berlin, Germany.,MLL Munich Leukaemia Laboratory, Munich, Germany
| | - Anja Möricke
- Department of Paediatrics, Universitätsklinikum Schleswig Holstein, Kiel, Germany
| | | | - Joachim B Kunz
- Department of Paediatric Oncology, Haematology and Immunology, Angelika Lautenschläger Children's Hospital, University of Heidelberg, Heidelberg, Germany
| | - Andreas E Kulozik
- Department of Paediatric Oncology, Haematology and Immunology, Angelika Lautenschläger Children's Hospital, University of Heidelberg, Heidelberg, Germany
| | - Wolf-Dieter Ludwig
- Department of Haematology and Stem Cell Transplantation, Helios Klinikum Berlin Buch, Berlin, Germany
| | - Martin Schrappe
- Department of Paediatrics, Universitätsklinikum Schleswig Holstein, Kiel, Germany
| | - Leonid Karawajew
- Department of Paediatric Oncology/Haematology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Richard Ratei
- Department of Haematology and Stem Cell Transplantation, Helios Klinikum Berlin Buch, Berlin, Germany.,Helios Klinikum Bad Saarow, Bad Saarow, Germany
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Machiela MJ, Grünewald TG, Surdez D, Reynaud S, Mirabeau O, Karlins E, Rubio RA, Zaidi S, Grossetete-Lalami S, Ballet S, Lapouble E, Laurence V, Michon J, Pierron G, Kovar H, Gaspar N, Kontny U, González-Neira A, Picci P, Alonso J, Patino-Garcia A, Corradini N, Freedman ND, Rothman N, Dagnall CL, Burdette L, Jones K, Manning M, Wyatt K, Zhou W, Yeager M, Cox DG, Hoover RN, Khan J, Armstrong GT, Leisenring WM, Bhatia S, Robison LL, Dirksen U, Metzler M, Hartmann W, Strauch K, Kirchner T, Kulozik AE, Morton LM, Mirabello L, Tucker MA, Tirode F, Chanock SJ, Delattre O. Abstract 2970: Multiple new susceptibility loci identified in genome-wide association study of Ewing sarcoma. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-2970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Ewing sarcoma (EWS) is a rare pediatric tumor predominantly occurring in children of European ancestry and is characterized by the pathognomonic EWSR1-FLI1 fusion oncogene. To identify germline susceptibility loci associated with EWS risk, we performed a genome-wide association study (GWAS) meta-analysis of 749 EWS cases and 1,378 unaffected individuals of European ancestry from sample collections within the Institut Curie, National Cancer Institute and the Childhood Cancer Survivor Study. Our study replicated previously reported susceptibility loci at 1p36.22, 10q21.3 and 15q15.1 as well as identified novel loci at 6p25.1, 8q24.23, 20p11.22 and 20p11.23 (P-values<5×10-8). These seven EWS susceptibility loci discovered in only 749 cases make EWS one of the most productive GWAS studied cancers when considering a locus to case discovery ratio. All estimated effect estimates were high for cancer GWAS with odds ratios in excess of 1.7 observed. These high per allele effects among relatively common germline variants are striking in light of the rarity of EWS cases and lack of evidence of EWS as part of a familial cancer syndrome and therefore suggest a distinctive genetic architecture for EWS. Interestingly, in silico bioinformatics analysis identified that most EWS susceptibility loci reside near GGAA nucleotide repeat sequences where binding of the EWSR1-FLI1 fusion protein occurs. ChIP-seq analyses confirmed in vivo binding of EWSR1-FLI1, suggesting germline variation in these regions could alter EWSR1-FLI1 binding and potentially deregulate neighboring genes. To identify genes with allele specific expression differences, we carried out expression quantitative trait locus (eQTL) analyses at each identified EWS susceptibility locus. We identified eQTLs for plausible candidate genes at 6p25.1 with RREB1, a RAS-responsive element, and at 20p11.23 with KIZ, a centrosomal stabilization protein. We also noted the 20p11.22 locus is near NKX2-2, a highly overexpressed gene in EWS, although no eQTL was observed in our expression data. Furthermore, knockdown of EWSR1-FLI1 in EWS cell lines indicated a more than 2-fold difference in expression of RREB1 and NKX2-2, further supporting the role of specific regulation of these genes by EWSR1-FLI1 and suggesting RREB1 and NKX2-2 may be transcription factors involved in core regulatory circuitries of EWS. Overall, our study suggests a distinctive underlying genetic architecture for EWS in which moderate risk common germline variants interact with EWSR1-FLI1 binding to alter expression of nearby target genes.
Citation Format: Mitchell J. Machiela, Thomas G. Grünewald, Didier Surdez, Stephanie Reynaud, Olivier Mirabeau, Eric Karlins, Rebeca Alba Rubio, Sakina Zaidi, Sandrine Grossetete-Lalami, Stelly Ballet, Eve Lapouble, Valérie Laurence, Jean Michon, Gaelle Pierron, Heinrich Kovar, Nathalie Gaspar, Udo Kontny, Anna González-Neira, Piero Picci, Javier Alonso, Ana Patino-Garcia, Nadège Corradini, Neal D. Freedman, Nathaniel Rothman, Casey L. Dagnall, Laurie Burdette, Kristine Jones, Michelle Manning, Kathleen Wyatt, Weiyin Zhou, Meredith Yeager, David G. Cox, Robert N. Hoover, Javed Khan, Gregory T. Armstrong, Wendy M. Leisenring, Smita Bhatia, Leslie L. Robison, Uta Dirksen, Markus Metzler, Wolfgang Hartmann, Konstantin Strauch, Thomas Kirchner, Andreas E. Kulozik, Lindsay M. Morton, Lisa Mirabello, Margaret A. Tucker, Franck Tirode, Stephen J. Chanock, Olivier Delattre. Multiple new susceptibility loci identified in genome-wide association study of Ewing sarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2970.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Heinrich Kovar
- 4Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Austria
| | | | | | | | - Piero Picci
- 8Istituto Ortopedico Rizzoli di Bologna, Italy
| | - Javier Alonso
- 9Instituto de Investigación de Enfermedades Raras, Spain
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Javed Khan
- 1National Cancer Institute, Bethesda, MD
| | | | | | | | | | - Uta Dirksen
- 16University Children's Hospital of Essen, Germany
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Suttorp M, Schulze P, Glauche I, Göhring G, von Neuhoff N, Metzler M, Sedlacek P, de Bont ESJM, Balduzzi A, Lausen B, Aleinikova O, Sufliarska S, Henze G, Strauss G, Eggert A, Kremens B, Groll AH, Berthold F, Klein C, Groß-Wieltsch U, Sykora KW, Borkhardt A, Kulozik AE, Schrappe M, Nowasz C, Krumbholz M, Tauer JT, Claviez A, Harbott J, Kreipe HH, Schlegelberger B, Thiede C. Front-line imatinib treatment in children and adolescents with chronic myeloid leukemia: results from a phase III trial. Leukemia 2018; 32:1657-1669. [PMID: 29925908 DOI: 10.1038/s41375-018-0179-9] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 04/26/2018] [Accepted: 05/01/2018] [Indexed: 12/16/2022]
Abstract
A total of 156 patients (age range 1.3-18.0 years, median 13.2 years; 91 (58.3%) male) with newly diagnosed CML (N = 146 chronic phase (CML-CP), N = 3 accelerated phase (CML-AP), N = 7 blastic phase (CML-BP)) received imatinib up-front (300, 400, 500 mg/m2, respectively) within a prospective phase III trial. Therapy response, progression-free survival, causes of treatment failure, and side effects were analyzed in 148 children and adolescents with complete data. Event-free survival rate by 18 months for patients in CML-CP (median follow-up time 25 months, range: 1-120) was 97% (95% CI, 94.2-99.9%). According to the 2006 ELN-criteria complete hematologic response by month 3, complete cytogenetic response (CCyR) by month 12, and major molecular response (MMR) by month 18 were achieved in 98, 63, and 59% of the patients, respectively. By month 36, 86% of the patients achieved CCyR and 74% achieved MMR. Thirty-eight patients (27%) experienced imatinib failure because of unsatisfactory response or intolerance (N = 9). In all, 28/148 patients (19%) underwent stem cell transplantation (SCT). In the SCT sub-cohort 2/23 patients diagnosed in CML-CP, 0/1 in CML-AP, and 2/4 in CML-BP, respectively, died of relapse (N = 3) or SCT-related complications (N = 2). This large pediatric trial extends and confirms data from smaller series that first-line imatinib in children is highly effective.
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Affiliation(s)
- Meinolf Suttorp
- Pediatric Hematology and Oncology, Department of Pediatrics, University Hospital "Carl Gustav Carus", TU Dresden, Dresden, Germany.
| | - Philipp Schulze
- Institute for Medical Informatics and Biometry, Faculty of Medicine "Carl Gustav Carus", TU Dresden, Dresden, Germany
| | - Ingmar Glauche
- Institute for Medical Informatics and Biometry, Faculty of Medicine "Carl Gustav Carus", TU Dresden, Dresden, Germany
| | - Gudrun Göhring
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Nils von Neuhoff
- Department of Human Genetics, Hannover Medical School, Hannover, Germany.,Department of Pediatrics III, University Hospital, University of Duisburg-Essen, Duisberg, Germany
| | - Markus Metzler
- Pediatric Hematology and Oncology, University Children's Hospital, Erlangen, Germany
| | - Petr Sedlacek
- Pediatric Hematology and Oncology, Teaching Hospital Motol, 2nd Medical School, Charles University Motol, Prague, Czech Republic
| | - Eveline S J M de Bont
- Pediatric Hematology and Oncology, University Children's Hospital, Groningen, The Netherlands.,Dutch Childhood Oncology Group (DCOG), The Hague, The Netherlands
| | - Adriana Balduzzi
- Pediatric Hematology and Hematopoietic Stem Cell Transplantation Unit, Clinica Pediatrica Università degli Studi di Milano Bicocca, Ospedale San Gerardo, Monza, Italy
| | - Birgitte Lausen
- Department of Pediatric and Adolescent Medicine, University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Olga Aleinikova
- Belarus Research Center for Pediatric Oncology, Hematology, and Immunology, Minsk, Belarus
| | - Sabina Sufliarska
- Department of Pediatrics, BMT Unit, Comenius University Children's Hospital, Bratislava, Slovakia
| | - Günter Henze
- Pediatric Hematology and Oncology, University Children's Hospital, Charité Berlin, Germany
| | - Gabriele Strauss
- Pediatric Hematology and Oncology, University Children's Hospital, Charité Berlin, Germany.,Pediatric Hematology and Oncology, Helios KlinikenBerlin-Buch, Berlin, Germany
| | - Angelika Eggert
- Pediatric Hematology and Oncology, University Children's Hospital, Charité Berlin, Germany
| | - Bernhard Kremens
- Department of Pediatrics III, University Hospital, University of Duisburg-Essen, Duisberg, Germany
| | - Andreas H Groll
- Pediatric Hematology and Oncology, University Children's Hospital, Münster, Germany
| | - Frank Berthold
- Pediatric Hematology and Oncology, University Children's Hospital, Cologne, Germany
| | - Christoph Klein
- University Children's Hospital, Ludwig Maximilians University, Munich, Germany
| | - Ute Groß-Wieltsch
- Pediatric Oncology, Hematology, Immunology, Stuttgart Cancer Center, Klinikum Stuttgart-Olgahospital, Stuttgart, Germany
| | - Karl Walter Sykora
- Paediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Arndt Borkhardt
- Pediatric Hematology, Oncology, and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Andreas E Kulozik
- Pediatric Oncology, Hematology, and Immunology, University Children's Hospital, Heidelberg, Germany
| | - Martin Schrappe
- Pediatric Hematology and Oncology, University Children's Hospital, Kiel, Germany
| | - Christina Nowasz
- Pediatric Hematology and Oncology, Department of Pediatrics, University Hospital "Carl Gustav Carus", TU Dresden, Dresden, Germany
| | - Manuela Krumbholz
- Pediatric Hematology and Oncology, University Children's Hospital, Erlangen, Germany
| | - Josephine T Tauer
- Pediatric Hematology and Oncology, Department of Pediatrics, University Hospital "Carl Gustav Carus", TU Dresden, Dresden, Germany.,Shriners Hospitals for Children, Montréal, Canada
| | - Alexander Claviez
- Pediatric Hematology and Oncology, University Children's Hospital, Kiel, Germany
| | - Jochen Harbott
- Oncogenetic Laboratory, Pediatric Hematology and Oncology, University Children's Hospital, Giessen, Germany
| | - Hans H Kreipe
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | | | - Christian Thiede
- Medical Department I, University Hospital "Carl Gustav Carus", TU Dresden, Dresden, Germany
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Cordas Dos Santos DM, Eilers J, Sosa Vizcaino A, Orlova E, Zimmermann M, Stanulla M, Schrappe M, Börner K, Grimm D, Muckenthaler MU, Kulozik AE, Kunz JB. MAP3K7 is recurrently deleted in pediatric T-lymphoblastic leukemia and affects cell proliferation independently of NF-κB. BMC Cancer 2018; 18:663. [PMID: 29914415 PMCID: PMC6006985 DOI: 10.1186/s12885-018-4525-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 05/18/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Deletions of 6q15-16.1 are recurrently found in pediatric T-cell acute lymphoblastic leukemia (T-ALL). This chromosomal region includes the mitogen-activated protein kinase kinase kinase 7 (MAP3K7) gene which has a crucial role in innate immune signaling and was observed to be functionally and prognostically relevant in different cancer entities. Therefore, we correlated the presence of MAP3K7 deletions with clinical parameters in a cohort of 327 pediatric T-ALL patients and investigated the function of MAP3K7 in the T-ALL cell lines CCRF-CEM, Jurkat and MOLT-4. METHODS MAP3K7 deletions were detected by multiplex ligation-dependent probe amplification (MLPA). T-ALL cell lines were transduced with adeno-associated virus (AAV) vectors expressing anti-MAP3K7 shRNA or a non-silencing shRNA together with a GFP reporter. Transduction efficiency was measured by flow cytometry and depletion efficiency by RT-PCR and Western blots. Induction of apoptosis was measured by flow cytometry after staining with PE-conjugated Annexin V. In order to assess the contribution of NF-κB signaling to the effects of MAP3K7 depletion, cells were treated with TNF-α and cell lysates analyzed for components of the NF-κB pathway by Western blotting and for expression of the NF-κB target genes BCL2, CMYC, FAS, PTEN and TNF-α by RT-PCR. RESULTS MAP3K7 is deleted in approximately 10% and point-mutated in approximately 1% of children with T-ALL. In 32 of 33 leukemias the deletion of MAP3K7 also included the adjacent CASP8AP2 gene. MAP3K7 deletions were associated with the occurrence of SIL-TAL1 fusions and a mature immunophenotype, but not with response to treatment and outcome. Depletion of MAP3K7 expression in T-ALL cell lines by shRNAs slowed down proliferation and induced apoptosis, but neither changed protein levels of components of NF-κB signaling nor NF-κB target gene expression after stimulation with TNF-α. CONCLUSIONS This study revealed that the recurrent deletion of MAP3K7/CASP8AP2 is associated with SIL-TAL1 fusions and a mature immunophenotype, but not with response to treatment and risk of relapse. Homozygous deletions of MAP3K7 were not observed, and efficient depletion of MAP3K7 interfered with viability of T-ALL cells, indicating that a residual expression of MAP3K7 is indispensable for T-lymphoblasts.
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Affiliation(s)
- David M Cordas Dos Santos
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Children's Hospital, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Juliane Eilers
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Children's Hospital, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Alfonso Sosa Vizcaino
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Children's Hospital, Heidelberg, Germany
| | - Elena Orlova
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Children's Hospital, Heidelberg, Germany
| | - Martin Zimmermann
- Department of Pediatric Hematology and Oncology, MH Hannover, Hannover, Germany
| | - Martin Stanulla
- Department of Pediatric Hematology and Oncology, MH Hannover, Hannover, Germany
| | - Martin Schrappe
- Department of Pediatrics, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Kathleen Börner
- Department of Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany.,German Center for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany.,BioQuant Center, Heidelberg University, Heidelberg, Germany
| | - Dirk Grimm
- Department of Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany.,German Center for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany.,BioQuant Center, Heidelberg University, Heidelberg, Germany.,Cluster of Excellence CellNetworks, Heidelberg University, Heidelberg, Germany
| | - Martina U Muckenthaler
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Children's Hospital, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Andreas E Kulozik
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Children's Hospital, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Joachim B Kunz
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Children's Hospital, Heidelberg, Germany. .,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany. .,German Cancer Consortium (DKTK), Heidelberg, Germany.
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Vendramini E, Giordan M, Giarin E, Michielotto B, Fazio G, Cazzaniga G, Biondi A, Silvestri D, Valsecchi MG, Muckenthaler MU, Kulozik AE, Gattei V, Izraeli S, Basso G, Te Kronnie G. High expression of miR-125b-2 and SNORD116 noncoding RNA clusters characterize ERG-related B cell precursor acute lymphoblastic leukemia. Oncotarget 2018; 8:42398-42413. [PMID: 28415578 PMCID: PMC5522075 DOI: 10.18632/oncotarget.16392] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 03/04/2017] [Indexed: 12/19/2022] Open
Abstract
ERG-related leukemia is a B cell precursor acute lymphoblastic leukemia (BCP ALL) subtype characterized by aberrant expression of DUX4 and ERG transcription factors, and highly recurrent ERG intragenic deletions. ERG-related patients have remarkably favorable outcome despite a high incidence of inauspicious IKZF1 aberrations. We describe clinical and genomic features of the ERG-related cases in an unselected cohort of B-other BCP ALL pediatric patients enrolled in the AIEOP ALL 2000 therapeutic protocol. We report a small noncoding RNA signature specific of ERG-related group, with up-regulation of miR-125b-2 cluster on chromosome 21 and several snoRNAs in the Prader-Willi locus at 15q11.2, including the orphan SNORD116 cluster.
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Affiliation(s)
- Elena Vendramini
- Department of Women's and Children's Health, University of Padova, Padova, Italy.,Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel.,Tel Aviv University, Tel Aviv, Israel
| | - Marco Giordan
- Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - Emanuela Giarin
- Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - Barbara Michielotto
- Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - Grazia Fazio
- Centro Ricerca Tettamanti, Clinica Pediatrica, University of Milano-Bicocca, Monza, Italy
| | - Gianni Cazzaniga
- Centro Ricerca Tettamanti, Clinica Pediatrica, University of Milano-Bicocca, Monza, Italy
| | - Andrea Biondi
- Centro Ricerca Tettamanti, Clinica Pediatrica, University of Milano-Bicocca, Monza, Italy
| | - Daniela Silvestri
- Centro Ricerca Tettamanti, Clinica Pediatrica, University of Milano-Bicocca, Monza, Italy
| | | | - Martina U Muckenthaler
- Department of Pediatric Oncology Hematology, University of Heidelberg, Heidelberg, Germany
| | - Andreas E Kulozik
- Department of Pediatric Oncology Hematology, University of Heidelberg, Heidelberg, Germany
| | - Valter Gattei
- Clinical and Experimental Onco-Hematology Unit, Centro di Riferimento Oncologico, I.R.C.C.S., Aviano (PN), Italy
| | - Shai Izraeli
- Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel.,Tel Aviv University, Tel Aviv, Israel
| | - Giuseppe Basso
- Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - Geertruy Te Kronnie
- Department of Women's and Children's Health, University of Padova, Padova, Italy
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48
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Palmi C, Savino AM, Silvestri D, Bronzini I, Cario G, Paganin M, Buldini B, Galbiati M, Muckenthaler MU, Bugarin C, Della Mina P, Nagel S, Barisone E, Casale F, Locatelli F, Lo Nigro L, Micalizzi C, Parasole R, Pession A, Putti MC, Santoro N, Testi AM, Ziino O, Kulozik AE, Zimmermann M, Schrappe M, Villa A, Gaipa G, Basso G, Biondi A, Valsecchi MG, Stanulla M, Conter V, Te Kronnie G, Cazzaniga G. CRLF2 over-expression is a poor prognostic marker in children with high risk T-cell acute lymphoblastic leukemia. Oncotarget 2018; 7:59260-59272. [PMID: 27449287 PMCID: PMC5312310 DOI: 10.18632/oncotarget.10610] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 07/01/2016] [Indexed: 12/01/2022] Open
Abstract
Pediatric T-ALL patients have a worse outcome compared to BCP-ALL patients and they could benefit from new prognostic marker identification. Alteration of CRLF2 gene, a hallmark correlated with poor outcome in BCP-ALL, has not been reported in T-ALL. We analyzed CRLF2 expression in 212 T-ALL pediatric patients enrolled in AIEOP-BFM ALL2000 study in Italian and German centers. Seventeen out of 120 (14.2%) Italian patients presented CRLF2 mRNA expression 5 times higher than the median (CRLF2-high); they had a significantly inferior event-free survival (41.2%±11.9 vs. 68.9%±4.6, p=0.006) and overall survival (47.1%±12.1 vs. 73.8%±4.3, p=0.009) and an increased cumulative incidence of relapse/resistance (52.9%±12.1 vs. 26.2%±4.3, p=0.007) compared to CRLF2-low patients. The prognostic value of CRLF2 over-expression was validated in the German cohort. Of note, CRLF2 over-expression was associated with poor prognosis in the high risk (HR) subgroup where CRLF2-high patients were more frequently allocated. Interestingly, although in T-ALL CRLF2 protein was localized mainly in the cytoplasm, in CRLF2-high blasts we found a trend towards a stronger TSLP-induced pSTAT5 response, sensitive to the JAK inhibitor Ruxolitinib. In conclusion, CRLF2 over-expression is a poor prognostic marker identifying a subset of HR T-ALL patients that could benefit from alternative therapy, potentially targeting the CRLF2 pathway.
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Affiliation(s)
- Chiara Palmi
- Centro Ricerca M. Tettamanti, Clinica Pediatrica, Università di Milano Bicocca, Fondazione MBBM/Ospedale San Gerardo, Monza, Italy
| | - Angela M Savino
- Centro Ricerca M. Tettamanti, Clinica Pediatrica, Università di Milano Bicocca, Fondazione MBBM/Ospedale San Gerardo, Monza, Italy
| | - Daniela Silvestri
- Center of Biostatistics for Clinical Epidemiology, Department of Health Sciences, University of Milano-Bicocca, Milan, Italy.,Clinica Pediatrica, Università di Milano Bicocca, Fondazione MBBM/Ospedale San Gerardo, Monza, Italy
| | - Ilaria Bronzini
- Laboratory of Onco-Hematology, Department SDB, Università di Padova, Padova, Italy
| | - Gunnar Cario
- Department of Pediatrics, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Maddalena Paganin
- Laboratory of Onco-Hematology, Department SDB, Università di Padova, Padova, Italy
| | - Barbara Buldini
- Laboratory of Onco-Hematology, Department SDB, Università di Padova, Padova, Italy
| | - Marta Galbiati
- Centro Ricerca M. Tettamanti, Clinica Pediatrica, Università di Milano Bicocca, Fondazione MBBM/Ospedale San Gerardo, Monza, Italy
| | - Martina U Muckenthaler
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg and EMBL/Medical Faculty Molecular Medicine Partnership Unit, Heidelberg, Germany
| | - Cristina Bugarin
- Centro Ricerca M. Tettamanti, Clinica Pediatrica, Università di Milano Bicocca, Fondazione MBBM/Ospedale San Gerardo, Monza, Italy
| | - Pamela Della Mina
- Microscopy and Image Analysis Consortium, Università di Milano-Bicocca, Monza, Italy
| | - Stefan Nagel
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Elena Barisone
- Pediatric Onco-Hematology, Stem Cell Transplantation and Cellular Therapy Division, Regina Margherita Children's Hospital, Turin, Italy
| | - Fiorina Casale
- Pediatric Oncology Service, Pediatric Department of 2nd University of Naples, Naples, Italy
| | - Franco Locatelli
- Department of Pediatric Hematology/Oncology, IRCCS Ospedale Bambino Gesù, Rome - University of Pavia, Pavia, Italy
| | - Luca Lo Nigro
- Center of Pediatric Hematology Oncology, Azienda Ospedaliero-Universitaria "Policlinico Vittorio Emanuele", Catania, Italy
| | | | - Rosanna Parasole
- Department of Pediatric Hemato-Oncology, Ospedale Pausilipon, Napoli, Italy
| | - Andrea Pession
- Department of Pediatrics, "Lalla Seràgnoli" Hematology-Oncology Unit, University of Bologna, Bologna, Italy
| | - Maria C Putti
- Laboratory of Onco-Hematology, Department SDB, Università di Padova, Padova, Italy
| | - Nicola Santoro
- Department of Pediatrics, Division of Pediatric Hematology-Oncology, University "A. Moro" of Bari, Bari, Italy
| | - Anna M Testi
- Division of Hematology, Department of Biotechnologies and Hematology, "Sapienza" University of Rome, Rome, Italy
| | - Ottavio Ziino
- Pediatric Hematology and Oncology Unit, A.R.N.A.S. Civico, Di Cristina and Benfratelli Hospital, Palermo, Italy
| | - Andreas E Kulozik
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg and EMBL/Medical Faculty Molecular Medicine Partnership Unit, Heidelberg, Germany
| | - Martin Zimmermann
- Department of Paediatric Haematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Martin Schrappe
- Department of Pediatrics, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Antonello Villa
- Microscopy and Image Analysis Consortium, Università di Milano-Bicocca, Monza, Italy
| | - Giuseppe Gaipa
- Centro Ricerca M. Tettamanti, Clinica Pediatrica, Università di Milano Bicocca, Fondazione MBBM/Ospedale San Gerardo, Monza, Italy
| | - Giuseppe Basso
- Laboratory of Onco-Hematology, Department SDB, Università di Padova, Padova, Italy
| | - Andrea Biondi
- Clinica Pediatrica, Università di Milano Bicocca, Fondazione MBBM/Ospedale San Gerardo, Monza, Italy
| | - Maria G Valsecchi
- Center of Biostatistics for Clinical Epidemiology, Department of Health Sciences, University of Milano-Bicocca, Milan, Italy
| | - Martin Stanulla
- Department of Paediatric Haematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Valentino Conter
- Clinica Pediatrica, Università di Milano Bicocca, Fondazione MBBM/Ospedale San Gerardo, Monza, Italy
| | - Geertruy Te Kronnie
- Laboratory of Onco-Hematology, Department SDB, Università di Padova, Padova, Italy
| | - Giovanni Cazzaniga
- Centro Ricerca M. Tettamanti, Clinica Pediatrica, Università di Milano Bicocca, Fondazione MBBM/Ospedale San Gerardo, Monza, Italy
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49
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Hundsdoerfer P, Vetter B, Stöver B, Bassir C, Scholz T, Grimmer I, Mönch E, Ziemer S, Rossi R, Kulozik AE. Homozygous and double heterozygous Factor V Leiden and Factor II G20210A genotypes predispose infants to thromboembolism but are not associated with an increase of foetal loss. Thromb Haemost 2017; 90:628-35. [PMID: 14515183 DOI: 10.1160/th03-02-0096] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
SummaryProspective and controlled data about the individual risk profile in asymptomatic children with homozygous or double heterozygous risk genotypes for Factor V Leiden (FVL) and factor II (FII) G20210A are currently unavailable. The systematic and prospective observational study presented here was designed to determine the impact of the homozygous and double heterozygous FVL and FII G20210A genotypes on the prenatal and postnatal risk profiles of affected children. Risk infants and heterozygous controls were identified by screening of 85,304 neonates. Follow-up included the comparison of prenatal and postnatal development, ultrasonography of brain and kidneys, and a panel of independent determinants of thrombophilia. The numbers of identified or expected FVL homozygotes and double heterozygotes did not differ significantly (FVL: 116 ver-sus 91, p=0.08; FVL/FII: 94 versus 76, p=0.17), indicating the absence of a prenatal disadvantage. A prenatal advantage was suggested in FII homozygotes, whose identified number far exceeded the expected (19 versus 4, p=0.002). Clinical and/or imaging abnormalities indicated spontaneous thromboembolic events in 4 of 129 risk infants (3%) but in none of the 178 controls (p=0.02). Physical and neurological development was normal in both groups during the first 2 years of life. The risk genotypes appear to confer a significant predisposition for spontaneous thromboembolic events in infancy without impeding development within the first two years of life. Foetal risk genotypes do not cause an increased foetal loss rate. Moreover, homozygous FII G20210A appears to be associated with a prenatal advantage.
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Affiliation(s)
- Patrick Hundsdoerfer
- Department of General Paediatrics, Charité, Humboldt University, Berlin, Germany
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50
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Neu-Yilik G, Raimondeau E, Eliseev B, Yeramala L, Amthor B, Deniaud A, Huard K, Kerschgens K, Hentze MW, Schaffitzel C, Kulozik AE. Dual function of UPF3B in early and late translation termination. EMBO J 2017; 36:2968-2986. [PMID: 28899899 PMCID: PMC5641913 DOI: 10.15252/embj.201797079] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 08/07/2017] [Accepted: 08/10/2017] [Indexed: 11/09/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is a cellular surveillance pathway that recognizes and degrades mRNAs with premature termination codons (PTCs). The mechanisms underlying translation termination are key to the understanding of RNA surveillance mechanisms such as NMD and crucial for the development of therapeutic strategies for NMD-related diseases. Here, we have used a fully reconstituted in vitro translation system to probe the NMD proteins for interaction with the termination apparatus. We discovered that UPF3B (i) interacts with the release factors, (ii) delays translation termination and (iii) dissociates post-termination ribosomal complexes that are devoid of the nascent peptide. Furthermore, we identified UPF1 and ribosomes as new interaction partners of UPF3B. These previously unknown functions of UPF3B during the early and late phases of translation termination suggest that UPF3B is involved in the crosstalk between the NMD machinery and the PTC-bound ribosome, a central mechanistic step of RNA surveillance.
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Affiliation(s)
- Gabriele Neu-Yilik
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany.,Hopp Kindertumorzentrum am NCT Heidelberg, Heidelberg, Germany
| | | | - Boris Eliseev
- European Molecular Biology Laboratory, Grenoble, France
| | | | - Beate Amthor
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Karine Huard
- European Molecular Biology Laboratory, Grenoble, France
| | - Kathrin Kerschgens
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany
| | - Matthias W Hentze
- Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany .,European Molecular Biology Laboratory, Heidelberg, Germany
| | - Christiane Schaffitzel
- European Molecular Biology Laboratory, Grenoble, France .,School of Biochemistry, University of Bristol, Bristol, UK
| | - Andreas E Kulozik
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany .,Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany.,Hopp Kindertumorzentrum am NCT Heidelberg, Heidelberg, Germany
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