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Reuss DE, Downing SM, Camacho CV, Wang YD, Piro RM, Herold-Mende C, Wang ZQ, Hofmann TG, Sahm F, von Deimling A, McKinnon PJ, Frappart PO. Simultaneous Nbs1 and p53 inactivation in neural progenitors triggers high-grade gliomas. Neuropathol Appl Neurobiol 2023; 49:e12915. [PMID: 37296499 DOI: 10.1111/nan.12915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 04/25/2023] [Accepted: 06/02/2023] [Indexed: 06/12/2023]
Abstract
AIMS Nijmegen breakage syndrome (NBS) is a rare autosomal recessive disorder caused by hypomorphic mutations of NBS1. NBS1 is a member of the MRE11-RAD50-NBS1 (MRN) complex that binds to DNA double-strand breaks and activates the DNA damage response (DDR). Nbs1 inactivation in neural progenitor cells leads to microcephaly and premature death. Interestingly, p53 homozygous deletion rescues the NBS1-deficient phenotype allowing long-term survival. The objective of this work was to determine whether simultaneous inactivation of Nbs1 and p53 in neural progenitors triggered brain tumorigenesis and if so in which category this tumour could be classified. METHODS We generated a mouse model with simultaneous genetic inactivation of Nbs1 and p53 in embryonic neural stem cells and analysed the arising tumours with in-depth molecular analyses including immunohistochemistry, array comparative genomic hybridisation (aCGH), whole exome-sequencing and RNA-sequencing. RESULTS NBS1/P53-deficient mice develop high-grade gliomas (HGG) arising in the olfactory bulbs and in the cortex along the rostral migratory stream. In-depth molecular analyses using immunohistochemistry, aCGH, whole exome-sequencing and RNA-sequencing revealed striking similarities to paediatric human HGG with shared features with radiation-induced gliomas (RIGs). CONCLUSIONS Our findings show that concomitant inactivation of Nbs1 and p53 in mice promotes HGG with RIG features. This model could be useful for preclinical studies to improve the prognosis of these deadly tumours, but it also highlights the singularity of NBS1 among the other DNA damage response proteins in the aetiology of brain tumours.
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Affiliation(s)
- David E Reuss
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Ruprecht-Karls-Universität Heidelberg, Heidelberg, Germany
| | - Susanna M Downing
- Center for Pediatric Neurological Disease Research, St. Jude Translational Neuroscience, Departments of Genetics and Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Cristel V Camacho
- Center for Pediatric Neurological Disease Research, St. Jude Translational Neuroscience, Departments of Genetics and Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Yong-Dong Wang
- Center for Pediatric Neurological Disease Research, St. Jude Translational Neuroscience, Departments of Genetics and Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Rosario M Piro
- Dipartimento di Elettronica, Informazione e Bioingegneria (DEIB), Politecnico di Milano, Milan, Italy
| | - Christel Herold-Mende
- Department of Neurosurgery, Ruprecht-Karls-Universität Heidelberg, Heidelberg, Germany
| | - Zhao-Qi Wang
- Leibniz Institute on Ageing-Fritz Lipmann Institute, Jena, Germany
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Thomas G Hofmann
- Institute of Toxicology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Felix Sahm
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Ruprecht-Karls-Universität Heidelberg, Heidelberg, Germany
| | - Andreas von Deimling
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Ruprecht-Karls-Universität Heidelberg, Heidelberg, Germany
| | - Peter J McKinnon
- Center for Pediatric Neurological Disease Research, St. Jude Translational Neuroscience, Departments of Genetics and Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Pierre-Olivier Frappart
- Institute of Toxicology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
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2
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de Melo Costa VR, Pfeuffer J, Louloupi A, Ørom UAV, Piro RM. SPLICE-q: a Python tool for genome-wide quantification of splicing efficiency. BMC Bioinformatics 2021; 22:368. [PMID: 34266387 PMCID: PMC8281633 DOI: 10.1186/s12859-021-04282-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 07/06/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Introns are generally removed from primary transcripts to form mature RNA molecules in a post-transcriptional process called splicing. An efficient splicing of primary transcripts is an essential step in gene expression and its misregulation is related to numerous human diseases. Thus, to better understand the dynamics of this process and the perturbations that might be caused by aberrant transcript processing it is important to quantify splicing efficiency. RESULTS Here, we introduce SPLICE-q, a fast and user-friendly Python tool for genome-wide SPLICing Efficiency quantification. It supports studies focusing on the implications of splicing efficiency in transcript processing dynamics. SPLICE-q uses aligned reads from strand-specific RNA-seq to quantify splicing efficiency for each intron individually and allows the user to select different levels of restrictiveness concerning the introns' overlap with other genomic elements such as exons of other genes. We applied SPLICE-q to globally assess the dynamics of intron excision in yeast and human nascent RNA-seq. We also show its application using total RNA-seq from a patient-matched prostate cancer sample. CONCLUSIONS Our analyses illustrate that SPLICE-q is suitable to detect a progressive increase of splicing efficiency throughout a time course of nascent RNA-seq and it might be useful when it comes to understanding cancer progression beyond mere gene expression levels. SPLICE-q is available at: https://github.com/vrmelo/SPLICE-q.
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Affiliation(s)
- Verônica R de Melo Costa
- Institute of Computer Science and Institute of Bioinformatics, Freie Universität Berlin, Berlin, Germany.
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany.
| | - Julianus Pfeuffer
- Institute of Computer Science and Institute of Bioinformatics, Freie Universität Berlin, Berlin, Germany
- Department of Computer Science, Eberhard Karls Universität Tübingen, Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics Tübingen, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Annita Louloupi
- Max Delbrück Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Ulf A V Ørom
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Rosario M Piro
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milan, Italy.
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3
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Gulino A, Stamoulakatou E, Piro RM. MutViz 2.0: visual analysis of somatic mutations and the impact of mutational signatures on selected genomic regions. NAR Cancer 2021; 3:zcab012. [PMID: 34316703 PMCID: PMC8210215 DOI: 10.1093/narcan/zcab012] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/24/2021] [Accepted: 03/12/2021] [Indexed: 01/28/2023] Open
Abstract
Patterns of somatic single nucleotide variants observed in human cancers vary widely between different tumor types. They depend not only on the activity of diverse mutational processes, such as exposure to ultraviolet light and the deamination of methylated cytosines, but largely also on the sequence content of different genomic regions on which these processes act. With MutViz (http://gmql.eu/mutviz/), we have presented a user-friendly web tool for the identification of mutation enrichments that offers preloaded mutations from public datasets for a variety of cancer types, well organized within an effective database architecture. Somatic mutation patterns can be visually and statistically analyzed within arbitrary sets of small, user-provided genomic regions, such as promoters or collections of transcription factor binding sites. Here, we present MutViz 2.0, a largely extended and consolidated version of the tool: we took into account the immediate (trinucleotide) sequence context of mutations, improved the representation of clinical annotation of tumor samples and devised a method for signature refitting on limited genomic regions to infer the contribution of individual mutational processes to the mutation patterns observed in these regions. We described both the features of MutViz 2.0, concentrating on the novelties, and the substantial re-engineering of the cloud-based architecture.
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Affiliation(s)
- Andrea Gulino
- Correspondence may also be addressed to Andrea Gulino. Tel: +39 02 2399 3538;
| | - Eirini Stamoulakatou
- Dipartimento di Elettronica, Informazione e Bioingegneria (DEIB), Politecnico di Milano, Via Ponzio 34/5, 20133 Milan, Italy
| | - Rosario M Piro
- To whom correspondence should be addressed. Tel: +39 02 2399 3538; Fax: +39 02 2399 3411;
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4
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Soni H, Bode J, Nguyen CDL, Puccio L, Neßling M, Piro RM, Bub J, Phillips E, Ahrends R, Eipper BA, Tews B, Goidts V. PERK-mediated expression of peptidylglycine α-amidating monooxygenase supports angiogenesis in glioblastoma. Oncogenesis 2020; 9:18. [PMID: 32054826 PMCID: PMC7018722 DOI: 10.1038/s41389-020-0201-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 08/09/2019] [Revised: 12/19/2019] [Accepted: 01/20/2020] [Indexed: 12/17/2022] Open
Abstract
PKR-like kinase (PERK) plays a significant role in inducing angiogenesis in various cancer types including glioblastoma. By proteomics analysis of the conditioned medium from a glioblastoma cell line treated with a PERK inhibitor, we showed that peptidylglycine α-amidating monooxygenase (PAM) expression is regulated by PERK under hypoxic conditions. Moreover, PERK activation via CCT020312 (a PERK selective activator) increased the cleavage and thus the generation of PAM cleaved cytosolic domain (PAM sfCD) that acts as a signaling molecule from the cytoplasm to the nuclei. PERK was also found to interact with PAM, suggesting a possible involvement in the generation of PAM sfCD. Knockdown of PERK or PAM reduced the formation of tubes by HUVECs in vitro. Furthermore, in vivo data highlighted the importance of PAM in the growth of glioblastoma with reduction of PAM expression in engrafted tumor significantly increasing the survival in mice. In summary, our data revealed PAM as a potential target for antiangiogenic therapy in glioblastoma.
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Affiliation(s)
- Himanshu Soni
- Brain Tumor Translational Targets, DKFZ Junior Group, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Molecular Mechanisms of Tumor Invasion, Schaller Research Group, University of Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Julia Bode
- Molecular Mechanisms of Tumor Invasion, Schaller Research Group, University of Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Chi D L Nguyen
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V, Dortmund, Germany
| | - Laura Puccio
- Brain Tumor Translational Targets, DKFZ Junior Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michelle Neßling
- Central Unit Electron Microscopy, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rosario M Piro
- Institute of Computer Science, Institute of Bioinformatics, Freie Universität Berlin, Berlin, Germany.,Institute of Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany.,German Cancer Consortium (DKTK) partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jonas Bub
- Brain Tumor Translational Targets, DKFZ Junior Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Emma Phillips
- Brain Tumor Translational Targets, DKFZ Junior Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Robert Ahrends
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V, Dortmund, Germany.,Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Wien, Austria
| | | | - Björn Tews
- Molecular Mechanisms of Tumor Invasion, Schaller Research Group, University of Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Violaine Goidts
- Brain Tumor Translational Targets, DKFZ Junior Group, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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5
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Stamoulakatou E, Pinoli P, Ceri S, Piro RM. Impact of mutational signatures on microRNA and their response elements. Pac Symp Biocomput 2020; 25:250-261. [PMID: 31797601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
MicroRNAs are a class of small non-coding RNA molecules with great importance for regulating a large number of diverse biological processes in health and disease, mostly by binding to complementary microRNA response elements (MREs) on protein-coding messenger RNAs and other non-coding RNAs and subsequently inducing their degradation. A growing body of evidence indicates that the dysregulation of certain microRNAs may either drive or suppress oncogenesis.The seed region of a microRNA is of crucial importance for its target recognition. Mutations in these seed regions may disrupt the binding of microRNAs to their target genes. In this study, we investigate the theoretical impact of cancer-associated mutagenic processes and their mutational signatures on microRNA seeds and their MREs. To our knowledge, this is the first study which provides a probabilistic framework for microRNA and MRE sequence alteration analysis based on mutational signatures and computationally assessing the disruptive impact of mutational signatures on human microRNA-target interactions.
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Affiliation(s)
- Eirini Stamoulakatou
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milano, Italy,
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6
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Abstract
BACKGROUND The somatic mutations found in a tumor have in most cases been caused by multiple mutational processes such as those related to extrinsic carcinogens like cigarette smoke, and those related to intrinsic processes like age-related spontaneous deamination of 5-methylcytosine. The effect of such mutational processes can be modeled by mutational signatures, of which two different conceptualizations exist: the model introduced by Alexandrov et al., Nature 500:415-421, 2013, and the model introduced by Shiraishi et al., PLoS Genetics 11(12):e1005657, 2015. The initial identification and definition of mutational signatures requires large sets of tumor samples. RESULTS Here, we present decompTumor2Sig, an easy to use R package that can decompose an individual tumor genome into a given set of Alexandrov-type or Shiraishi-type signatures, thus quantifying the contribution of the corresponding mutational processes to the somatic mutations identified in the tumor. Until now, such tools were available only for Alexandrov signatures. We demonstrate the correctness and usefulness of our approach with three test cases, using somatic mutations from 21 breast cancer genomes, from 435 tumor genomes of ten different tumor entities, and from simulated tumor genomes, respectively. CONCLUSIONS The decompTumor2Sig package is freely available and has been accepted for inclusion in Bioconductor.
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Affiliation(s)
- Sandra Krüger
- Institute of Computer Science and Institute of Bioinformatics, Freie Universität Berlin, Berlin, Germany
| | - Rosario M Piro
- Institute of Computer Science and Institute of Bioinformatics, Freie Universität Berlin, Berlin, Germany. .,Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany. .,German Cancer Consortium (DKTK) partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany.
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7
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Schweizer Y, Meszaros Z, Jones DT, Koelsche C, Boudalil M, Fiesel P, Schrimpf D, Piro RM, Brehmer S, von Deimling A, Kerl U, Seiz-Rosenhagen M, Capper D. Molecular Transition of an Adult Low-Grade Brain Tumor to an Atypical Teratoid/Rhabdoid Tumor Over a Time-Course of 14 Years. J Neuropathol Exp Neurol 2017; 76:655-664. [DOI: 10.1093/jnen/nlx044] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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8
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Hutter S, Piro RM, Waszak SM, Kehrer-Sawatzki H, Friedrich RE, Lassaletta A, Witt O, Korbel JO, Lichter P, Schuhmann MU, Pfister SM, Tabori U, Mautner VF, Jones DTW. No correlation between NF1 mutation position and risk of optic pathway glioma in 77 unrelated NF1 patients. Hum Genet 2016; 135:469-475. [PMID: 26969325 DOI: 10.1007/s00439-016-1646-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 02/06/2016] [Indexed: 01/08/2023]
Abstract
Neurofibromatosis type 1 (NF1) is a common monogenic disorder whereby affected individuals are predisposed to developing CNS tumors, including optic pathway gliomas (OPGs, occurring in ~15 to 20 % of cases). So far, no definite genotype-phenotype correlation determining NF1 patients at risk for tumor formation has been described, although enrichment for mutations in the 5' region of the NF1 gene in OPG patients has been suggested. We used whole exome sequencing, targeted sequencing, and copy number analysis to screen 77 unrelated NF1 patients with (n = 41) or without (n = 36; age ≥10 years) optic pathway glioma for germline NF1 alterations. We identified germline NF1 mutations in 69 of 77 patients (90 %), but no genotype-phenotype correlation was observed. Our data using a larger patient cohort did not confirm the previously reported clustering of mutations in the 5' region of the NF1 gene in patients with OPG. Thus, NF1 mutation location should not currently be used as a clinical criterion to assess the risk of developing OPGs.
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Affiliation(s)
- Sonja Hutter
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Rosario M Piro
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK) Core Center Heidelberg, Heidelberg, Germany.,Institute of Computer Science, Freie Universität Berlin, Berlin, Germany.,Institute of Medical Genetics and Human Genetics, Charité University Hospital, Berlin, Germany
| | - Sebastian M Waszak
- European Molecular Biology Laboratory (EMBL), Genome Biology Research Unit, Heidelberg, Germany
| | | | - Reinhard E Friedrich
- Department of Oral and Cranio-Maxillofacial Surgery, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Alvaro Lassaletta
- Division of Hematology/Oncology, Department of Pediatrics, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Olaf Witt
- German Cancer Consortium (DKTK) Core Center Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Jan O Korbel
- European Molecular Biology Laboratory (EMBL), Genome Biology Research Unit, Heidelberg, Germany
| | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK) Core Center Heidelberg, Heidelberg, Germany
| | - Martin U Schuhmann
- Department of Neurosurgery, University Hospital Tübingen, Tübingen, Germany.,Centre for Neurofibromatosis, Centre for Rare Diseases Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK) Partner Site Tübingen, Tübingen, Germany
| | - Stefan M Pfister
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,German Cancer Consortium (DKTK) Core Center Heidelberg, Heidelberg, Germany.,Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Uri Tabori
- Division of Hematology/Oncology, Department of Pediatrics, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Victor F Mautner
- Department of Neurology, University Hospital Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany.
| | - David T W Jones
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany. .,German Cancer Consortium (DKTK) Core Center Heidelberg, Heidelberg, Germany.
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9
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Hutter S, Piro RM, Reuss DE, Hovestadt V, Sahm F, Farschtschi S, Kehrer-Sawatzki H, Wolf S, Lichter P, von Deimling A, Schuhmann MU, Pfister SM, Jones DTW, Mautner VF. Whole exome sequencing reveals that the majority of schwannomatosis cases remain unexplained after excluding SMARCB1 and LZTR1 germline variants. Acta Neuropathol 2014; 128:449-52. [PMID: 25008767 DOI: 10.1007/s00401-014-1311-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 06/06/2014] [Accepted: 06/16/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Sonja Hutter
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
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10
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Piro RM, Wiesberg S, Schramm G, Rebel N, Oswald M, Eils R, Reinelt G, König R. Network topology-based detection of differential gene regulation and regulatory switches in cell metabolism and signaling. BMC Syst Biol 2014; 8:56. [PMID: 24886210 PMCID: PMC4031158 DOI: 10.1186/1752-0509-8-56] [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] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 04/29/2014] [Indexed: 11/10/2022]
Abstract
Background Common approaches to pathway analysis treat pathways merely as lists of genes disregarding their topological structures, that is, ignoring the genes' interactions on which a pathway's cellular function depends. In contrast, PathWave has been developed for the analysis of high-throughput gene expression data that explicitly takes the topology of networks into account to identify both global dysregulation of and localized (switch-like) regulatory shifts within metabolic and signaling pathways. For this purpose, it applies adjusted wavelet transforms on optimized 2D grid representations of curated pathway maps. Results Here, we present the new version of PathWave with several substantial improvements including a new method for optimally mapping pathway networks unto compact 2D lattice grids, a more flexible and user-friendly interface, and pre-arranged 2D grid representations. These pathway representations are assembled for several species now comprising H. sapiens, M. musculus, D. melanogaster, D. rerio, C. elegans, and E. coli. We show that PathWave is more sensitive than common approaches and apply it to RNA-seq expression data, identifying crucial metabolic pathways in lung adenocarcinoma, as well as microarray expression data, identifying pathways involved in longevity of Drosophila. Conclusions PathWave is a generic method for pathway analysis complementing established tools like GSEA, and the update comprises efficient new features. In contrast to the tested commonly applied approaches which do not take network topology into account, PathWave enables identifying pathways that are either known be involved in or very likely associated with such diverse conditions as human lung cancer or aging of D. melanogaster. The PathWave R package is freely available at http://www.ichip.de/software/pathwave.html.
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Affiliation(s)
| | | | | | | | | | | | | | - Rainer König
- Division of Theoretical Bioinformatics, German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ), Heidelberg, Germany.
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11
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Groebner SN, Zapatka M, Piro RM, Pfister SM. Signatures of Mutational Processes in Childhood Cancers. Klin Padiatr 2014. [DOI: 10.1055/s-0034-1374847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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12
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Kool M, Jones DTW, Jäger N, Northcott PA, Pugh TJ, Hovestadt V, Piro RM, Esparza LA, Markant SL, Remke M, Milde T, Bourdeaut F, Ryzhova M, Sturm D, Pfaff E, Stark S, Hutter S, Seker-Cin H, Johann P, Bender S, Schmidt C, Rausch T, Shih D, Reimand J, Sieber L, Wittmann A, Linke L, Witt H, Weber UD, Zapatka M, König R, Beroukhim R, Bergthold G, van Sluis P, Volckmann R, Koster J, Versteeg R, Schmidt S, Wolf S, Lawerenz C, Bartholomae CC, von Kalle C, Unterberg A, Herold-Mende C, Hofer S, Kulozik AE, von Deimling A, Scheurlen W, Felsberg J, Reifenberger G, Hasselblatt M, Crawford JR, Grant GA, Jabado N, Perry A, Cowdrey C, Croul S, Zadeh G, Korbel JO, Doz F, Delattre O, Bader GD, McCabe MG, Collins VP, Kieran MW, Cho YJ, Pomeroy SL, Witt O, Brors B, Taylor MD, Schüller U, Korshunov A, Eils R, Wechsler-Reya RJ, Lichter P, Pfister SM. Genome sequencing of SHH medulloblastoma predicts genotype-related response to smoothened inhibition. Cancer Cell 2014; 25:393-405. [PMID: 24651015 PMCID: PMC4493053 DOI: 10.1016/j.ccr.2014.02.004] [Citation(s) in RCA: 548] [Impact Index Per Article: 54.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 11/19/2013] [Accepted: 02/13/2014] [Indexed: 01/07/2023]
Abstract
Smoothened (SMO) inhibitors recently entered clinical trials for sonic-hedgehog-driven medulloblastoma (SHH-MB). Clinical response is highly variable. To understand the mechanism(s) of primary resistance and identify pathways cooperating with aberrant SHH signaling, we sequenced and profiled a large cohort of SHH-MBs (n = 133). SHH pathway mutations involved PTCH1 (across all age groups), SUFU (infants, including germline), and SMO (adults). Children >3 years old harbored an excess of downstream MYCN and GLI2 amplifications and frequent TP53 mutations, often in the germline, all of which were rare in infants and adults. Functional assays in different SHH-MB xenograft models demonstrated that SHH-MBs harboring a PTCH1 mutation were responsive to SMO inhibition, whereas tumors harboring an SUFU mutation or MYCN amplification were primarily resistant.
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Affiliation(s)
- Marcel Kool
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany.
| | - David T W Jones
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Natalie Jäger
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Paul A Northcott
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Trevor J Pugh
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | - Volker Hovestadt
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Rosario M Piro
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | | | | | - Marc Remke
- The Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G 1L7, Canada
| | - Till Milde
- Department of Pediatric Oncology, Hematology and Immunology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Franck Bourdeaut
- Institut Curie, 75005 Paris, France; Institut Curie/INSERM U830, 75248 Paris, France
| | - Marina Ryzhova
- Department of Neuropathology, NN Burdenko Neurosurgical Institute, Moscow 125047, Russia
| | - Dominik Sturm
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Elke Pfaff
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Sebastian Stark
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Sonja Hutter
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Huriye Seker-Cin
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Pascal Johann
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Sebastian Bender
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Christin Schmidt
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Tobias Rausch
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - David Shih
- The Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G 1L7, Canada
| | - Jüri Reimand
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Laura Sieber
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Andrea Wittmann
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Linda Linke
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Hendrik Witt
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany; Department of Pediatric Oncology, Hematology and Immunology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Ursula D Weber
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Marc Zapatka
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Rainer König
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany; Integrated Research and Treatment Center, Center for Sepsis Control and Care, Jena University Hospital, 07747 Jena, Germany; Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute (HKI), 07745 Jena, Germany
| | - Rameen Beroukhim
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA; Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Guillaume Bergthold
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA; Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA; UMR 8203, CNRS Vectorology and Anticancer Therapeutics, Gustave Roussy Cancer Institute, University Paris XI, 94805 Villejuif Cedex, France
| | - Peter van Sluis
- Department of Oncogenomics, Academic Medical Center, Amsterdam 1105 AZ, the Netherlands
| | - Richard Volckmann
- Department of Oncogenomics, Academic Medical Center, Amsterdam 1105 AZ, the Netherlands
| | - Jan Koster
- Department of Oncogenomics, Academic Medical Center, Amsterdam 1105 AZ, the Netherlands
| | - Rogier Versteeg
- Department of Oncogenomics, Academic Medical Center, Amsterdam 1105 AZ, the Netherlands
| | - Sabine Schmidt
- Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Stephan Wolf
- Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Chris Lawerenz
- Data Management Facility, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Cynthia C Bartholomae
- Division of Translational Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), 69121 Heidelberg, Germany
| | - Christof von Kalle
- Division of Translational Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), 69121 Heidelberg, Germany
| | - Andreas Unterberg
- Division of Translational Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), 69121 Heidelberg, Germany
| | - Christel Herold-Mende
- Division of Translational Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), 69121 Heidelberg, Germany
| | - Silvia Hofer
- Department of Oncology, University Hospital Zürich, 8006 Zürich, Switzerland
| | - Andreas E Kulozik
- Department of Pediatric Oncology, Hematology and Immunology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, University of Heidelberg, 69120 Heidelberg, Germany; Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Wolfram Scheurlen
- Cnopf'sche Kinderklinik, Nürnberg Children's Hospital, 90419 Nürnberg, Germany
| | - Jörg Felsberg
- Department of Neuropathology, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Guido Reifenberger
- Department of Neuropathology, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Martin Hasselblatt
- Institute for Neuropathology, University Hospital Münster, 48149 Münster, Germany
| | - John R Crawford
- Departments of Pediatrics and Neurosciences, University of California San Diego, La Jolla, CA 92093; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Gerald A Grant
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Duke University Medical Center, Durham, NC 27710, USA; Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
| | - Nada Jabado
- Departments of Pediatrics and Human Genetics, McGill University Health Centre Research Institute, Montreal, QC H3H 1P3, Canada
| | - Arie Perry
- Departments of Pathology and Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Cynthia Cowdrey
- Departments of Pathology and Neurological Surgery, Brain Tumor Research Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sydney Croul
- Department of Neuropathology, The Arthur and Sonia Labatt Brain Tumour Research Centre, Toronto, ON M5G 1L7, Canada
| | - Gelareh Zadeh
- Department of Neuropathology, The Arthur and Sonia Labatt Brain Tumour Research Centre, Toronto, ON M5G 1L7, Canada
| | - Jan O Korbel
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Francois Doz
- Institut Curie, 75005 Paris, France; Université Paris Descartes, 75006 Paris, France
| | - Olivier Delattre
- Institut Curie, 75005 Paris, France; Institut Curie/INSERM U830, 75248 Paris, France
| | - Gary D Bader
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Martin G McCabe
- Manchester Academic Health Science Centre, Manchester M13 9NT, UK
| | - V Peter Collins
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - Mark W Kieran
- Pediatric Medical Neuro-Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02215, USA
| | - Yoon-Jae Cho
- Department of Neurology and Neurosurgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Scott L Pomeroy
- Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Olaf Witt
- CCU Pediatric Oncology, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Benedikt Brors
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Michael D Taylor
- The Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G 1L7, Canada
| | - Ulrich Schüller
- Center for Neuropathology and Prion Research, Ludwig-Maximilians-Universität, 81377 München, Germany
| | - Andrey Korshunov
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany; Department of Neuropathology, University of Heidelberg, 69120 Heidelberg, Germany; Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Roland Eils
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | | | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Stefan M Pfister
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany; Department of Pediatric Oncology, Hematology and Immunology, University Hospital Heidelberg, 69120 Heidelberg, Germany
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13
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Tönjes M, Barbus S, Park YJ, Wang W, Schlotter M, Lindroth AM, Pleier SV, Bai AHC, Karra D, Piro RM, Felsberg J, Addington A, Lemke D, Weibrecht I, Hovestadt V, Rolli CG, Campos B, Turcan S, Sturm D, Witt H, Chan TA, Herold-Mende C, Kemkemer R, König R, Schmidt K, Hull WE, Pfister SM, Jugold M, Hutson SM, Plass C, Okun JG, Reifenberger G, Lichter P, Radlwimmer B. BCAT1 promotes cell proliferation through amino acid catabolism in gliomas carrying wild-type IDH1. Nat Med 2013; 19:901-908. [PMID: 23793099 DOI: 10.1038/nm.3217] [Citation(s) in RCA: 340] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Accepted: 05/01/2013] [Indexed: 12/11/2022]
Abstract
Here we show that glioblastoma express high levels of branched-chain amino acid transaminase 1 (BCAT1), the enzyme that initiates the catabolism of branched-chain amino acids (BCAAs). Expression of BCAT1 was exclusive to tumors carrying wild-type isocitrate dehydrogenase 1 (IDH1) and IDH2 genes and was highly correlated with methylation patterns in the BCAT1 promoter region. BCAT1 expression was dependent on the concentration of α-ketoglutarate substrate in glioma cell lines and could be suppressed by ectopic overexpression of mutant IDH1 in immortalized human astrocytes, providing a link between IDH1 function and BCAT1 expression. Suppression of BCAT1 in glioma cell lines blocked the excretion of glutamate and led to reduced proliferation and invasiveness in vitro, as well as significant decreases in tumor growth in a glioblastoma xenograft model. These findings suggest a central role for BCAT1 in glioma pathogenesis, making BCAT1 and BCAA metabolism attractive targets for the development of targeted therapeutic approaches to treat patients with glioblastoma.
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Affiliation(s)
- Martje Tönjes
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sebastian Barbus
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Yoon Jung Park
- Division of Epigenomics and Cancer Risk Factors, DKFZ, Heidelberg, Germany.,Department of Nutritional Science and Food Management, College of Health Science, Ewha Womans University, Seoul, South Korea
| | - Wei Wang
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Magdalena Schlotter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Anders M Lindroth
- Division of Epigenomics and Cancer Risk Factors, DKFZ, Heidelberg, Germany
| | - Sabrina V Pleier
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, DKFZ, Heidelberg, Germany
| | - Alfa H C Bai
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniela Karra
- Department of Neuropathology, Heinrich Heine University, Düsseldorf, Germany
| | - Rosario M Piro
- Department of Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology and Bioquant, University of Heidelberg, Heidelberg, Germany.,Division of Theoretical Bioinformatics, DKFZ, Heidelberg, Germany
| | - Jörg Felsberg
- Department of Neuropathology, Heinrich Heine University, Düsseldorf, Germany
| | - Adele Addington
- Department of Human Nutrition, Foods and Exercise, Virginia Polytechnic Institute, Blacksburg, Virginia, USA
| | - Dieter Lemke
- Clinical Cooperation Unit Neurooncology, DKFZ, Heidelberg, Germany
| | - Irene Weibrecht
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Volker Hovestadt
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Claudio G Rolli
- Department of New Materials and Biosystems, Max Planck Institute for Intelligent Systems, Stuttgart, Germany
| | - Benito Campos
- Division of Experimental Neurosurgery, University of Heidelberg, Heidelberg, Germany.,Department of Neurosurgery, University of Heidelberg, Heidelberg, Germany
| | - Sevin Turcan
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | - Dominik Sturm
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, DKFZ, Heidelberg, Germany.,Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Hendrik Witt
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, DKFZ, Heidelberg, Germany.,Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Timothy A Chan
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | - Christel Herold-Mende
- Division of Experimental Neurosurgery, University of Heidelberg, Heidelberg, Germany.,Department of Neurosurgery, University of Heidelberg, Heidelberg, Germany
| | - Ralf Kemkemer
- Department of New Materials and Biosystems, Max Planck Institute for Intelligent Systems, Stuttgart, Germany.,Reutlingen University of Applied Science, Reutlingen, Germany
| | - Rainer König
- Department of Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology and Bioquant, University of Heidelberg, Heidelberg, Germany.,Division of Theoretical Bioinformatics, DKFZ, Heidelberg, Germany
| | - Kathrin Schmidt
- Department of General Pediatrics, Division of Inborn Metabolic Diseases, University Children's Hospital, Heidelberg, Germany
| | | | - Stefan M Pfister
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, DKFZ, Heidelberg, Germany.,Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Manfred Jugold
- Core Facility, Small Animal Imaging Center, DKFZ, Heidelberg, Germany
| | - Susan M Hutson
- Department of Human Nutrition, Foods and Exercise, Virginia Polytechnic Institute, Blacksburg, Virginia, USA
| | - Christoph Plass
- Division of Epigenomics and Cancer Risk Factors, DKFZ, Heidelberg, Germany
| | - Jürgen G Okun
- Department of General Pediatrics, Division of Inborn Metabolic Diseases, University Children's Hospital, Heidelberg, Germany
| | - Guido Reifenberger
- Department of Neuropathology, Heinrich Heine University, Düsseldorf, Germany.,German Cancer Consortium (DKTK), DKFZ, Heidelberg, Germany
| | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bernhard Radlwimmer
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
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14
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Schweizer L, Koelsche C, Sahm F, Piro RM, Capper D, Reuss DE, Pusch S, Habel A, Meyer J, Göck T, Jones DTW, Mawrin C, Schittenhelm J, Becker A, Heim S, Simon M, Herold-Mende C, Mechtersheimer G, Paulus W, König R, Wiestler OD, Pfister SM, von Deimling A. Meningeal hemangiopericytoma and solitary fibrous tumors carry the NAB2-STAT6 fusion and can be diagnosed by nuclear expression of STAT6 protein. Acta Neuropathol 2013; 125:651-8. [PMID: 23575898 DOI: 10.1007/s00401-013-1117-6] [Citation(s) in RCA: 241] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 04/03/2013] [Accepted: 04/03/2013] [Indexed: 10/27/2022]
Abstract
Non-central nervous system hemangiopericytoma (HPC) and solitary fibrous tumor (SFT) are considered by pathologists as two variants of a single tumor entity now subsumed under the entity SFT. Recent detection of frequent NAB2-STAT6 fusions in both, HPC and SFT, provided additional support for this view. On the other hand, current neuropathological practice still distinguishes between HPC and SFT. The present study set out to identify genes involved in the formation of meningeal HPC. We performed exome sequencing and detected the NAB2-STAT6 fusion in DNA of 8/10 meningeal HPC thereby providing evidence of close relationship of these tumors with peripheral SFT. Due to the considerable effort required for exome sequencing, we sought to explore surrogate markers for the NAB2-STAT6 fusion protein. We adopted the Duolink proximity ligation assay and demonstrated the presence of NAB2-STAT6 fusion protein in 17/17 HPC and the absence in 15/15 meningiomas. More practical, presence of the NAB2-STAT6 fusion protein resulted in a strong nuclear signal in STAT6 immunohistochemistry. The nuclear reallocation of STAT6 was detected in 35/37 meningeal HPC and 25/25 meningeal SFT but not in 87 meningiomas representing the most important differential diagnosis. Tissues not harboring the NAB2-STAT6 fusion protein presented with nuclear expression of NAB2 and cytoplasmic expression of STAT6 proteins. In conclusion, we provide strong evidence for meningeal HPC and SFT to constitute variants of a single entity which is defined by NAB2-STAT6 fusion. In addition, we demonstrate that this fusion can be rapidly detected by STAT6 immunohistochemistry which shows a consistent nuclear reallocation. This immunohistochemical assay may prove valuable for the differentiation of HPC and SFT from other mesenchymal neoplasms.
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15
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Piro RM, Molineris I, Di Cunto F, Eils R, König R. Disease-gene discovery by integration of 3D gene expression and transcription factor binding affinities. ACTA ACUST UNITED AC 2012; 29:468-75. [PMID: 23267172 DOI: 10.1093/bioinformatics/bts720] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
MOTIVATION The computational evaluation of candidate genes for hereditary disorders is a non-trivial task. Several excellent methods for disease-gene prediction have been developed in the past 2 decades, exploiting widely differing data sources to infer disease-relevant functional relationships between candidate genes and disorders. We have shown recently that spatially mapped, i.e. 3D, gene expression data from the mouse brain can be successfully used to prioritize candidate genes for human Mendelian disorders of the central nervous system. RESULTS We improved our previous work 2-fold: (i) we demonstrate that condition-independent transcription factor binding affinities of the candidate genes' promoters are relevant for disease-gene prediction and can be integrated with our previous approach to significantly enhance its predictive power; and (ii) we define a novel similarity measure-termed Relative Intensity Overlap-for both 3D gene expression patterns and binding affinity profiles that better exploits their disease-relevant information content. Finally, we present novel disease-gene predictions for eight loci associated with different syndromes of unknown molecular basis that are characterized by mental retardation.
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Affiliation(s)
- Rosario M Piro
- Department of Theoretical Bioinformatics, German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ), University of Heidelberg, Im 69120 Heidelberg, Germany.
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16
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Abstract
The identification of genes involved in human hereditary diseases often requires the time-consuming and expensive examination of a great number of possible candidate genes, since genome-wide techniques such as linkage analysis and association studies frequently select many hundreds of 'positional' candidates. Even considering the positive impact of next-generation sequencing technologies, the prioritization of candidate genes may be an important step for disease-gene identification. In this paper we develop a basic classification scheme for computational approaches to disease-gene prediction and apply it to exhaustively review bioinformatics tools that have been developed for this purpose, focusing on conceptual aspects rather than technical detail and performance. Finally, we discuss some past successes obtained by computational approaches to illustrate their beneficial contribution to medical research.
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Affiliation(s)
- Rosario M Piro
- Department of Theoretical Bioinformatics, German Cancer Research Center, (DKFZ), Heidelberg, Germany.
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17
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Piro RM, Molineris I, Ala U, Di Cunto F. Evaluation of candidate genes from orphan FEB and GEFS+ loci by analysis of human brain gene expression atlases. PLoS One 2011; 6:e23149. [PMID: 21858011 PMCID: PMC3157479 DOI: 10.1371/journal.pone.0023149] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Accepted: 07/07/2011] [Indexed: 12/19/2022] Open
Abstract
Febrile seizures, or febrile convulsions (FEB), represent the most common form of childhood seizures and are believed to be influenced by variations in several susceptibility genes. Most of the associated loci, however, remain ‘orphan’, i.e. the susceptibility genes they contain still remain to be identified. Further orphan loci have been mapped for a related disorder, genetic (generalized) epilepsy with febrile seizures plus (GEFS+). We show that both spatially mapped and ‘traditional’ gene expression data from the human brain can be successfully employed to predict the most promising candidate genes for FEB and GEFS+, apply our prediction method to the remaining orphan loci and discuss the validity of the predictions. For several of the orphan FEB/GEFS+ loci we propose excellent, and not always obvious, candidates for mutation screening in order to aid in gaining a better understanding of the genetic origin of the susceptibility to seizures.
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Affiliation(s)
- Rosario M Piro
- Molecular Biotechnology Center and Department of Genetics, Biology and Biochemistry, University of Torino, Torino, Italy.
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18
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Fagoonee S, Hobbs RM, De Chiara L, Cantarella D, Piro RM, Tolosano E, Medico E, Provero P, Pandolfi PP, Silengo L, Altruda F. Generation of functional hepatocytes from mouse germ line cell-derived pluripotent stem cells in vitro. Stem Cells Dev 2011; 19:1183-94. [PMID: 20331356 DOI: 10.1089/scd.2009.0496] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Germ line cell-derived pluripotent stem cells (GPSCs) are similar to embryonic stem (ES) cells in that they can proliferate intensively and differentiate into a variety of cell types. Previous studies have revealed some inherent differences in gene expression between undifferentiated mouse ES cells and GPSCs. Our aims were to generate functional hepatocytes from mouse GPSCs in vitro and to investigate whether the differences in gene expression may impact on the hepatocyte differentiation capacity of the GPSCs compared with ES cells. Mouse GPSCs and ES cells were induced to differentiate into hepatocytes through embryoid body formation, with very high efficiency. These hepatocytes were characterized at cellular, molecular, and functional levels. The GPSC-derived hepatocytes expressed hepatic markers and were metabolically active as shown by albumin and haptoglobin secretion, urea synthesis, glycogen storage, and indocyanine green uptake. We also performed an unprecedented DNA microarray analysis comparing different stages of hepatocyte differentiation. Gene expression profiling demonstrated a strong similarity between GPSC and ES cells at different stages of induced hepatic differentiation. Moreover, Pearson correlation analysis of the microarray datasets suggested that, at late hepatic differentiation stages, the in vitro-derived cells were closer to fetal mouse primary hepatocytes than to those obtained from neonates. We have shown for the first time that adult GPSCs can be induced to differentiate into functional hepatocytes in vitro. These GPSC-derived hepatocytes offer great potential for cell replacement therapy for a wide variety of liver diseases.
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Affiliation(s)
- Sharmila Fagoonee
- Department of Genetics, Biology and Biochemistry and Molecular Biotechnology Center, University of Turin, Turin, Italy.
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19
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Abstract
Motivation: The identification of genes involved in specific phenotypes, such as human hereditary diseases, often requires the time-consuming and expensive examination of a large number of positional candidates selected by genome-wide techniques such as linkage analysis and association studies. Even considering the positive impact of next-generation sequencing technologies, the prioritization of these positional candidates may be an important step for disease-gene identification. Results: Here, we report a large-scale analysis of spatial, i.e. 3D, gene-expression data from an entire organ (the mouse brain) for the purpose of evaluating and ranking positional candidate genes, showing that the spatial gene-expression patterns can be successfully exploited for the prediction of gene–phenotype associations not only for mouse phenotypes, but also for human central nervous system-related Mendelian disorders. We apply our method to the case of X-linked mental retardation, compare the predictions to the results obtained from a previous large-scale resequencing study of chromosome X and discuss some promising novel candidates. Contact:rosario.piro@unito.it Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Rosario M Piro
- Molecular Biotechnology Center, Biology and Biochemistry, University of Torino, Torino, Italy.
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