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Abstract
Feline leukemia virus (FeLV) occurs in nature not as a single genomic species but as a family of closely related viruses. The disease outcome of natural FeLV infection is variable and likely reflects genetic variation both in the virus and the naturally outbreeding host population. A series of studies have been undertaken with the objectives of examining natural FeLV genetic variation, the selective pressures operative in FeLV infection that lead to predominance of natural variants, and the consequences for infection and disease progression. Genetic variation among FeLV isolates was examined in a cohort of naturally infected cats with thymic lymphoma of T-cell origin, non-T-cell multicentric lymphoma, myeloproliferative disorder or anemia. The predominant isolate in the cohort, designated FeLV-945, was identified exclusively in disorders of non-T-cell origin. The FeLV-945 LTR was shown to contain a unique 21-bp repeat element, triplicated in tandem downstream of enhancer. The 21-bp triplication was shown to act as a transcriptional enhancer and to confer a replicative advantage through the assembly of a distinctive transcription factor complex. Oncogene utilization during tumor induction by FeLV-945 was studied using a recombinant Moloney murine leukemia virus containing the FeLV-945 LTR. This approach identified novel loci of common proviral integration in tumors, including the regulatory subunit of PI-3Kgamma. Mutational changes identified in FeLV-945 SU were shown not to alter receptor usage as measured by host range and superinfection interference, but to significantly increase the efficiency of receptor binding. To determine whether the unique sequence elements of FeLV-945 influence the course of infection and disease in vivo, recombinant viruses were constructed in which the FeLV-945 LTR alone, or the FeLV-945 SU gene and LTR were substituted into the prototype isolate FeLV-A/61E. Longitudinal studies of infected animals showed that substitution of the FeLV-945 LTR into FeLV-A/61E resulted in a significantly more rapid disease onset, but did not alter the tumorigenic spectrum. In contrast, substitution of both the FeLV-945 LTR and SU gene changed the disease outcome entirely. Together, these observations indicate that the distinctive LTR and SU gene of FeLV-945 mediate a rapid pathogenesis with distinctive clinical features and oncogenic mechanisms.
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Affiliation(s)
- Laura S Levy
- Department of Microbiology and Immunology and Tulane Cancer Center, Tulane University School of Medicine, 1430 Tulane Avenue SL-38, New Orleans, LA 70112, USA.
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52
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Hackett CS, Geurts AM, Hackett PB. Predicting preferential DNA vector insertion sites: implications for functional genomics and gene therapy. Genome Biol 2007; 8 Suppl 1:S12. [PMID: 18047689 PMCID: PMC2106846 DOI: 10.1186/gb-2007-8-s1-s12] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Viral and transposon vectors have been employed in gene therapy as well as functional genomics studies. However, the goals of gene therapy and functional genomics are entirely different; gene therapists hope to avoid altering endogenous gene expression (especially the activation of oncogenes), whereas geneticists do want to alter expression of chromosomal genes. The odds of either outcome depend on a vector's preference to integrate into genes or control regions, and these preferences vary between vectors. Here we discuss the relative strengths of DNA vectors over viral vectors, and review methods to overcome barriers to delivery inherent to DNA vectors. We also review the tendencies of several classes of retroviral and transposon vectors to target DNA sequences, genes, and genetic elements with respect to the balance between insertion preferences and oncogenic selection. Theoretically, knowing the variables that affect integration for various vectors will allow researchers to choose the vector with the most utility for their specific purposes. The three principle benefits from elucidating factors that affect preferences in integration are as follows: in gene therapy, it allows assessment of the overall risks for activating an oncogene or inactivating a tumor suppressor gene that could lead to severe adverse effects years after treatment; in genomic studies, it allows one to discern random from selected integration events; and in gene therapy as well as functional genomics, it facilitates design of vectors that are better targeted to specific sequences, which would be a significant advance in the art of transgenesis.
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Affiliation(s)
- Christopher S Hackett
- Biomedical Sciences Graduate Program and Department of Neurology, University of California San Francisco, Room U441K, Parnassus Ave, San Francisco, California 94143-0663, USA
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Bronner C, Achour M, Arima Y, Chataigneau T, Saya H, Schini-Kerth VB. The UHRF family: Oncogenes that are drugable targets for cancer therapy in the near future? Pharmacol Ther 2007; 115:419-34. [PMID: 17658611 DOI: 10.1016/j.pharmthera.2007.06.003] [Citation(s) in RCA: 121] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2007] [Accepted: 06/07/2007] [Indexed: 12/21/2022]
Abstract
In this paper, we review the current literature about the UHRF family that in particular includes the UHRF1 and UHRF2 genes. Its members play a fundamental role in cell proliferation through different structural domains. These domains include a ubiquitin-like domain (NIRF_N), a plant homeodomain (PHD) domain, a SRA domain and a RING domain. The SRA domain has only been observed in this family probably conferring unique properties to it. The unique enzymatic activity so far identified in this family involves the RING finger that contains a ubiquitin E3 ligase activity toward, for instance, histones. The physiological roles played by the UHRF family are most likely exerted during embryogenic development and when proliferation is required in adults. Interestingly, UHRF members are putative oncogenes regulated by tumor suppressor genes, but they exert also a feedback control on these latter. Finally, we propose some new roles for this family, including regulation and/or inheritance of the epigenetic code. Alteration of these regulatory mechanisms, such as those occurring in cancer cells, may be involved in carcinogenesis. The reasons why the UHRF family could be an interesting target for developing anticancer drugs is also developed.
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Affiliation(s)
- Christian Bronner
- CNRS UMR 7175, Département de Pharmacologie et Pharmacochimie des Interactions Moléculaires et Cellulaires, Faculté de Pharmacie, 74 route du Rhin, BP 60024, 67401, Illkirch Cedex, France.
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54
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Sørensen AB, Lund AH, Kunder S, Quintanilla-Martinez L, Schmidt J, Wang B, Wabl M, Pedersen FS. Impairment of alternative splice sites defining a novel gammaretroviral exon within gag modifies the oncogenic properties of Akv murine leukemia virus. Retrovirology 2007; 4:46. [PMID: 17617899 PMCID: PMC1936429 DOI: 10.1186/1742-4690-4-46] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2007] [Accepted: 07/06/2007] [Indexed: 01/25/2023] Open
Abstract
Background Mutations of an alternative splice donor site located within the gag region has previously been shown to broaden the pathogenic potential of the T-lymphomagenic gammaretrovirus Moloney murine leukemia virus, while the equivalent mutations in the erythroleukemia inducing Friend murine leukemia virus seem to have no influence on the disease-inducing potential of this virus. In the present study we investigate the splice pattern as well as the possible effects of mutating the alternative splice sites on the oncogenic properties of the B-lymphomagenic Akv murine leukemia virus. Results By exon-trapping procedures we have identified a novel gammaretroviral exon, resulting from usage of alternative splice acceptor (SA') and splice donor (SD') sites located in the capsid region of gag of the B-cell lymphomagenic Akv murine leukemia virus. To analyze possible effects in vivo of this novel exon, three different alternative splice site mutant viruses, mutated in either the SA', in the SD', or in both sites, respectively, were constructed and injected into newborn inbred NMRI mice. Most of the infected mice (about 90%) developed hematopoietic neoplasms within 250 days, and histological examination of the tumors showed that the introduced synonymous gag mutations have a significant influence on the phenotype of the induced tumors, changing the distribution of the different types as well as generating tumors of additional specificities such as de novo diffuse large B cell lymphoma (DLBCL) and histiocytic sarcoma. Interestingly, a broader spectrum of diagnoses was made from the two single splice-site mutants than from as well the wild-type as the double splice-site mutant. Both single- and double-spliced transcripts are produced in vivo using the SA' and/or the SD' sites, but the mechanisms underlying the observed effects on oncogenesis remain to be clarified. Likewise, analyses of provirus integration sites in tumor tissues, which identified 111 novel RISs (retroviral integration sites) and 35 novel CISs (common integration sites), did not clearly point to specific target genes or pathways to be associated with specific tumor diagnoses or individual viral mutants. Conclusion We present here the first example of a doubly spliced transcript within the group of gammaretroviruses, and we show that mutation of the alternative splice sites that define this novel RNA product change the oncogenic potential of Akv murine leukemia virus.
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Affiliation(s)
- Annette Balle Sørensen
- Department of Molecular Biology, University of Aarhus, Denmark
- The State and University Library, Universitetsparken, DK-8000 Aarhus C, Denmark
| | - Anders H Lund
- Department of Molecular Biology, University of Aarhus, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Sandra Kunder
- Institute of Pathology, GSF-National Research Center for Environment and Health, Neuherberg, Germany
| | | | - Jörg Schmidt
- Department of Comparative Medicine GSF-National Research Center for Environment and Health, Neuherberg, Germany
| | | | - Matthias Wabl
- Department of Microbiology and Immunology, University of California-San Francisco, San Francisco, CA, USA
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Li Z, Kustikova OS, Kamino K, Neumann T, Rhein M, Grassman E, Fehse B, Baum C. Insertional Mutagenesis by Replication-Deficient Retroviral Vectors Encoding the Large T Oncogene. Ann N Y Acad Sci 2007; 1106:95-113. [PMID: 17395733 DOI: 10.1196/annals.1392.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Insertion sites of replication-deficient retroviral vectors may trigger clonal dominance of hematopoietic cells in vivo. Here, we tested whether this would also be the case when using vectors that express powerful oncogenes, such as the large tumor antigen (TAg) of simian virus 40. TAg inactivates the tumor-suppressor proteins p53 and Rb by virtue of a chaperone-like activity. Primary hematopoietic stem/progenitor cells transduced with retroviral vectors encoding TAg-induced histiocytic sarcoma (HS) or myeloid leukemia (ML) in transplanted mice (average survival of 21 weeks). Retrovirally introducing TAg into pretransformed 32D cells generated a monocytic leukemia, with faster kinetics ( approximately 8 weeks). Leukemic clones showed retroviral insertions in genes contributing to all known TAg cooperation pathways, acting mitogenic and/or modulating apoptosis (such as BclX, Crk, Pim2, Csfr1/Pdgfrb, Osm/Lif, Axl, Fli, Sema4b, Sox4). 32D-derived monocytic leukemias showed hits in Pim2 and Max proto-oncogenes, or the chaperone Hspa4, plus additional signaling genes. Vector-mediated insertional mutagenesis thus revealed a broad spectrum of potential TAg complementation genes. These findings have important implications for the use of retroviral transgenesis in cancer research, and the expression of signaling genes in somatic gene therapy.
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Affiliation(s)
- Zhixiong Li
- Department of Experimental Hematology, OE6960, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
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56
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Kustikova OS, Geiger H, Li Z, Brugman MH, Chambers SM, Shaw CA, Pike-Overzet K, de Ridder D, Staal FJT, von Keudell G, Cornils K, Nattamai KJ, Modlich U, Wagemaker G, Goodell MA, Fehse B, Baum C. Retroviral vector insertion sites associated with dominant hematopoietic clones mark "stemness" pathways. Blood 2006; 109:1897-907. [PMID: 17119121 PMCID: PMC1801061 DOI: 10.1182/blood-2006-08-044156] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Evidence from model organisms and clinical trials reveals that the random insertion of retrovirus-based vectors in the genome of long-term repopulating hematopoietic cells may increase self-renewal or initiate malignant transformation. Clonal dominance of nonmalignant cells is a particularly interesting phenotype as it may be caused by the dysregulation of genes that affect self-renewal and competitive fitness. We have accumulated 280 retrovirus vector insertion sites (RVISs) from murine long-term studies resulting in benign or malignant clonal dominance. RVISs (22.5%) are located in or near (up to 100 kb [kilobase]) to known proto-oncogenes, 49.6% in signaling genes, and 27.9% in other or unknown genes. The resulting insertional dominance database (IDDb) shows substantial overlaps with the transcriptome of hematopoietic stem/progenitor cells and the retrovirus-tagged cancer gene database (RTCGD). RVISs preferentially marked genes with high expression in hematopoietic stem/progenitor cells, and Gene Ontology revealed an overrepresentation of genes associated with cell-cycle control, apoptosis signaling, and transcriptional regulation, including major "stemness" pathways. The IDDb forms a powerful resource for the identification of genes that stimulate or transform hematopoietic stem/progenitor cells and is an important reference for vector biosafety studies in human gene therapy.
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Affiliation(s)
- Olga S Kustikova
- Department of Experimental Hematology, Hannover Medical School, Germany
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57
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Rodenburg M, Fischer M, Engelmann A, Harbers SO, Ziegler M, Löhler J, Stocking C. Importance of receptor usage, Fli1 activation, and mouse strain for the stem cell specificity of 10A1 murine leukemia virus leukemogenicity. J Virol 2006; 81:732-42. [PMID: 17079317 PMCID: PMC1797452 DOI: 10.1128/jvi.01430-06] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Murine leukemia viruses (MuLV) induce leukemia through a multistage process, a critical step being the activation of oncogenes through provirus integration. Transcription elements within the long terminal repeats (LTR) are prime determinants of cell lineage specificity; however, the influence of other factors, including the Env protein that modulates cell tropism through receptor recognition, has not been rigorously addressed. The ability of 10A1-MuLV to use both PiT1 and PiT2 receptors has been implicated in its induction of blast cell leukemia. Here we show that restricting receptor usage of 10A1-MuLV to PiT2 results in loss of blast cell transformation capacity. However, the pathogenicity was unaltered when the env gene is exchanged with Moloney MuLV, which uses the Cat1 receptor. Significantly, the leukemic blasts express erythroid markers and consistently contain proviral integrations in the Fli1 locus, a target of Friend MuLV (F-MuLV) during erythroleukemia induction. Furthermore, an NB-tropic variant of 10A1 was unable to induce blast cell leukemia in C57BL/6 mice, which are also resistant to F-MuLV transformation. We propose that 10A1- and F-MuLV actually induce identical (erythro)blastic leukemia by a mechanism involving Fli1 activation and cooperation with inherent genetic mutations in susceptible mouse strains. Furthermore, we demonstrate that deletion of the Icsbp tumor suppressor gene in C57BL/6 mice is sufficient to confer susceptibility to 10A1-MuLV leukemia induction but with altered specificity. In summary, we validate the significance of the env gene in leukemia specificity and underline the importance of a complex interplay of cooperating oncogenes and/or tumor suppressors in determining the pathogenicity of MuLV variants.
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MESH Headings
- Animals
- Cells, Cultured
- Fibroblasts
- Gene Products, env/genetics
- Gene Products, env/metabolism
- Hematopoietic Stem Cells/pathology
- Hematopoietic Stem Cells/virology
- Leukemia Virus, Murine/genetics
- Leukemia Virus, Murine/metabolism
- Leukemia Virus, Murine/pathogenicity
- Leukemia, Experimental/pathology
- Leukemia, Experimental/virology
- Mice
- Mice, Inbred C57BL
- Proto-Oncogene Protein c-fli-1/genetics
- Proto-Oncogene Protein c-fli-1/metabolism
- Receptors, Virus/metabolism
- Retroviridae Infections/pathology
- Retroviridae Infections/virology
- Species Specificity
- Tumor Virus Infections/pathology
- Tumor Virus Infections/virology
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58
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de Ridder J, Uren A, Kool J, Reinders M, Wessels L. Detecting statistically significant common insertion sites in retroviral insertional mutagenesis screens. PLoS Comput Biol 2006; 2:e166. [PMID: 17154714 PMCID: PMC1676030 DOI: 10.1371/journal.pcbi.0020166] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2006] [Accepted: 10/24/2006] [Indexed: 01/09/2023] Open
Abstract
Retroviral insertional mutagenesis screens, which identify genes involved in tumor development in mice, have yielded a substantial number of retroviral integration sites, and this number is expected to grow substantially due to the introduction of high-throughput screening techniques. The data of various retroviral insertional mutagenesis screens are compiled in the publicly available Retroviral Tagged Cancer Gene Database (RTCGD). Integrally analyzing these screens for the presence of common insertion sites (CISs, i.e., regions in the genome that have been hit by viral insertions in multiple independent tumors significantly more than expected by chance) requires an approach that corrects for the increased probability of finding false CISs as the amount of available data increases. Moreover, significance estimates of CISs should be established taking into account both the noise, arising from the random nature of the insertion process, as well as the bias, stemming from preferential insertion sites present in the genome and the data retrieval methodology. We introduce a framework, the kernel convolution (KC) framework, to find CISs in a noisy and biased environment using a predefined significance level while controlling the family-wise error (FWE) (the probability of detecting false CISs). Where previous methods use one, two, or three predetermined fixed scales, our method is capable of operating at any biologically relevant scale. This creates the possibility to analyze the CISs in a scale space by varying the width of the CISs, providing new insights in the behavior of CISs across multiple scales. Our method also features the possibility of including models for background bias. Using simulated data, we evaluate the KC framework using three kernel functions, the Gaussian, triangular, and rectangular kernel function. We applied the Gaussian KC to the data from the combined set of screens in the RTCGD and found that 53% of the CISs do not reach the significance threshold in this combined setting. Still, with the FWE under control, application of our method resulted in the discovery of eight novel CISs, which each have a probability less than 5% of being false detections. A potent method for the identification of novel cancer genes is retroviral insertional mutagenesis. Mice infected with slow transforming retroviruses develop tumors because the virus inserts randomly in their genome and mutates cancer genes. The regions in the genome that are mutated in multiple independent tumors are likely to contain genes involved in tumorigenesis. As the size of these datasets increases, conventional methods to detect these so-called common insertion sites (CISs) no longer suffice, and an approach is required that can control the error independent of the dataset size. The authors introduce a framework that uses a technique called kernel density estimation to find the regions in the genome that show a significant increase in insertion density. This method is implemented over a range of scales, allowing the data to be evaluated at any relevant scale. The authors demonstrate that the framework is capable of compensating for the inherent biases in the data, such as preference for retroviruses to insert near transcriptional start sites. By better balancing the error, they are able to show that from the 361 published CISs, 150 can be identified that have a low probability of being a false detection. In addition, they discover eight novel CISs.
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Affiliation(s)
- Jeroen de Ridder
- Information and Communication Theory Group, Faculty of Electrical Engineering, Mathematics, and Computer Science, Delft University of Technology, Delft, The Netherlands
- Division of Molecular Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Anthony Uren
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jaap Kool
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Marcel Reinders
- Information and Communication Theory Group, Faculty of Electrical Engineering, Mathematics, and Computer Science, Delft University of Technology, Delft, The Netherlands
- * To whom correspondence should be addressed. E-mail: (MR); (LW)
| | - Lodewyk Wessels
- Information and Communication Theory Group, Faculty of Electrical Engineering, Mathematics, and Computer Science, Delft University of Technology, Delft, The Netherlands
- Division of Molecular Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- * To whom correspondence should be addressed. E-mail: (MR); (LW)
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59
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Modlich U, Bohne J, Schmidt M, von Kalle C, Knöss S, Schambach A, Baum C. Cell-culture assays reveal the importance of retroviral vector design for insertional genotoxicity. Blood 2006; 108:2545-53. [PMID: 16825499 PMCID: PMC1895590 DOI: 10.1182/blood-2005-08-024976] [Citation(s) in RCA: 262] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Retroviral vectors with long terminal repeats (LTRs), which contain strong enhancer/promoter sequences at both ends of their genome, are widely used for stable gene transfer into hematopoietic cells. However, recent clinical data and mouse models point to insertional activation of cellular proto-oncogenes as a dose-limiting side effect of retroviral gene delivery that potentially induces leukemia. Self-inactivating (SIN) retroviral vectors do not contain the terminal repetition of the enhancer/promoter, theoretically attenuating the interaction with neighboring cellular genes. With a new assay based on in vitro expansion of primary murine hematopoietic cells and selection in limiting dilution, we showed that SIN vectors using a strong internal retroviral enhancer/promoter may also transform cells by insertional mutagenesis. Most transformed clones, including those obtained after dose escalation of SIN vectors, showed insertions upstream of the third exon of Evi1 and in reverse orientation to its transcriptional orientation. Normalizing for the vector copy number, we found the transforming capacity of SIN vectors to be significantly reduced when compared with corresponding LTR vectors. Additional modifications of SIN vectors may further increase safety. Improved cell-culture assays will likely play an important role in the evaluation of insertional mutagenesis.
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Affiliation(s)
- Ute Modlich
- Department of Experimental Hematology, Hannover Medical School, Carl-Neuberg-Strasse 1, D-30625 Hannover, Germany
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60
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Geurts AM, Hackett CS, Bell JB, Bergemann TL, Collier LS, Carlson CM, Largaespada DA, Hackett PB. Structure-based prediction of insertion-site preferences of transposons into chromosomes. Nucleic Acids Res 2006; 34:2803-11. [PMID: 16717285 PMCID: PMC1464413 DOI: 10.1093/nar/gkl301] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Mobile genetic elements with the ability to integrate genetic information into chromosomes can cause disease over short periods of time and shape genomes over eons. These elements can be used for functional genomics, gene transfer and human gene therapy. However, their integration-site preferences, which are critically important for these uses, are poorly understood. We analyzed the insertion sites of several transposons and retroviruses to detect patterns of integration that might be useful for prediction of preferred integration sites. Initially we found that a mathematical description of DNA-deformability, called Vstep, could be used to distinguish preferential integration sites for Sleeping Beauty (SB) transposons into a particular 100 bp region of a plasmid [G. Liu, A. M. Geurts, K. Yae, A. R. Srinivassan, S. C. Fahrenkrug, D. A. Largaespada,J. Takeda, K. Horie, W. K. Olson and P. B. Hackett (2005) J. Mol. Biol., 346, 161–173 ]. Based on these findings, we extended our examination of integration of SB transposons into whole plasmids and chromosomal DNA. To accommodate sequences up to 3 Mb for these analyses, we developed an automated method, ProTIS©, that can generate profiles of predicted integration events. However, a similar approach did not reveal any structural pattern of DNA that could be used to predict favored integration sites for other transposons as well as retroviruses and lentiviruses due to a limitation of available data sets. Nonetheless, ProTIS© has the utility for predicting likely SB transposon integration sites in investigator-selected regions of genomes and our general strategy may be useful for other mobile elements once a sufficiently high density of sites in a single region are obtained. ProTIS analysis can be useful for functional genomic, gene transfer and human gene therapy applications using the SB system.
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Affiliation(s)
- Aron M. Geurts
- Department of Genetics, Cell Biology and Development, The Arnold and Mabel Beckman Center for Transposon Research, University of MinnesotaMinneapolis, MN 55455, USA
| | - Christopher S. Hackett
- Biomedical Sciences Graduate Program, University of California San FranciscoSan Francisco, CA 94143-0452, USA
| | - Jason B. Bell
- Department of Genetics, Cell Biology and Development, The Arnold and Mabel Beckman Center for Transposon Research, University of MinnesotaMinneapolis, MN 55455, USA
| | - Tracy L. Bergemann
- Biostatistics Core, University of Minnesota Cancer CenterMinneapolis, MN 55455, USA
| | - Lara S. Collier
- University of Minnesota Cancer CenterMinneapolis, MN 55455, USA
| | | | - David A. Largaespada
- Department of Genetics, Cell Biology and Development, The Arnold and Mabel Beckman Center for Transposon Research, University of MinnesotaMinneapolis, MN 55455, USA
- University of Minnesota Cancer CenterMinneapolis, MN 55455, USA
| | - Perry B. Hackett
- Department of Genetics, Cell Biology and Development, The Arnold and Mabel Beckman Center for Transposon Research, University of MinnesotaMinneapolis, MN 55455, USA
- University of Minnesota Cancer CenterMinneapolis, MN 55455, USA
- To whom correspondence should be addressed at Department of Genetics, Cell Biology, and Development, University of Minnesota, 6-160 Jackson Hall, 321 Church Street SE, Minneapolis, MN 55455, USA. Tel: +1 612 624 6736; Fax: +1 612 625 6140;
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61
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Baum C, Kustikova O, Modlich U, Li Z, Fehse B. Mutagenesis and oncogenesis by chromosomal insertion of gene transfer vectors. Hum Gene Ther 2006; 17:253-63. [PMID: 16544975 DOI: 10.1089/hum.2006.17.253] [Citation(s) in RCA: 266] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Increasing evidence reveals that random insertion of gene transfer vectors into the genome of repopulating hematopoietic cells may alter their fate in vivo. Although most insertional mutations are expected to have few if any consequences for cellular survival, clonal dominance caused by retroviral vector insertions in (or in the vicinity of) proto-oncogenes or other signaling genes has been described for both normal and malignant hematopoiesis. Important insights into these side effects were initially obtained in murine models. Results from ongoing clinical studies have revealed that similar adverse events may also occur in human gene therapy. However, it remains unknown to what extent the outcome of insertional mutagenesis induced by gene vectors is related to (1) the architecture and type of vector used, (2) intrinsic properties of the target cell, and (3) extrinsic and potentially disease-specific factors influencing clonal competition in vivo. This review discusses reports addressing these questions, underlining the need for models that demonstrate and quantify the functional consequences of insertional mutagenesis. Improving vector design appears to be the most straightforward approach to increase safety, provided all relevant cofactors are considered.
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Affiliation(s)
- Christopher Baum
- Experimental Cell Therapy, Department of Hematology and Oncology, Hannover Medical School, 30625 Hannover, Germany.
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62
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Baum C, Kustikova O, Modlich U, Li Z, Fehse B. Mutagenesis and Oncogenesis by Chromosomal Insertion of Gene Transfer Vectors. Hum Gene Ther 2006. [DOI: 10.1089/hum.2006.17.ft-190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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63
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Baum C, Kustikova O, Modlich U, Li Z, Fehse B. Mutagenesis and Oncogenesis by Chromosomal Insertion of Gene Transfer Vectors. Hum Gene Ther 2006. [DOI: 10.1089/hum.2006.17.ft-181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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64
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Hilkens J. Recent translational research: oncogene discovery by insertional mutagenesis gets a new boost. Breast Cancer Res 2006; 8:102. [PMID: 16469121 PMCID: PMC1413991 DOI: 10.1186/bcr1376] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Knowledge of the genes and genetic pathways involved in onco-genesis is essential if we are to identify novel targets for cancer therapy. Insertional mutagenesis in mouse models is among the most efficient tools to detect novel cancer genes. Retrovirus-mediated insertional mutagenesis received a tremendous boost by the availability of the mouse genome sequence and new PCR methods. Application of such advances were limited to lympho-magenesis but are now also being applied to mammary tumourigenesis. Novel transposons that allow insertional muta-genesis studies to be conducted in tumors of any mouse tissue may give cancer gene discovery a further boost.
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Affiliation(s)
- John Hilkens
- Division of Tumor Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
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Du Y, Spence SE, Jenkins NA, Copeland NG. Cooperating cancer-gene identification through oncogenic-retrovirus-induced insertional mutagenesis. Blood 2005; 106:2498-505. [PMID: 15961513 PMCID: PMC1895273 DOI: 10.1182/blood-2004-12-4840] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Multiple cooperating mutations that deregulate different signaling pathways are required to induce cancer. Identifying these cooperating mutations is a prerequisite for developing better combinatorial therapies for treating cancer. Here we show that cooperating cancer mutations can be identified through oncogenic-retrovirus-induced insertional mutagenesis. Among 13 myeloid leukemias induced by transplanting into mice bone marrow cells infected in vitro with a replication-defective retrovirus carrying the Sox4 oncogene, 9 contained insertional mutations at known or suspected cancer genes. This likely occurred because rare bone marrow cells, in which the oncogenic retrovirus happened to integrate and in which it mutated a cooperating cancer gene, were selected because the host harbored a cooperating cancer mutation. Cooperativity between Sox4 and another gene, Mef2c, was subsequently confirmed in transplantation studies, in which deregulated Mef2c expression was shown to accelerate the myeloid leukemia induced by Sox4. Insertional mutagenesis of cooperating cancer genes by a defective oncogenic retrovirus provides a new method for identifying cooperating cancer genes and could aid in the development of better therapies for treating cancer.
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Affiliation(s)
- Yang Du
- Mouse Cancer Genetics Program, National Cancer Institute, Center for Cancer Research, Frederick, MD, USA
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66
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Nielsen AA, Sørensen AB, Schmidt J, Pedersen FS. Analysis of wild-type and mutant SL3-3 murine leukemia virus insertions in the c-myc promoter during lymphomagenesis reveals target site hot spots, virus-dependent patterns, and frequent error-prone gap repair. J Virol 2005; 79:67-78. [PMID: 15596802 PMCID: PMC538719 DOI: 10.1128/jvi.79.1.67-78.2005] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The murine leukemia retrovirus SL3-3 induces lymphomas in the T-cell compartment of the hematopoetic system when it is injected into newborn mice of susceptible strains. Previously, our laboratory reported on a deletion mutant of SL3-3 that induces T-cell tumors faster than the wild-type virus (S. Ethelberg, A. B. Sorensen, J. Schmidt, A. Luz, and F. S. Pedersen, J. Virol. 71:9796-9799, 1997). PCR analyses of proviral integrations in the promoter region of the c-myc proto-oncogene in lymphomas induced by wild-type SL3-3 [SL3-3(wt)] and the enhancer deletion mutant displayed a difference in targeting frequency into this locus. We here report on patterns of proviral insertions into the c-myc promoter region from SL3-3(wt), the faster variant, as well as other enhancer variants from a total of approximately 250 tumors. The analysis reveals (i) several integration site hot spots in the c-myc promoter region, (ii) differences in integration patterns between SL3-3(wt) and enhancer deletion mutant viruses, (iii) a correlation between tumor latency and the number of proviral insertions into the c-myc promoter, and (iv) a [5'-(A/C/G)TA(C/G/T)-3'] integration site consensus sequence. Unexpectedly, about 12% of the sequenced insertions were associated with point mutations in the direct repeat flanking the provirus. Based on these results, we propose a model for error-prone gap repair of host-provirus junctions.
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MESH Headings
- Animals
- Animals, Newborn
- Base Sequence
- Consensus Sequence
- DNA Repair
- Enhancer Elements, Genetic
- Female
- Gene Deletion
- Genes, myc
- Leukemia Virus, Murine/genetics
- Leukemia Virus, Murine/pathogenicity
- Leukemia, Experimental/pathology
- Leukemia, Experimental/virology
- Lymphoma, T-Cell/pathology
- Lymphoma, T-Cell/virology
- Male
- Mice
- Molecular Sequence Data
- Mutation
- Promoter Regions, Genetic
- Proto-Oncogene Proteins c-myc/genetics
- Proviruses/genetics
- Retroviridae Infections/pathology
- Retroviridae Infections/virology
- Tumor Virus Infections/pathology
- Tumor Virus Infections/virology
- Virus Integration/genetics
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67
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Beverly LJ, Capobianco AJ. Targeting promiscuous signaling pathways in cancer: another Notch in the bedpost. Trends Mol Med 2004; 10:591-8. [PMID: 15567329 DOI: 10.1016/j.molmed.2004.10.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The chromosomal translocation t(7;9)(q34;q34.3) in human T-cell acute lymphoblastic leukemia results in the constitutive activation of Notch (Nic). Reported mutations in Ikaros cause the loss of DNA-binding, which in turn leads to a loss of repressive activity. Recently, these two mutations have been shown to cooperate in leukemogenesis. The current model proposes that the combination of the loss of Ikaros activity and the gain of constitutive Notch activity disrupts the normal balance between repression and activation at common regulatory elements. Furthermore, the model is extended to suggest that multiple transcription factors coordinate transcriptional repression and activation through these common regulatory elements. In leukemogenesis, the breakdown of this coordinate regulation underlies one of the pathophysiological mechanisms. Finally, using Notch as a template, potential points of interdiction by designer therapeutics are discussed.
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Affiliation(s)
- Levi J Beverly
- The Wistar Institute, Molecular and Cellular Oncogenesis Program, 3601 Spruce Street, Philadelphia, PA 19104, USA
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68
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von Kalle C, Fehse B, Layh-Schmitt G, Schmidt M, Kelly P, Baum C. Stem cell clonality and genotoxicity in hematopoietic cells: Gene activation side effects should be avoidable. Semin Hematol 2004; 41:303-18. [PMID: 15508116 DOI: 10.1053/j.seminhematol.2004.07.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Two serious adverse events involving activation of the LMO2 oncogene through retrovirus vector insertion in the otherwise extremely successful first gene therapy trial for X-linked severe combined immunodeficieny type 1 (SCID-X1) had initially caused widespread concern in the patient and research communities. Careful consideration 1 year after diagnosis of the second case still finds 12 of the treated patients clearly benefiting from gene therapy (freedom from treatment failure, 80%; survival 100%), a situation that should not portend the end of gene therapy for this disease, and is, in fact encouraging. While current approaches are justified to treat patients with otherwise life-threatening disorders, a broad consensus has developed that systematic basic research is required to further understand the pathophysiology of these serious adverse events and to provide new insights, enabling safer and more effective gene therapy strategies. With the continued success of SCID-X1 gene therapy in the majority of patients treated, it is of even greater importance to understand exactly which vector element or combination of elements predispose to toxicity. An in-depth study of the mechanisms behind the activation of the LMO2 and gammac genes will be highly instructive for the development of safer procedures and vectors. We summarize the central observations, ongoing experimental approaches, new concepts, and developments relevant to understanding, interpreting, and eventually overcoming the real and perceived obstacles posed by insertional mutagenesis due to gene transfer vectors.
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Affiliation(s)
- C von Kalle
- Division of Experimental Hematology, Cincinnati Children's Hospital Research Foundation, Cincinnati, OH 45229, USA.
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69
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Erkeland SJ, Valkhof M, Heijmans-Antonissen C, van Hoven-Beijen A, Delwel R, Hermans MHA, Touw IP. Large-scale identification of disease genes involved in acute myeloid leukemia. J Virol 2004; 78:1971-80. [PMID: 14747562 PMCID: PMC369447 DOI: 10.1128/jvi.78.4.1971-1980.2004] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2003] [Accepted: 10/27/2003] [Indexed: 11/20/2022] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous group of diseases in which chromosomal aberrations, small insertions or deletions, or point mutations in certain genes have profound consequences for prognosis. However, the majority of AML patients present without currently known genetic defects. Retroviral insertion mutagenesis in mice has become a powerful tool for identifying new disease genes involved in the pathogenesis of leukemia and lymphoma. Here we have used the Graffi-1.4 strain of murine leukemia virus, which causes predominantly AML, in a screen to identify novel genes involved in the pathogenesis of this disease. We report 79 candidate disease genes in common integration sites (CISs) and 15 genes whose family members previously were found to be affected in other studies. The majority of the identified sequences (60%) were not found in lymphomas and monocytic leukemias in previous screens, suggesting a specific involvement in AML. Although most of the virus integrations occurred in or near the 5' or 3' ends of the genes, suggesting deregulation of gene expression as a consequence of virus integration, 18 CISs were located exclusively within the genes, conceivably causing gene disruption.
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Affiliation(s)
- Stefan J Erkeland
- Department of Hematology, Erasmus Medical Center, Rotterdam, The Netherlands
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70
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Akagi K, Suzuki T, Stephens RM, Jenkins NA, Copeland NG. RTCGD: retroviral tagged cancer gene database. Nucleic Acids Res 2004; 32:D523-7. [PMID: 14681473 PMCID: PMC308748 DOI: 10.1093/nar/gkh013] [Citation(s) in RCA: 275] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Retroviral insertional mutagenesis in mouse hematopoietic tumors provides a potent cancer gene discovery tool in the post-genome-sequence era. To manage multiple high-throughput insertional mutagenesis screening projects, we developed the Retroviral Tagged Cancer Gene Database (RTCGD; http://RTCGD.ncifcrf.gov). A sequence analysis pipeline determines the genomic position of each retroviral integration site cloned from a mouse tumor, the distance between it and the nearest candidate disease gene(s) and its orientation with respect to the candidate gene(s). The pipeline also identifies genomic regions that are targets of retroviral integration in more than one tumor (common integration sites, CISs) and are thus likely to encode a disease gene. Users can search the database using a specified gene symbol, chromosome number or tumor model to identify both CIS genes and unique viral integration sites or compare the integration sites cloned by different laboratories using different models. As a default setting, users first review the CIS Lists and then Clone Lists. CIS Lists describe CISs and their candidate disease genes along with links to other public databases and clone lists. Clone Lists describe the viral integration site clones along with the tumor model and tumor type from which they were cloned, candidate disease gene(s), genomic position and orientation of the integrated provirus with respect to the candidate gene(s). It also provides a pictorial view of the genomic location of each integration site relative to neighboring genes and markers. Researchers can identify integrations of interest and compare their results with those for multiple tumor models and tumor types using RTCGD.
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Affiliation(s)
- Keiko Akagi
- Mouse Cancer Genetics Program, National Cancer Institute, Frederick, MD 21701, USA
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