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Giordano FA, Hotz-Wagenblatt A, Lauterborn D, Appelt JU, Fellenberg K, Nagy KZ, Zeller WJ, Suhai S, Fruehauf S, Laufs S. New Bioinformatic Strategies to Rapidly Characterize Retroviral Integration Sites of Gene Therapy Vectors. Methods Inf Med 2018. [DOI: 10.1160/me0423] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Summary
Objective:
Increasing use of retroviral vector-mediated gene transfer created intense interest to characterize vector integrations on the genomic level. Techniques to determine insertion sites, mainly based on time-consuming manual data processing, are commonly applied. Since a high variability in processing methods hampers further data comparison, there is an urgent need to systematically process the data arising from such analysis.
Methods:
To allow large-scale and standardized comparison of insertion sites of viral vectors we developed two programs, IntegrationSeqand IntegrationMap. IntegrationSeq can trim sequences, and valid integration sequences get further processed with IntegrationMap for automatic genomic mapping. IntegrationMap retrieves detailed information about whether integrations are located in or close to genes, the name of the gene, the exact localization in the transcriptional units, and further parameters like the distance from the transcription start site to the integration.
Results:
We validated the method using 259 files originating from integration site analysis (LM-PCR). Sequences processed by IntegrationSeq led to an increased yield of valid integration sequence detection, which were shown to be more sensitive than conventional analysis and 15 times faster, while the specificities are equal. Output files generated by IntegrationMap were found to be 99.8% identical with results retrieved by much slower conventional mapping with the ENSEMBL alignment tool.
Conclusion:
Using IntegrationSeq and IntegrationMap, a validated, fast and standardized high-throughput analysis of insertion sites can be achieved for the first time.
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Blume CJ, Hotz-Wagenblatt A, Hüllein J, Sellner L, Jethwa A, Stolz T, Slabicki M, Lee K, Sharathchandra A, Benner A, Dietrich S, Oakes CC, Dreger P, te Raa D, Kater AP, Jauch A, Merkel O, Oren M, Hielscher T, Zenz T. p53-dependent non-coding RNA networks in chronic lymphocytic leukemia. Leukemia 2015; 29:2015-23. [DOI: 10.1038/leu.2015.119] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Revised: 04/02/2015] [Accepted: 04/30/2015] [Indexed: 12/23/2022]
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Amaravadi M, Bauer A, Hotz-Wagenblatt A, Botla S, Löchelt M, Pawlita M, Büchler M, Giese N, Hoheisel J. 382: Identification of pathogenic virus sequences in pancreatic cancer. Eur J Cancer 2014. [DOI: 10.1016/s0959-8049(14)50340-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Blume C, Hielscher T, Hotz-Wagenblatt A, Sellner L, Hüllein J, Stolz T, Oakes C, Merkel O, Zenz T. 535: Small RNA sequencing identifies microRNAs involved in B-cell receptor signaling in chronic lymphocytic leukemia. Eur J Cancer 2014. [DOI: 10.1016/s0959-8049(14)50477-7] [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: 11/15/2022]
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del Val C, Ernst P, Falkenhahn M, Fladerer C, Glatting KH, Suhai S, Hotz-Wagenblatt A. ProtSweep, 2Dsweep and DomainSweep: protein analysis suite at DKFZ. Nucleic Acids Res 2007; 35:W444-50. [PMID: 17526514 PMCID: PMC1933246 DOI: 10.1093/nar/gkm364] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [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] [Indexed: 11/13/2022] Open
Abstract
The wealth of transcript information that has been made publicly available in recent years has led to large pools of individual web sites offering access to bioinformatics software. However, finding out which services exist, what they can or cannot do, how to use them and how to feed results from one service to the next one in the right format can be very time and resource consuming, especially for non-experts. Automating this task, we present a suite of protein annotation pipelines (tasks) developed at the German Cancer Research Centre (DKFZ) oriented to protein annotation by homology (ProtSweep), by domain analysis (DomainSweep), and by secondary structure elements (2Dsweep). The aim of these tasks is to perform an exhaustive structural and functional analysis employing a wide variety of methods in combination with the most updated public databases. The three servers are available for academic users at the HUSAR open server http://genius.embnet.dkfz-heidelberg.de/menu/biounit/open-husar/
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Affiliation(s)
- C del Val
- DKFZ, German Cancer Research Center, Division of Molecular Biophysics, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany.
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Kenzelmann M, Maertens S, Hergenhahn M, Kueffer S, Hotz-Wagenblatt A, Li L, Wang S, Ittrich C, Lemberger T, Arribas R, Jonnakuty S, Hollstein MC, Schmid W, Gretz N, Gröne HJ, Schütz G. Microarray analysis of newly synthesized RNA in cells and animals. Proc Natl Acad Sci U S A 2007; 104:6164-9. [PMID: 17405863 PMCID: PMC1851046 DOI: 10.1073/pnas.0610439104] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Current methods to analyze gene expression measure steady-state levels of mRNA. To specifically analyze mRNA transcription, we have developed a technique that can be applied in vivo in intact cells and animals. Our method makes use of the cellular pyrimidine salvage pathway and is based on affinity-chromatographic isolation of thiolated mRNA. When combined with data on mRNA steady-state levels, this method is able to assess the relative contributions of mRNA synthesis and degradation/stabilization. It overcomes limitations associated with currently available methods such as mechanistic intervention that disrupts cellular physiology, or the inability to apply the techniques in vivo. Our method was first tested in serum response of cultured fibroblast cells and then applied to the study of renal ischemia reperfusion injury, demonstrating its applicability for whole organs in vivo. Combined with data on mRNA steady-state levels, this method provided a detailed analysis of regulatory mechanisms of mRNA expression and the relative contributions of RNA synthesis and turnover within distinct pathways, and identification of genes expressed at low abundance at the transcriptional level.
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Affiliation(s)
- M Kenzelmann
- Department of Molecular Biology of the Cell I, German Cancer Research Center, 69120 Heidelberg, Germany.
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Giordano FA, Hotz-Wagenblatt A, Lauterborn D, Appelt JU, Fellenberg K, Nagy KZ, Zeller WJ, Suhai S, Fruehauf S, Laufs S. New bioinformatic strategies to rapidly characterize retroviral integration sites of gene therapy vectors. Methods Inf Med 2007; 46:542-547. [PMID: 17938776] [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: 05/25/2023]
Abstract
OBJECTIVE Increasing use of retroviral vector-mediated gene transfer created intense interest to characterize vector integrations on the genomic level. Techniques to determine insertion sites, mainly based on time-consuming manual data processing, are commonly applied. Since a high variability in processing methods hampers further data comparison, there is an urgent need to systematically process the data arising from such analysis. METHODS To allow large-scale and standardized comparison of insertion sites of viral vectors we developed two programs, IntegrationSeq and IntegrationMap. IntegrationSeq can trim sequences, and valid integration sequences get further processed with IntegrationMap for automatic genomic mapping. IntegrationMap retrieves detailed information about whether integrations are located in or close to genes, the name of the gene, the exact localization in the transcriptional units, and further parameters like the distance from the transcription start site to the integration. RESULTS We validated the method using 259 files originating from integration site analysis (LM-PCR). Sequences processed by IntegrationSeq led to an increased yield of valid integration sequence detection, which were shown to be more sensitive than conventional analysis and 15 times faster, while the specificities are equal. Output files generated by IntegrationMap were found to be 99.8% identical with results retrieved by much slower conventional mapping with the ENSEMBL alignment tool. CONCLUSION Using IntegrationSeq and IntegrationMap, a validated, fast and standardized high-throughput analysis of insertion sites can be achieved for the first time.
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Affiliation(s)
- F A Giordano
- Research Program Innovative Cancer Diagnostics and Therapy, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
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Giordano FA, Fehse B, Hotz-Wagenblatt A, Jonnakuty S, del Val C, Appelt JU, Nagy KZ, Kuehlcke K, Naundorf S, Zander AR, Zeller WJ, Ho AD, Fruehauf S, Laufs S. Retroviral vector insertions in T-lymphocytes used for suicide gene therapy occur in gene groups with specific molecular functions. Bone Marrow Transplant 2006; 38:229-35. [PMID: 16785865 DOI: 10.1038/sj.bmt.1705424] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Graft-versus-host disease (GvHD) is a severe complication in the context of allogeneic stem cell transplantation and adoptive immunotherapy. The transfer of a suicide gene into donor T-lymphocytes (TLCs) allows selective elimination of GvHD-causing cells. As retroviral gene transfer into hematopoietic stem cells can induce leukaemia, there is an urgent need also to analyze retroviral integration sites in TLCs. We examined suicide gene-transduced TLCs in four grafts and from four transplanted patients. One-hundred and fifteen integration sites were detected in vitro. Of these 90 could be mapped to the human genome; 50% (45) were located in genes and 32% (29) were detected 10 kb upstream or downstream of transcription start sites. We found a significant overrepresentation of genes encoding for proteins with receptor activity, signal transducer activity, transcription regulator activity, nucleic acid binding activity and translation regulator activity. Similar data were obtained from patient samples. Our results point to preferred vector integration patterns, which are specific for the target cell population and probably independent of selection processes. Thus, future preclinical analysis of the integration repertoire with abundant amounts of transduced cells could allow a prediction also for the in vivo situation, where target cells are scarce.
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Affiliation(s)
- F A Giordano
- Research Program Innovative Cancer Diagnostics and Therapy, German Cancer Research Center (DKFZ), Heidelberg, Germany
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Schmid E, Hotz-Wagenblatt A, Hacj V, Dröge W. Phosphorylation of the insulin receptor kinase by phosphocreatine in combination with hydrogen peroxide: the structural basis of redox priming. FASEB J 1999; 13:1491-500. [PMID: 10463939 DOI: 10.1096/fasebj.13.12.1491] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Signaling by insulin requires autophosphorylation of the insulin receptor kinase (IRK) at Tyr1158, Tyr1162, and Tyr1163. Earlier experiments with (32)P-gamma-ATP indicated that the nonphosphorylated IRK (IRK-0P) is relatively inactive, and crystallographic data indicated that the ATP binding site of IRK-0P is blocked by its activation loop. We now show that phosphocreatine (PCr) in combination with hydrogen peroxide serves as an alternative phosphate donor and that ATP and PCr use distinct binding sites. Whereas phosphorylation of the IRK by ATP is inhibited by the nonhydrolyzable competitor adenylyl-imidodiphosphate, phosphorylation by PCr is enhanced. The IRK mutant Tyr1158Phe showed no phosphorylation with PCr but almost normal phosphorylation with ATP, whereas Tyr1162Phe was phosphorylated well with PCr but less then normal with ATP. 3-Dimensional models of IRK-0P revealed that the conversion of any of the four cysteine residues 1056, 1138, 1234, and 1245 into sulfenic acid produces structural changes that bring Tyr1158 into close contact with Asp1083 and render the well-known catalytic site at Asp1132 and Tyr1162 accessible from a direction that differs from the known ATP binding site. The mutant Cys1138Ala, in contrast, showed relatively inaccessible catalytic sites and weak catalytic activity in functional experiments. Taken together, these findings indicate that 'redox priming' of the IRK facilitates its autophosphorylation by PCr in the activation loop.
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Affiliation(s)
- E Schmid
- Division of Immunochemistry and Division of Molecular Biophysics, Deutsches Krebsforschungszentrum, D-69120 Heidelberg, Germany
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Abstract
Previous studies on cultured skeletal muscle cells have indicated that the insulin-induced expression of GLUT4 transporter protein is inhibited by nitric oxide (NO). Therefore, we determined the effect of NO on the insulin-induced autophosphorylation of the insulin receptor kinase (IRK), i.e., the first step in the insulin-mediated signal transduction pathway. The experiments showed that the insulin-induced autophosphorylation of the insulin receptor beta-chain is strongly inhibited by the NO donors 1,1-diethyl-2-hydroxy-2-nitrosohydrazine (DEA-NO) or S-nitroso-N-acetylpenicillamine (SNAP). The inhibitory effect was ameliorated in cells depleted of glutathione (GSH), suggesting the possibility that S-nitroso-glutathione may operate as an intermediate NO donor. Complementary experiments with different Cys --> Ala mutant proteins showed, surprisingly, that all mutant proteins were inhibited by DEA-NO. Three-dimensional models of the nonphosphorylated IR beta-chain nitrosylated at the accessible cysteine residues 1056, 1138, 1234, or 1245 revealed that derivatization of any of these four cysteine residues leads essentially to the same structural changes of the IRK domain. These changes involve a movement of the amino-terminal lobe against the carboxy-terminal lobe in a direction opposite to the direction of the "lobe closure" that was previously proposed to facilitate the accessibility for ATP and the expression of catalytic activity. Our findings suggest that the occurrence of several functionally relevant cysteine residues in distinct regions of the IRK protein increases the probability of regulatory redox interactions and thus the redox sensitivity of the IRK.
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Affiliation(s)
- E Schmid
- Division of Immunochemistry, Deutsches Krebsforschungszentrum, Heidelberg, Germany
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Abstract
MOTIVATION The user-friendly, graphical X-windows interface (WPI) to the GCG sequence analysis package can often not be used due to the lack of an X-server on PC or Macintosh computers. Because Web browsers like Netscape are much more common on those platforms, we decided to develop W2H, a WWW interface to the GCG Sequence Analysis Software Package with nearly the same functionality as the X-windows interface WPI. RESULTS The new WWW interface (W2H) to the GCG Sequence Analysis Software Package (Wisconsin Package) supports modern Web technologies, like client-pull method, or embedded scripting language, and provides a reasonable platform independence. The interface is quite comprehensive with advanced features like sequence selector, search set builder, enzyme chooser, access to sequence databases, uploading client files to the GCG server or displaying and manipulating graphical outputs in addition to GCG analysis programs. W2H also manages secure access to both GCG server and user data. For special environments, like workshops, conferences and company intranets, there is a special mode (Intranet mode) with less security constraints. The behaviour of W2H is mostly controlled by meta-data files describing the applications and giving a base for dynamic creation of HTML documents. This paper presents mainly the development approaches used, and architectural design aspects of W2H. AVAILABILITY W2H is available by ftp://ftp.ebi.ac. uk/pub/software/unix/w2h or ftp://genome.dkfz-heidelberg.de/pub/w2h CONTACT m.senger@ebi.ac.uk
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Affiliation(s)
- M Senger
- DKFZ - German Cancer Research Center, Department of Molecular Biophysics, Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany.
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Mehta PP, Hotz-Wagenblatt A, Rose B, Shalloway D, Loewenstein WR. Incorporation of the gene for a cell-cell channel protein into transformed cells leads to normalization of growth. J Membr Biol 1991; 124:207-25. [PMID: 1664859 DOI: 10.1007/bf01994355] [Citation(s) in RCA: 146] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Incorporation of the gene for connexin43, a cell-cell channel protein of gap junction, into the genome of communication-deficient transformed mouse 10T1/2 cells restored junctional communication and inhibited growth. Growth was slowed, saturation density reduced and focus formation suppressed, and these effects were contingent on overexpression of the exogenous gene and the consequent enhancement of communication. In coculture with normal cells the growth of the connexin overexpressors was completely arrested, as these cells established strong communication with the normal ones. Thus, in culture by themselves or in coculture, the connexin overexpressor cells grew like normal cells. These results demonstrate that the cell-cell channel is instrumental in growth control; they are the expected behavior if the channel transmits cytoplasmic growth-regulatory signals.
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Affiliation(s)
- P P Mehta
- Department of Physiology and Biophysics, University of Miami School of Medicine, Florida 33136
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