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König E, Nicoletti A, Pattaro C, Annesi G, Melotti R, Gialluisi A, Schwienbacher C, Picard A, Blankenburg H, Pichler I, Modugno N, Ciullo M, Esposito T, Domingues FS, Hicks AA, Zappia M, Pramstaller PP. Exome-wide association study of levodopa-induced dyskinesia in Parkinson's disease. Sci Rep 2021; 11:19582. [PMID: 34599261 PMCID: PMC8486836 DOI: 10.1038/s41598-021-99393-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 09/16/2021] [Indexed: 11/09/2022] Open
Abstract
Levodopa is the standard long-term dopamine replacement therapy to treat Parkinson's disease (PD) symptoms. With time, levodopa may induce debilitating dyskinesias (LID), the treatment of which represents a large clinically unmet need. However, time-to-LID onset varies between patients, reflecting a possible genetic component. We performed an hypothesis-free whole-exome sequencing (WES)-based screening of time-to-LID onset and attempted replication of previously published candidate gene studies. A WES association analysis was carried out in 134 PD patients in a meta-analytical framework. Replication was attempted in an independent study of 97 PD patients. Variants from previously reported candidate genes (OPRM1, COMT, BDNF) were also specifically examined. We significantly replicated, for the first time, an association of variant rs1799971 in the OPRM1 gene with time-to-LID onset. Furthermore, we identified two novel potentially functional variants, in the MAD2L2 (rs2233019) and MAP7 (rs35350783) genes, which were significantly associated at the discovery stage. In the replication study, the two variants showed direction-consistent effects but did not achieve the replication significance threshold. Our study provides the first WES results for time-to-LID onset, where we replicate association at OPRM1, and suggest new variants in MAD2L2 and MAP7 genes that are significant in discovery, but require larger datasets for replication. The results are being made publicly available to allow for independent external validation.
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Affiliation(s)
- Eva König
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Via Luigi Galvani 31, 39100, Bozen/Bolzano, Italy
| | - Alessandra Nicoletti
- Section of Neurosciences, Department G.F. Ingrassia, University of Catania, Catania, Italy
| | - Cristian Pattaro
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Via Luigi Galvani 31, 39100, Bozen/Bolzano, Italy
| | - Grazia Annesi
- Institute for Biomedical Research and Innovation, National Research Council, Mangone (Cosenza), Italy
| | - Roberto Melotti
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Via Luigi Galvani 31, 39100, Bozen/Bolzano, Italy
| | | | - Christine Schwienbacher
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Via Luigi Galvani 31, 39100, Bozen/Bolzano, Italy
| | - Anne Picard
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Via Luigi Galvani 31, 39100, Bozen/Bolzano, Italy
| | - Hagen Blankenburg
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Via Luigi Galvani 31, 39100, Bozen/Bolzano, Italy
| | - Irene Pichler
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Via Luigi Galvani 31, 39100, Bozen/Bolzano, Italy
| | - Nicola Modugno
- Mediterranean Neurological Institute (MNI), IRCCS Neuromed, Pozzilli, Italy
| | - Marina Ciullo
- Mediterranean Neurological Institute (MNI), IRCCS Neuromed, Pozzilli, Italy.,Institute of Genetics and Biophysics "Adriano Buzzati-Traverso", National Research Council, Naples, Italy
| | - Teresa Esposito
- Mediterranean Neurological Institute (MNI), IRCCS Neuromed, Pozzilli, Italy.,Institute of Genetics and Biophysics "Adriano Buzzati-Traverso", National Research Council, Naples, Italy
| | - Francisco S Domingues
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Via Luigi Galvani 31, 39100, Bozen/Bolzano, Italy
| | - Andrew A Hicks
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Via Luigi Galvani 31, 39100, Bozen/Bolzano, Italy.
| | - Mario Zappia
- Section of Neurosciences, Department G.F. Ingrassia, University of Catania, Catania, Italy
| | - Peter P Pramstaller
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Via Luigi Galvani 31, 39100, Bozen/Bolzano, Italy
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2
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Rainer J, Meraviglia V, Blankenburg H, Piubelli C, Pramstaller PP, Paolin A, Cogliati E, Pompilio G, Sommariva E, Domingues FS, Rossini A. The arrhythmogenic cardiomyopathy-specific coding and non-coding transcriptome in human cardiac stromal cells. BMC Genomics 2018; 19:491. [PMID: 29940860 PMCID: PMC6019788 DOI: 10.1186/s12864-018-4876-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 06/18/2018] [Indexed: 01/05/2023] Open
Abstract
Background Arrhythmogenic cardiomyopathy (ACM) is a genetic autosomal disease characterized by abnormal cell-cell adhesion, cardiomyocyte death, progressive fibro-adipose replacement of the myocardium, arrhythmias and sudden death. Several different cell types contribute to the pathogenesis of ACM, including, as recently described, cardiac stromal cells (CStCs). In the present study, we aim to identify ACM-specific expression profiles of human CStCs derived from endomyocardial biopsies of ACM patients and healthy individuals employing TaqMan Low Density Arrays for miRNA expression profiling, and high throughput sequencing for gene expression quantification. Results We identified 3 miRNAs and 272 genes as significantly differentially expressed at a 5% false discovery rate. Both the differentially expressed genes as well as the target genes of the ACM-specific miRNAs were found to be enriched in cell adhesion-related biological processes. Functional similarity and protein interaction-based network analyses performed on the identified deregulated genes, miRNA targets and known ACM-causative genes revealed clusters of highly related genes involved in cell adhesion, extracellular matrix organization, lipid transport and ephrin receptor signaling. Conclusions We determined for the first time the coding and non-coding transcriptome characteristic of ACM cardiac stromal cells, finding evidence for a potential contribution of miRNAs, specifically miR-29b-3p, to ACM pathogenesis or phenotype maintenance. Electronic supplementary material The online version of this article (10.1186/s12864-018-4876-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Johannes Rainer
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Viale Druso 1, 39100, Bolzano, Italy.
| | - Viviana Meraviglia
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Viale Druso 1, 39100, Bolzano, Italy.
| | - Hagen Blankenburg
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Viale Druso 1, 39100, Bolzano, Italy
| | - Chiara Piubelli
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Viale Druso 1, 39100, Bolzano, Italy
| | - Peter P Pramstaller
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Viale Druso 1, 39100, Bolzano, Italy
| | - Adolfo Paolin
- Treviso Tissue Bank Foundation, Piazzalo Ospedale 1, 31100, Treviso, Italy
| | - Elisa Cogliati
- Treviso Tissue Bank Foundation, Piazzalo Ospedale 1, 31100, Treviso, Italy
| | - Giulio Pompilio
- Vascular Biology and Regenerative Medicine Unit, Centro Cardiologico Monzino IRCCS, via Parea 4, 20138, Milan, Italy
| | - Elena Sommariva
- Vascular Biology and Regenerative Medicine Unit, Centro Cardiologico Monzino IRCCS, via Parea 4, 20138, Milan, Italy
| | - Francisco S Domingues
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Viale Druso 1, 39100, Bolzano, Italy
| | - Alessandra Rossini
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Viale Druso 1, 39100, Bolzano, Italy
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Blankenburg H, Falla M, Schwienbacher C, Fabbrini G, Berardelli A, Pramstaller PP, Domingues FS. A Web Resource for Levodopa-Induced Dyskinesia Genetics in Parkinson's Disease. Neuroinformatics 2017; 15:297-300. [PMID: 28417316 DOI: 10.1007/s12021-017-9327-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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]
Affiliation(s)
- Hagen Blankenburg
- Institute for Biomedicine, Eurac Research, Eurac Research, Bolzano, Italy.
| | - Marika Falla
- Institute for Biomedicine, Eurac Research, Eurac Research, Bolzano, Italy.,Department of Neurology, General Central Hospital, Bolzano, Italy.,Department of Neurology and Psychiatry, Sapienza University of Rome, Rome, Italy
| | | | - Giovanni Fabbrini
- Department of Neurology and Psychiatry, Sapienza University of Rome, Rome, Italy.,Neuromed Institute IRCCS, Pozzilli, Italy
| | - Alfredo Berardelli
- Department of Neurology and Psychiatry, Sapienza University of Rome, Rome, Italy.,Neuromed Institute IRCCS, Pozzilli, Italy
| | - Peter P Pramstaller
- Institute for Biomedicine, Eurac Research, Eurac Research, Bolzano, Italy.,Department of Neurology, General Central Hospital, Bolzano, Italy.,Department of Neurology, University of Lübeck, Lübeck, Germany
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Weichenberger CX, Blankenburg H, Palermo A, D'Elia Y, König E, Bernstein E, Domingues FS. Dintor: functional annotation of genomic and proteomic data. BMC Genomics 2015; 16:1081. [PMID: 26691694 PMCID: PMC4687148 DOI: 10.1186/s12864-015-2279-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 12/08/2015] [Indexed: 11/16/2022] Open
Abstract
Background During the last decade, a great number of extremely valuable large-scale genomics and proteomics datasets have become available to the research community. In addition, dropping costs for conducting high-throughput sequencing experiments and the option to outsource them considerably contribute to an increasing number of researchers becoming active in this field. Even though various computational approaches have been developed to analyze these data, it is still a laborious task involving prudent integration of many heterogeneous and frequently updated data sources, creating a barrier for interested scientists to accomplish their own analysis. Results We have implemented Dintor, a data integration framework that provides a set of over 30 tools to assist researchers in the exploration of genomics and proteomics datasets. Each of the tools solves a particular task and several tools can be combined into data processing pipelines. Dintor covers a wide range of frequently required functionalities, from gene identifier conversions and orthology mappings to functional annotation of proteins and genetic variants up to candidate gene prioritization and Gene Ontology-based gene set enrichment analysis. Since the tools operate on constantly changing datasets, we provide a mechanism to unambiguously link tools with different versions of archived datasets, which guarantees reproducible results for future tool invocations. We demonstrate a selection of Dintor’s capabilities by analyzing datasets from four representative publications. The open source software can be downloaded and installed on a local Unix machine. For reasons of data privacy it can be configured to retrieve local data only. In addition, the Dintor tools are available on our public Galaxy web service at http://dintor.eurac.edu. Conclusions Dintor is a computational annotation framework for the analysis of genomic and proteomic datasets, providing a rich set of tools that cover the most frequently encountered tasks. A major advantage is its capability to consistently handle multiple versions of tool-associated datasets, supporting the researcher in delivering reproducible results. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2279-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christian X Weichenberger
- Center for Biomedicine, European Academy of Bolzano/Bozen (EURAC), (Affiliated to the University of Lübeck, Lübeck, Germany), Viale Druso 1, 39100, Bolzano, Italy.
| | - Hagen Blankenburg
- Center for Biomedicine, European Academy of Bolzano/Bozen (EURAC), (Affiliated to the University of Lübeck, Lübeck, Germany), Viale Druso 1, 39100, Bolzano, Italy.
| | - Antonia Palermo
- Center for Biomedicine, European Academy of Bolzano/Bozen (EURAC), (Affiliated to the University of Lübeck, Lübeck, Germany), Viale Druso 1, 39100, Bolzano, Italy.
| | - Yuri D'Elia
- Center for Biomedicine, European Academy of Bolzano/Bozen (EURAC), (Affiliated to the University of Lübeck, Lübeck, Germany), Viale Druso 1, 39100, Bolzano, Italy.
| | - Eva König
- Center for Biomedicine, European Academy of Bolzano/Bozen (EURAC), (Affiliated to the University of Lübeck, Lübeck, Germany), Viale Druso 1, 39100, Bolzano, Italy.
| | - Erik Bernstein
- Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.
| | - Francisco S Domingues
- Center for Biomedicine, European Academy of Bolzano/Bozen (EURAC), (Affiliated to the University of Lübeck, Lübeck, Germany), Viale Druso 1, 39100, Bolzano, Italy.
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5
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Serafin A, Foco L, Zanigni S, Blankenburg H, Picard A, Zanon A, Giannini G, Pichler I, Facheris MF, Cortelli P, Pramstaller PP, Hicks AA, Domingues FS, Schwienbacher C. Overexpression of blood microRNAs 103a, 30b, and 29a in L-dopa-treated patients with PD. Neurology 2015; 84:645-53. [PMID: 25596505 DOI: 10.1212/wnl.0000000000001258] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE The aims of the present study were to profile the expression of several candidate microRNAs (miRNAs) in blood from L-dopa-treated and drug-naive patients with Parkinson disease (PD) vs unaffected controls and to interpret the miRNA expression data in a biological context. METHODS We analyzed RNAs from peripheral blood of 36 L-dopa-treated, 10 drug-naive patients with PD and unaffected controls matched 1:1 by sex and age. We evaluated expression by reverse transcription-quantitative real-time PCR, and we analyzed data using a 2-tailed paired t test. To detect miRNA targets, several miRNA resources were combined to generate an overall score for each candidate gene using weighted rank aggregation. RESULTS Significant overexpression of miR-103a-3p (p < 0.0001), miR-30b-5p (p = 0.002), and miR-29a-3p (p = 0.005) in treated patients with PD was observed, and promising candidate target genes for these were revealed by an integrated in silico analysis. CONCLUSIONS We revealed 3 candidate biomarkers for PD. miRNAs 30b-5p and 29a-3p replicated a documented deregulation in PD albeit opposite to published data, while for miR-103a-3p, we demonstrated for the first time an overexpression in treated patients with PD. Expression studies in patients and/or in isolated peripheral blood mononuclear cells before and after L-dopa administration are necessary to define the involvement of L-dopa treatment in the observed overexpression. Our in silico analysis to prioritize targets of deregulated miRNAs identified candidate target genes, including genes related to neurodegeneration and PD. Despite the preliminary character of our study, the results provide a rationale for further clarifying the role of the identified miRNAs in the pathogenesis of PD and for validating their diagnostic potential.
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Affiliation(s)
- Alice Serafin
- From the Center for Biomedicine (A.S., L.F., S.Z., H.B., A.P., A.Z., G.G., I.P., M.F.F., P.P.P., A.A.H., F.S.D., C.S.), European Academy Bozen/Bolzano (EURAC), Bolzano, Italy, affiliated institute of the University of Lübeck, Germany; Department of Neurology (S.Z., P.P.P.), General Central Hospital, Bolzano; IRCCS Institute of Neurological Sciences of Bologna (P.C.); Department of Biomedical and NeuroMotor Sciences (P.C.), Alma Mater Studiorum-University of Bologna, Italy; Department of Neurology (P.P.P.), University of Lübeck, Germany
| | - Luisa Foco
- From the Center for Biomedicine (A.S., L.F., S.Z., H.B., A.P., A.Z., G.G., I.P., M.F.F., P.P.P., A.A.H., F.S.D., C.S.), European Academy Bozen/Bolzano (EURAC), Bolzano, Italy, affiliated institute of the University of Lübeck, Germany; Department of Neurology (S.Z., P.P.P.), General Central Hospital, Bolzano; IRCCS Institute of Neurological Sciences of Bologna (P.C.); Department of Biomedical and NeuroMotor Sciences (P.C.), Alma Mater Studiorum-University of Bologna, Italy; Department of Neurology (P.P.P.), University of Lübeck, Germany
| | - Stefano Zanigni
- From the Center for Biomedicine (A.S., L.F., S.Z., H.B., A.P., A.Z., G.G., I.P., M.F.F., P.P.P., A.A.H., F.S.D., C.S.), European Academy Bozen/Bolzano (EURAC), Bolzano, Italy, affiliated institute of the University of Lübeck, Germany; Department of Neurology (S.Z., P.P.P.), General Central Hospital, Bolzano; IRCCS Institute of Neurological Sciences of Bologna (P.C.); Department of Biomedical and NeuroMotor Sciences (P.C.), Alma Mater Studiorum-University of Bologna, Italy; Department of Neurology (P.P.P.), University of Lübeck, Germany
| | - Hagen Blankenburg
- From the Center for Biomedicine (A.S., L.F., S.Z., H.B., A.P., A.Z., G.G., I.P., M.F.F., P.P.P., A.A.H., F.S.D., C.S.), European Academy Bozen/Bolzano (EURAC), Bolzano, Italy, affiliated institute of the University of Lübeck, Germany; Department of Neurology (S.Z., P.P.P.), General Central Hospital, Bolzano; IRCCS Institute of Neurological Sciences of Bologna (P.C.); Department of Biomedical and NeuroMotor Sciences (P.C.), Alma Mater Studiorum-University of Bologna, Italy; Department of Neurology (P.P.P.), University of Lübeck, Germany
| | - Anne Picard
- From the Center for Biomedicine (A.S., L.F., S.Z., H.B., A.P., A.Z., G.G., I.P., M.F.F., P.P.P., A.A.H., F.S.D., C.S.), European Academy Bozen/Bolzano (EURAC), Bolzano, Italy, affiliated institute of the University of Lübeck, Germany; Department of Neurology (S.Z., P.P.P.), General Central Hospital, Bolzano; IRCCS Institute of Neurological Sciences of Bologna (P.C.); Department of Biomedical and NeuroMotor Sciences (P.C.), Alma Mater Studiorum-University of Bologna, Italy; Department of Neurology (P.P.P.), University of Lübeck, Germany
| | - Alessandra Zanon
- From the Center for Biomedicine (A.S., L.F., S.Z., H.B., A.P., A.Z., G.G., I.P., M.F.F., P.P.P., A.A.H., F.S.D., C.S.), European Academy Bozen/Bolzano (EURAC), Bolzano, Italy, affiliated institute of the University of Lübeck, Germany; Department of Neurology (S.Z., P.P.P.), General Central Hospital, Bolzano; IRCCS Institute of Neurological Sciences of Bologna (P.C.); Department of Biomedical and NeuroMotor Sciences (P.C.), Alma Mater Studiorum-University of Bologna, Italy; Department of Neurology (P.P.P.), University of Lübeck, Germany
| | - Giulia Giannini
- From the Center for Biomedicine (A.S., L.F., S.Z., H.B., A.P., A.Z., G.G., I.P., M.F.F., P.P.P., A.A.H., F.S.D., C.S.), European Academy Bozen/Bolzano (EURAC), Bolzano, Italy, affiliated institute of the University of Lübeck, Germany; Department of Neurology (S.Z., P.P.P.), General Central Hospital, Bolzano; IRCCS Institute of Neurological Sciences of Bologna (P.C.); Department of Biomedical and NeuroMotor Sciences (P.C.), Alma Mater Studiorum-University of Bologna, Italy; Department of Neurology (P.P.P.), University of Lübeck, Germany
| | - Irene Pichler
- From the Center for Biomedicine (A.S., L.F., S.Z., H.B., A.P., A.Z., G.G., I.P., M.F.F., P.P.P., A.A.H., F.S.D., C.S.), European Academy Bozen/Bolzano (EURAC), Bolzano, Italy, affiliated institute of the University of Lübeck, Germany; Department of Neurology (S.Z., P.P.P.), General Central Hospital, Bolzano; IRCCS Institute of Neurological Sciences of Bologna (P.C.); Department of Biomedical and NeuroMotor Sciences (P.C.), Alma Mater Studiorum-University of Bologna, Italy; Department of Neurology (P.P.P.), University of Lübeck, Germany
| | - Maurizio F Facheris
- From the Center for Biomedicine (A.S., L.F., S.Z., H.B., A.P., A.Z., G.G., I.P., M.F.F., P.P.P., A.A.H., F.S.D., C.S.), European Academy Bozen/Bolzano (EURAC), Bolzano, Italy, affiliated institute of the University of Lübeck, Germany; Department of Neurology (S.Z., P.P.P.), General Central Hospital, Bolzano; IRCCS Institute of Neurological Sciences of Bologna (P.C.); Department of Biomedical and NeuroMotor Sciences (P.C.), Alma Mater Studiorum-University of Bologna, Italy; Department of Neurology (P.P.P.), University of Lübeck, Germany
| | - Pietro Cortelli
- From the Center for Biomedicine (A.S., L.F., S.Z., H.B., A.P., A.Z., G.G., I.P., M.F.F., P.P.P., A.A.H., F.S.D., C.S.), European Academy Bozen/Bolzano (EURAC), Bolzano, Italy, affiliated institute of the University of Lübeck, Germany; Department of Neurology (S.Z., P.P.P.), General Central Hospital, Bolzano; IRCCS Institute of Neurological Sciences of Bologna (P.C.); Department of Biomedical and NeuroMotor Sciences (P.C.), Alma Mater Studiorum-University of Bologna, Italy; Department of Neurology (P.P.P.), University of Lübeck, Germany
| | - Peter P Pramstaller
- From the Center for Biomedicine (A.S., L.F., S.Z., H.B., A.P., A.Z., G.G., I.P., M.F.F., P.P.P., A.A.H., F.S.D., C.S.), European Academy Bozen/Bolzano (EURAC), Bolzano, Italy, affiliated institute of the University of Lübeck, Germany; Department of Neurology (S.Z., P.P.P.), General Central Hospital, Bolzano; IRCCS Institute of Neurological Sciences of Bologna (P.C.); Department of Biomedical and NeuroMotor Sciences (P.C.), Alma Mater Studiorum-University of Bologna, Italy; Department of Neurology (P.P.P.), University of Lübeck, Germany
| | - Andrew A Hicks
- From the Center for Biomedicine (A.S., L.F., S.Z., H.B., A.P., A.Z., G.G., I.P., M.F.F., P.P.P., A.A.H., F.S.D., C.S.), European Academy Bozen/Bolzano (EURAC), Bolzano, Italy, affiliated institute of the University of Lübeck, Germany; Department of Neurology (S.Z., P.P.P.), General Central Hospital, Bolzano; IRCCS Institute of Neurological Sciences of Bologna (P.C.); Department of Biomedical and NeuroMotor Sciences (P.C.), Alma Mater Studiorum-University of Bologna, Italy; Department of Neurology (P.P.P.), University of Lübeck, Germany
| | - Francisco S Domingues
- From the Center for Biomedicine (A.S., L.F., S.Z., H.B., A.P., A.Z., G.G., I.P., M.F.F., P.P.P., A.A.H., F.S.D., C.S.), European Academy Bozen/Bolzano (EURAC), Bolzano, Italy, affiliated institute of the University of Lübeck, Germany; Department of Neurology (S.Z., P.P.P.), General Central Hospital, Bolzano; IRCCS Institute of Neurological Sciences of Bologna (P.C.); Department of Biomedical and NeuroMotor Sciences (P.C.), Alma Mater Studiorum-University of Bologna, Italy; Department of Neurology (P.P.P.), University of Lübeck, Germany
| | - Christine Schwienbacher
- From the Center for Biomedicine (A.S., L.F., S.Z., H.B., A.P., A.Z., G.G., I.P., M.F.F., P.P.P., A.A.H., F.S.D., C.S.), European Academy Bozen/Bolzano (EURAC), Bolzano, Italy, affiliated institute of the University of Lübeck, Germany; Department of Neurology (S.Z., P.P.P.), General Central Hospital, Bolzano; IRCCS Institute of Neurological Sciences of Bologna (P.C.); Department of Biomedical and NeuroMotor Sciences (P.C.), Alma Mater Studiorum-University of Bologna, Italy; Department of Neurology (P.P.P.), University of Lübeck, Germany.
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6
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Poenisch M, Metz P, Blankenburg H, Ruggieri A, Lee JY, Rupp D, Rebhan I, Diederich K, Kaderali L, Domingues FS, Albrecht M, Lohmann V, Erfle H, Bartenschlager R. Identification of HNRNPK as regulator of hepatitis C virus particle production. PLoS Pathog 2015; 11:e1004573. [PMID: 25569684 PMCID: PMC4287573 DOI: 10.1371/journal.ppat.1004573] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [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: 07/08/2014] [Accepted: 11/12/2014] [Indexed: 12/11/2022] Open
Abstract
Hepatitis C virus (HCV) is a major cause of chronic liver disease affecting around 130 million people worldwide. While great progress has been made to define the principle steps of the viral life cycle, detailed knowledge how HCV interacts with its host cells is still limited. To overcome this limitation we conducted a comprehensive whole-virus RNA interference-based screen and identified 40 host dependency and 16 host restriction factors involved in HCV entry/replication or assembly/release. Of these factors, heterogeneous nuclear ribonucleoprotein K (HNRNPK) was found to suppress HCV particle production without affecting viral RNA replication. This suppression of virus production was specific to HCV, independent from assembly competence and genotype, and not found with the related Dengue virus. By using a knock-down rescue approach we identified the domains within HNRNPK required for suppression of HCV particle production. Importantly, HNRNPK was found to interact specifically with HCV RNA and this interaction was impaired by mutations that also reduced the ability to suppress HCV particle production. Finally, we found that in HCV-infected cells, subcellular distribution of HNRNPK was altered; the protein was recruited to sites in close proximity of lipid droplets and colocalized with core protein as well as HCV plus-strand RNA, which was not the case with HNRNPK variants unable to suppress HCV virion formation. These results suggest that HNRNPK might determine efficiency of HCV particle production by limiting the availability of viral RNA for incorporation into virions. This study adds a new function to HNRNPK that acts as central hub in the replication cycle of multiple other viruses.
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Affiliation(s)
- Marion Poenisch
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Philippe Metz
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Hagen Blankenburg
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany
- Center for Biomedicine, European Academy Bozen/Bolzano (EURAC), Bolzano, Italy, Affiliated Institute of the University of Lübeck, Lübeck, Germany
| | - Alessia Ruggieri
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Ji-Young Lee
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Daniel Rupp
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Ilka Rebhan
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Kathrin Diederich
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Lars Kaderali
- ViroQuant Research Group Modeling, University of Heidelberg, Heidelberg, Germany
- Institute for Medical Informatics and Biometry, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Francisco S. Domingues
- Center for Biomedicine, European Academy Bozen/Bolzano (EURAC), Bolzano, Italy, Affiliated Institute of the University of Lübeck, Lübeck, Germany
| | - Mario Albrecht
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Volker Lohmann
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Holger Erfle
- ViroQuant-CellNetworks RNAi Screening Facility, University of Heidelberg, Heidelberg, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
- * E-mail:
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7
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Serafin A, Foco L, Blankenburg H, Picard A, Zanigni S, Zanon A, Pramstaller PP, Hicks AA, Schwienbacher C. Identification of a set of endogenous reference genes for miRNA expression studies in Parkinson's disease blood samples. BMC Res Notes 2014; 7:715. [PMID: 25304816 PMCID: PMC4209045 DOI: 10.1186/1756-0500-7-715] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 10/02/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Research on microRNAs (miRNAs) is becoming an increasingly attractive field, as these small RNA molecules are involved in several physiological functions and diseases. To date, only few studies have assessed the expression of blood miRNAs related to Parkinson's disease (PD) using microarray and quantitative real-time PCR (qRT-PCR). Measuring miRNA expression involves normalization of qRT-PCR data using endogenous reference genes for calibration, but their choice remains a delicate problem with serious impact on the resulting expression levels. The aim of the present study was to evaluate the suitability of a set of commonly used small RNAs as normalizers and to identify which of these miRNAs might be considered reliable reference genes in qRT-PCR expression analyses on PD blood samples. RESULTS Commonly used reference genes snoRNA RNU24, snRNA RNU6B, snoRNA Z30 and miR-103a-3p were selected from the literature. We then analyzed the effect of using these genes as reference, alone or in any possible combination, on the measured expression levels of the target genes miR-30b-5p and miR-29a-3p, which have been previously reported to be deregulated in PD blood samples. CONCLUSIONS We identified RNU24 and Z30 as a reliable and stable pair of reference genes in PD blood samples.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Christine Schwienbacher
- Center for Biomedicine, European Academy Bozen/Bolzano (EURAC), 39100 Bolzano, Italy, Affiliated Institute of the University of Lübeck, Lübeck, Germany.
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8
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Garai Á, Zeke A, Gógl G, Törő I, Fördős F, Blankenburg H, Bárkai T, Varga J, Alexa A, Emig D, Albrecht M, Reményi A. Specificity of linear motifs that bind to a common mitogen-activated protein kinase docking groove. Sci Signal 2012; 5:ra74. [PMID: 23047924 DOI: 10.1126/scisignal.2003004] [Citation(s) in RCA: 122] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Mitogen-activated protein kinases (MAPKs) have a docking groove that interacts with linear "docking" motifs in binding partners. To determine the structural basis of binding specificity between MAPKs and docking motifs, we quantitatively analyzed the ability of 15 docking motifs from diverse MAPK partners to bind to c-Jun amino-terminal kinase 1 (JNK1), p38α, and extracellular signal-regulated kinase 2 (ERK2). Classical docking motifs mediated highly specific binding only to JNK1, and only those motifs with a sequence pattern distinct from the classical MAPK binding docking motif consensus differentiated between the topographically similar docking grooves of ERK and p38α. Crystal structures of four complexes of MAPKs with docking peptides, representing JNK-specific, ERK-specific, or ERK- and p38-selective binding modes, revealed that the regions located between consensus positions in the docking motifs showed conformational diversity. Although the consensus positions in the docking motifs served as anchor points that bound to common MAPK surface features and mostly contributed to docking in a nondiscriminatory fashion, the conformation of the intervening region between the anchor points mostly determined specificity. We designed peptides with tailored MAPK binding profiles by rationally changing the length and amino acid composition of intervening regions located between anchor points. These results suggest a coherent structural model for MAPK docking specificity that reveals how short linear motifs binding to a common kinase docking groove can mediate diverse interaction patterns and contribute to correct MAPK partner selection in signaling networks.
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Affiliation(s)
- Ágnes Garai
- Department of Biochemistry, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary
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9
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Aranda B, Blankenburg H, Kerrien S, Brinkman FSL, Ceol A, Chautard E, Dana JM, De Las Rivas J, Dumousseau M, Galeota E, Gaulton A, Goll J, Hancock REW, Isserlin R, Jimenez RC, Kerssemakers J, Khadake J, Lynn DJ, Michaut M, O'Kelly G, Ono K, Orchard S, Prieto C, Razick S, Rigina O, Salwinski L, Simonovic M, Velankar S, Winter A, Wu G, Bader GD, Cesareni G, Donaldson IM, Eisenberg D, Kleywegt GJ, Overington J, Ricard-Blum S, Tyers M, Albrecht M, Hermjakob H. PSICQUIC and PSISCORE: accessing and scoring molecular interactions. Nat Methods 2011; 8:528-9. [PMID: 21716279 DOI: 10.1038/nmeth.1637] [Citation(s) in RCA: 233] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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10
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Blankenburg H, Diehl S, Ramírez F, Wörz I, Poenisch M, Bartenschlager R. Discovery and prioritization of human cellular factors required for HCV infection. N Biotechnol 2010. [DOI: 10.1016/j.nbt.2010.01.020] [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: 11/28/2022]
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11
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Blankenburg H, Finn RD, Prlić A, Jenkinson AM, Ramírez F, Emig D, Schelhorn SE, Büch J, Lengauer T, Albrecht M. DASMI: exchanging, annotating and assessing molecular interaction data. ACTA ACUST UNITED AC 2009; 25:1321-8. [PMID: 19420069 PMCID: PMC2677739 DOI: 10.1093/bioinformatics/btp142] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
MOTIVATION Ever increasing amounts of biological interaction data are being accumulated worldwide, but they are currently not readily accessible to the biologist at a single site. New techniques are required for retrieving, sharing and presenting data spread over the Internet. RESULTS We introduce the DASMI system for the dynamic exchange, annotation and assessment of molecular interaction data. DASMI is based on the widely used Distributed Annotation System (DAS) and consists of a data exchange specification, web servers for providing the interaction data and clients for data integration and visualization. The decentralized architecture of DASMI affords the online retrieval of the most recent data from distributed sources and databases. DASMI can also be extended easily by adding new data sources and clients. We describe all DASMI components and demonstrate their use for protein and domain interactions. AVAILABILITY The DASMI tools are available at http://www.dasmi.de/ and http://ipfam.sanger.ac.uk/graph. The DAS registry and the DAS 1.53E specification is found at http://www.dasregistry.org/.
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Affiliation(s)
- Hagen Blankenburg
- Max Planck Institute for Informatics, Campus E 1.4, 66123 Saarbrücken, Germany
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12
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Blankenburg H, Ramírez F, Büch J, Albrecht M. DASMIweb: online integration, analysis and assessment of distributed protein interaction data. Nucleic Acids Res 2009; 37:W122-8. [PMID: 19502495 PMCID: PMC2703953 DOI: 10.1093/nar/gkp438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
In recent years, we have witnessed a substantial increase of the amount of available protein interaction data. However, most data are currently not readily accessible to the biologist at a single site, but scattered over multiple online repositories. Therefore, we have developed the DASMIweb server that affords the integration, analysis and qualitative assessment of distributed sources of interaction data in a dynamic fashion. Since DASMIweb allows for querying many different resources of protein and domain interactions simultaneously, it serves as an important starting point for interactome studies and assists the user in finding publicly accessible interaction data with minimal effort. The pool of queried resources is fully configurable and supports the inclusion of own interaction data or confidence scores. In particular, DASMIweb integrates confidence measures like functional similarity scores to assess individual interactions. The retrieved results can be exported in different file formats like MITAB or SIF. DASMIweb is freely available at http://www.dasmiweb.de.
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Affiliation(s)
- Hagen Blankenburg
- Max Planck Institute for Informatics, Campus E1.4, 66123 Saarbrücken, Germany.
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13
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Jenkinson AM, Albrecht M, Birney E, Blankenburg H, Down T, Finn RD, Hermjakob H, Hubbard TJP, Jimenez RC, Jones P, Kähäri A, Kulesha E, Macías JR, Reeves GA, Prlić A. Integrating biological data--the Distributed Annotation System. BMC Bioinformatics 2008; 9 Suppl 8:S3. [PMID: 18673527 PMCID: PMC2500094 DOI: 10.1186/1471-2105-9-s8-s3] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Distributed Annotation System (DAS) is a widely adopted protocol for dynamically integrating a wide range of biological data from geographically diverse sources. DAS continues to expand its applicability and evolve in response to new challenges facing integrative bioinformatics. RESULTS Here we describe the various infrastructure components of DAS and present a new extended version of the DAS specification. Version 1.53E incorporates several recent developments, including its extension to serve new data types and an ontology for protein features. CONCLUSION Our extensions to the DAS protocol have facilitated the integration of new data types, and our improvements to the existing DAS infrastructure have addressed recent challenges. The steadily increasing numbers of available data sources demonstrates further adoption of the DAS protocol.
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14
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Tress ML, Martelli PL, Frankish A, Reeves GA, Wesselink JJ, Yeats C, Ólason PĹ, Albrecht M, Hegyi H, Giorgetti A, Raimondo D, Lagarde J, Laskowski RA, López G, Sadowski MI, Watson JD, Fariselli P, Rossi I, Nagy A, Kai W, Størling Z, Orsini M, Assenov Y, Blankenburg H, Huthmacher C, Ramírez F, Schlicker A, Denoeud F, Jones P, Kerrien S, Orchard S, Antonarakis SE, Reymond A, Birney E, Brunak S, Casadio R, Guigo R, Harrow J, Hermjakob H, Jones DT, Lengauer T, A. Orengo C, Patthy L, Thornton JM, Tramontano A, Valencia A. The implications of alternative splicing in the ENCODE protein complement. Proc Natl Acad Sci U S A 2007; 104:5495-500. [PMID: 17372197 PMCID: PMC1838448 DOI: 10.1073/pnas.0700800104] [Citation(s) in RCA: 180] [Impact Index Per Article: 10.6] [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: 10/20/2006] [Indexed: 12/22/2022] Open
Abstract
Alternative premessenger RNA splicing enables genes to generate more than one gene product. Splicing events that occur within protein coding regions have the potential to alter the biological function of the expressed protein and even to create new protein functions. Alternative splicing has been suggested as one explanation for the discrepancy between the number of human genes and functional complexity. Here, we carry out a detailed study of the alternatively spliced gene products annotated in the ENCODE pilot project. We find that alternative splicing in human genes is more frequent than has commonly been suggested, and we demonstrate that many of the potential alternative gene products will have markedly different structure and function from their constitutively spliced counterparts. For the vast majority of these alternative isoforms, little evidence exists to suggest they have a role as functional proteins, and it seems unlikely that the spectrum of conventional enzymatic or structural functions can be substantially extended through alternative splicing.
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Affiliation(s)
- Michael L. Tress
- Structural Computational Biology Programme, Spanish National Cancer Research Centre, E-28029 Madrid, Spain
| | | | - Adam Frankish
- HAVANA Group, The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Gabrielle A. Reeves
- European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Jan Jaap Wesselink
- Structural Computational Biology Programme, Spanish National Cancer Research Centre, E-28029 Madrid, Spain
| | - Corin Yeats
- Department of Biochemistry and Molecular Biology and
| | - Páll ĺsólfur Ólason
- Center for Biological Sequence Analysis, BioCentrum-DTU, DK-2800 Lyngby, Denmark
| | - Mario Albrecht
- Max Planck Institute for Informatics, 66123 Saarbrücken, Germany
| | - Hedi Hegyi
- Biological Research Center, Hungarian Academy of Sciences, 1113 Budapest, Hungary
| | - Alejandro Giorgetti
- Department of Biochemical Sciences, University of Rome “La Sapienza,” 2-00185 Rome, Italy
| | - Domenico Raimondo
- Department of Biochemical Sciences, University of Rome “La Sapienza,” 2-00185 Rome, Italy
| | - Julien Lagarde
- Research Unit on Biomedical Informatics, Institut Municipal d'Investigació Mèdica, E-8003 Barcelona, Spain
| | - Roman A. Laskowski
- European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Gonzalo López
- Structural Computational Biology Programme, Spanish National Cancer Research Centre, E-28029 Madrid, Spain
| | - Michael I. Sadowski
- Bioinformatics Unit, University College London, London WC1E 6BT, United Kingdom
| | - James D. Watson
- European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Piero Fariselli
- Department of Biology, University of Bologna, 33-40126 Bologna, Italy
| | - Ivan Rossi
- Department of Biology, University of Bologna, 33-40126 Bologna, Italy
| | - Alinda Nagy
- Biological Research Center, Hungarian Academy of Sciences, 1113 Budapest, Hungary
| | - Wang Kai
- Center for Biological Sequence Analysis, BioCentrum-DTU, DK-2800 Lyngby, Denmark
| | - Zenia Størling
- Center for Biological Sequence Analysis, BioCentrum-DTU, DK-2800 Lyngby, Denmark
| | - Massimiliano Orsini
- Center for Advanced Studies, Research and Development in Sardinia (CRS4), 09010 Pula, Italy
| | - Yassen Assenov
- Max Planck Institute for Informatics, 66123 Saarbrücken, Germany
| | | | | | - Fidel Ramírez
- Max Planck Institute for Informatics, 66123 Saarbrücken, Germany
| | | | - France Denoeud
- Research Unit on Biomedical Informatics, Institut Municipal d'Investigació Mèdica, E-8003 Barcelona, Spain
| | - Phil Jones
- European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Samuel Kerrien
- European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Sandra Orchard
- European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Stylianos E. Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
| | - Alexandre Reymond
- Center for Integrative Genomics, Genopode building, University of Lausanne, 1015 Lausanne, Switzerland; and
| | - Ewan Birney
- European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Søren Brunak
- Center for Biological Sequence Analysis, BioCentrum-DTU, DK-2800 Lyngby, Denmark
| | - Rita Casadio
- Department of Biology, University of Bologna, 33-40126 Bologna, Italy
| | - Roderic Guigo
- Research Unit on Biomedical Informatics, Institut Municipal d'Investigació Mèdica, E-8003 Barcelona, Spain
- Centre de Regulació Genòmica, Universitat Pompeu Fabra, E-08003 Barcelona, Spain
| | - Jennifer Harrow
- HAVANA Group, The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Henning Hermjakob
- European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - David T. Jones
- Bioinformatics Unit, University College London, London WC1E 6BT, United Kingdom
| | - Thomas Lengauer
- Max Planck Institute for Informatics, 66123 Saarbrücken, Germany
| | | | - László Patthy
- Biological Research Center, Hungarian Academy of Sciences, 1113 Budapest, Hungary
| | - Janet M. Thornton
- European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom
| | | | - Alfonso Valencia
- Structural Computational Biology Programme, Spanish National Cancer Research Centre, E-28029 Madrid, Spain
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15
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Seekamp A, Blankenburg H, van Griensven M, Regel G. [Intramuscular pO2 monitoring in compartment syndrome--an experimental study]. Zentralbl Chir 1998; 123:285-91; discussion 291-2. [PMID: 9586191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
HYPOTHESIS Measuring intracompartmental pressure is a well accepted method in evaluating a compartment syndrome, which may occur after limb ischemia followed by reperfusion. As a compartment syndrome is paralleled by a decreased microcirculation it should be possible to evaluate a compartment syndrome also by measuring intramuscular pO2. METHODS Anesthetized rats (spontaneous breathing via tracheotomy) were subjected to infrarenal ligation of the aorta. A pressure catheter was placed subfascial in the crural muscle group of one hind limb, whereas the contralateral side was prepared with a pO2 catheter. Besides a sham operated group, three experimental groups were subjected to either 2 hrs, 4 hrs or 6 hrs of ischemia followed by 4 hrs of reperfusion. One further group was also subjected to 4 hrs of ischemia and 4 hrs of reperfusion but received a fasciotomy at the time of reperfusion. Compartment pressure and intramuscular pO2 were recorded every 15 min. For histological examination muscle specimen were obtained after each experiment. RESULTS Two hours of ischemia followed by 4 hrs of reperfusion did not result in any morphological changes and also not in any significant change in compartment pressure during both phases, whereas pO2 significantly dropped during ischemia (from 19.0 mmHg to 3.0-5.0 mmHg) and returned to normal during reperfusion. In prolonged ischemia (4hrs) morphologically a severe interstitial edema was evident, compartment pressure increased during reperfusion (from 2.0 mmHg to 8.8 mmHg) and pO2 dropped during ischemia down to 3.0 mmHg and did not return to normal during reperfusion (10.5 mmHg versus 19.0 mmHg normal). In case of 6 hrs ischemia, partial necrosis and only little interstitial edema were found morphologically. There was no significant change in compartment pressure throughout the study; and pO2 remained significantly decreased even during reperfusion (2.0-3.0 mmHg). DISCUSSION Normal compartment pressure could mislead to false negative interpretation of compartment syndrome, whereas pO2 clearly identifies the microcirculatory state of the muscle. Thus, intramuscular pO2 monitoring presents a valuable method in evaluating compartment syndrome, especially in case of suspect clinical signs but normal compartment pressure.
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Affiliation(s)
- A Seekamp
- Unfallchirurgische Klinik, Medizinische Hochschule Hannover
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16
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Abstract
Measuring intracompartmental pressure is a well-accepted method in evaluating a compartment syndrome, which may occur after limb ischaemia followed by reperfusion. As a compartment syndrome is paralleled by a decreased microcirculation it should be possible also to evaluate a compartment syndrome by measuring intramuscular partial oxygen tension (PO2). In this study, anaesthetized rats (spontaneous breathing via tracheotomy) were subjected to infrarenal ligation of the aorta. A pressure catheter was placed subfascial in the crural muscle group of one hind limb, whereas the contralateral side was prepared with a PO2 catheter. Besides a sham operated group, three experimental groups were subjected to either 2, 4 or 6 h of ischaemia followed by 4 h of reperfusion. One further group was also subjected to 4 h of ischaemia and 4 h of reperfusion but received a fasciotomy at the time of reperfusion. Compartment pressure and intramuscular PO2 were recorded every 15 min. For histological examination muscle specimens were obtained after each experiment. Two hours of ischaemia followed by 4 h of reperfusion did not result in any morphological changes and also in no significant change in compartment pressure during both phases, whereas PO2 significantly dropped during ischaemia (from 19.0 mmHg to 3.0-5.0 mmHg) and returned to normal during reperfusion. In prolonged ischaemia (4 h) morphologically a severe interstitial oedema was evident, compartment pressure increased during reperfusion (from 2.0 mmHg to 8.8 mmHg) and PO2 dropped during ischaemia to 3.0 mmHg and did not return to normal during reperfusion (10.5 mmHg versus 19.0 mmHg normal). In the case of 6 h ischaemia, partial necrosis and no interstitial oedema was found morphologically. There was no significant change in compartment pressure throughout the study, and PO2 remained significantly decreased even during reperfusion (2.0-3.0 mmHg). Normal compartment pressure could mislead to false negative interpretation of microcirculatory disorders preceding or following compartment syndrome, whereas PO2 clearly identifies the microcirculatory state of the muscle. Thus, intramuscular PO2 monitoring presents a valuable method in evaluating compartment syndrome, especially where there are suspected clinical signs and risk of ischaemia but normal compartment pressure.
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Affiliation(s)
- A Seekamp
- Unfallchirurgische Klinik, Medizinische Hochschule Hannover, Germany
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17
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Blankenburg H, Müller-Stephann H, Pangert R. [Fitness evaluation and preliminary occupational medicine examination in employment with increased mechanical stress on the spine]. Beitr Orthop Traumatol 1988; 35:276-80. [PMID: 3214411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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18
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Oeser R, Blankenburg H, Konetzke G. [Expert assessment of occupationally-induced diseases caused by local body vibration]. Beitr Orthop Traumatol 1987; 34:579-84. [PMID: 2830878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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19
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Blankenburg H, Müller-Stephann H. [Evaluation of occupationally-induced spinal diseases]. Beitr Orthop Traumatol 1986; 33:12-7. [PMID: 3964197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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20
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Heuchert G, Blankenburg H, Bräunlich A. [Results and conclusions from an analysis of occupationally-induced degenerative damage of the locomotor system]. Beitr Orthop Traumatol 1983; 30:561-7. [PMID: 6667229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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21
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Blankenburg H, Dethloff E. [Differential diagnosis of dorsal hemispine]. Beitr Orthop Traumatol 1972; 19:415-9. [PMID: 4628220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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22
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Blankenburg H. [Naviculare tripartitum? Navicular pseudarthrosis?]. Beitr Orthop Traumatol 1971; 18:93-95. [PMID: 5575612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
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23
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Blankenburg H, Träger G. [Occurrence of false posture]. Beitr Orthop Traumatol 1970; 17:633-4. [PMID: 5512873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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24
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Blankenburg H. [Manifestations of fetal chondrodystrophia]. Dtsch Gesundheitsw 1970; 25:218-20. [PMID: 5422756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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25
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Blankenburg H. [Incidence of primary malignant tumors of the musculoskeletal system in a population from 11 countries]. Beitr Orthop Traumatol 1970; 17:31. [PMID: 5511197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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26
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Blankenburg H. [Multiple cartilaginous exostoses, their familial occurrence and parallel relationships to other systemic diseases]. Beitr Orthop Traumatol 1968; 15:98-100. [PMID: 5304882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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27
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Blankenburg H. [Cleft hand and cleft foot formations in typical and atypical forms]. Beitr Orthop Traumatol 1967; 14:209-15. [PMID: 5584775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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28
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Blankenburg H. [Polydactylia]. Beitr Orthop Traumatol 1967; 14:160-5. [PMID: 5594193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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29
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Blankenburg H. [The patella partita and its differential diagnosis]. Beitr Orthop Traumatol 1966; 13:83-9. [PMID: 5920120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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