1
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Sorel N, Díaz-Pascual F, Bessot B, Sadek H, Mollet C, Chouteau M, Zahn M, Gil-Farina I, Tajer P, van Eggermond M, Berghuis D, Lankester AC, André I, Gabriel R, Cavazzana M, Pike-Overzet K, Staal FJT, Lagresle-Peyrou C. Restoration of T and B Cell Differentiation after RAG1 Gene Transfer in Human RAG1 Defective Hematopoietic Stem Cells. Biomedicines 2024; 12:1495. [PMID: 39062069 PMCID: PMC11275127 DOI: 10.3390/biomedicines12071495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 06/22/2024] [Accepted: 06/25/2024] [Indexed: 07/28/2024] Open
Abstract
Recombinase-activating gene (RAG)-deficient SCID patients lack B and T lymphocytes due to the inability to rearrange immunoglobulin and T cell receptor genes. The two RAG genes act as a required dimer to initiate gene recombination. Gene therapy is a valid treatment alternative for RAG-SCID patients who lack a suitable bone marrow donor, but developing such therapy for RAG1/2 has proven challenging. Using a clinically approved lentiviral vector with a codon-optimized RAG1 gene, we report here preclinical studies using CD34+ cells from four RAG1-SCID patients. We used in vitro T cell developmental assays and in vivo assays in xenografted NSG mice. The RAG1-SCID patient CD34+ cells transduced with the RAG1 vector and transplanted into NSG mice led to restored human B and T cell development. Together with favorable safety data on integration sites, these results substantiate an ongoing phase I/II clinical trial for RAG1-SCID.
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Affiliation(s)
- Nataël Sorel
- Human Lymphohematopoiesis Laboratory, Université Paris Cité, Imagine Institute, INSERM UMR 1163, 75015 Paris, France (I.A.)
| | | | - Boris Bessot
- Biotherapy Clinical Investigation Center, Groupe Hospitalier Universitaire Ouest, AP-HP, INSERM, 75015 Paris, France
| | - Hanem Sadek
- Human Lymphohematopoiesis Laboratory, Université Paris Cité, Imagine Institute, INSERM UMR 1163, 75015 Paris, France (I.A.)
| | - Chloé Mollet
- Biotherapy Clinical Investigation Center, Groupe Hospitalier Universitaire Ouest, AP-HP, INSERM, 75015 Paris, France
| | - Myriam Chouteau
- Human Lymphohematopoiesis Laboratory, Université Paris Cité, Imagine Institute, INSERM UMR 1163, 75015 Paris, France (I.A.)
| | - Marco Zahn
- ProtaGene CGT GmbH, Im Neuenheimer Feld 582, 69120 Heidelberg, Germany
| | - Irene Gil-Farina
- ProtaGene CGT GmbH, Im Neuenheimer Feld 582, 69120 Heidelberg, Germany
| | - Parisa Tajer
- Department of Immunohematology and Blood Transfusion, L3-Q Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Marja van Eggermond
- Department of Immunohematology and Blood Transfusion, L3-Q Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Dagmar Berghuis
- Department of Pediatrics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (D.B.); (A.C.L.)
| | - Arjan C. Lankester
- Department of Pediatrics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (D.B.); (A.C.L.)
| | - Isabelle André
- Human Lymphohematopoiesis Laboratory, Université Paris Cité, Imagine Institute, INSERM UMR 1163, 75015 Paris, France (I.A.)
| | - Richard Gabriel
- ProtaGene CGT GmbH, Im Neuenheimer Feld 582, 69120 Heidelberg, Germany
| | - Marina Cavazzana
- Biotherapy Clinical Investigation Center, Groupe Hospitalier Universitaire Ouest, AP-HP, INSERM, 75015 Paris, France
- Biotherapy Department, Necker-Enfants Malades Hospital, AP-HP, 75015 Paris, France;
- Imagine Institute UMR1163, Université Paris Cité, Sorbonne Paris Cité, 75015 Paris, France
| | - Kasrin Pike-Overzet
- Biotherapy Department, Necker-Enfants Malades Hospital, AP-HP, 75015 Paris, France;
| | - Frank J. T. Staal
- Department of Immunohematology and Blood Transfusion, L3-Q Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
- Department of Pediatrics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (D.B.); (A.C.L.)
| | - Chantal Lagresle-Peyrou
- Human Lymphohematopoiesis Laboratory, Université Paris Cité, Imagine Institute, INSERM UMR 1163, 75015 Paris, France (I.A.)
- Biotherapy Clinical Investigation Center, Groupe Hospitalier Universitaire Ouest, AP-HP, INSERM, 75015 Paris, France
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2
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Borges B, Varthaliti A, Schwab M, Clarke MT, Pivetti C, Gupta N, Cadwell CR, Guibinga G, Phillips S, Del Rio T, Ozsolak F, Imai-Leonard D, Kong L, Laird DJ, Herzeg A, Sumner CJ, MacKenzie TC. Prenatal AAV9-GFP administration in fetal lambs results in transduction of female germ cells and maternal exposure to virus. Mol Ther Methods Clin Dev 2024; 32:101263. [PMID: 38827250 PMCID: PMC11141462 DOI: 10.1016/j.omtm.2024.101263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 05/01/2024] [Indexed: 06/04/2024]
Abstract
Prenatal somatic cell gene therapy (PSCGT) could potentially treat severe, early-onset genetic disorders such as spinal muscular atrophy (SMA) or muscular dystrophy. Given the approval of adeno-associated virus serotype 9 (AAV9) vectors in infants with SMA by the U.S. Food and Drug Administration, we tested the safety and biodistribution of AAV9-GFP (clinical-grade and dose) in fetal lambs to understand safety and efficacy after umbilical vein or intracranial injection on embryonic day 75 (E75) . Umbilical vein injection led to widespread biodistribution of vector genomes in all examined lamb tissues and in maternal uteruses at harvest (E96 or E140; term = E150). There was robust GFP expression in brain, spinal cord, dorsal root ganglia (DRGs), without DRG toxicity and excellent transduction of diaphragm and quadriceps muscles. However, we found evidence of systemic toxicity (fetal growth restriction) and maternal exposure to the viral vector (transient elevation of total bilirubin and a trend toward elevation in anti-AAV9 antibodies). There were no antibodies against GFP in ewes or lambs. Analysis of fetal gonads demonstrated GFP expression in female (but not male) germ cells, with low levels of integration-specific reads, without integration in select proto-oncogenes. These results suggest potential therapeutic benefit of AAV9 PSCGT for neuromuscular disorders, but warrant caution for exposure of female germ cells.
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Affiliation(s)
- Beltran Borges
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
- UCSF Center for Maternal-Fetal Precision Medicine, San Francisco, CA 94158, USA
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Antonia Varthaliti
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Marisa Schwab
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Maria T Clarke
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
- UCSF Center for Maternal-Fetal Precision Medicine, San Francisco, CA 94158, USA
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Christopher Pivetti
- Department of Surgery, University of California, Davis, Davis, CA 95817, USA
| | - Nalin Gupta
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
- Department of Pediatrics and Benioff Children's Hospital, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Cathryn R Cadwell
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
- Weill Neurohub, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ghiabe Guibinga
- Novartis Institutes for BioMedical Research Biologics Center, San Diego, CA 92121, USA
| | - Shirley Phillips
- Novartis Institutes for BioMedical Research Biologics Center, San Diego, CA 92121, USA
| | - Tony Del Rio
- Novartis Institutes for BioMedical Research Biologics Center, San Diego, CA 92121, USA
| | - Fatih Ozsolak
- Novartis Institutes for BioMedical Research Biologics Center, San Diego, CA 92121, USA
| | - Denise Imai-Leonard
- Comparative Pathology Laboratory, University of California, Davis, Davis, CA 95616, USA
| | - Lingling Kong
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21218, USA
| | - Diana J Laird
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
- Department of Obstetrics and Gynecology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Akos Herzeg
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
- UCSF Center for Maternal-Fetal Precision Medicine, San Francisco, CA 94158, USA
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Charlotte J Sumner
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21218, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21218, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21218, USA
| | - Tippi C MacKenzie
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
- UCSF Center for Maternal-Fetal Precision Medicine, San Francisco, CA 94158, USA
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
- Department of Pediatrics and Benioff Children's Hospital, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Obstetrics and Gynecology, University of California, San Francisco, San Francisco, CA 94158, USA
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3
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Fronza R, Vasciaveo A, Benso A, Schmidt M. A Graph Based Framework to Model Virus Integration Sites. Comput Struct Biotechnol J 2016; 14:69-77. [PMID: 27257470 PMCID: PMC4874582 DOI: 10.1016/j.csbj.2015.10.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 10/20/2015] [Accepted: 10/23/2015] [Indexed: 12/03/2022] Open
Abstract
With next generation sequencing thousands of virus and viral vector integration genome targets are now under investigation to uncover specific integration preferences and to define clusters of integration, termed common integration sites (CIS), that may allow to assess gene therapy safety or to detect disease related genomic features such as oncogenes. Here, we addressed the challenge to: 1) define the notion of CIS on graph models, 2) demonstrate that the structure of CIS enters in the category of scale-free networks and 3) show that our network approach analyzes CIS dynamically in an integrated systems biology framework using the Retroviral Transposon Tagged Cancer Gene Database (RTCGD) as a testing dataset.
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Affiliation(s)
- Raffaele Fronza
- Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Center, Im Neuenheimer Feld 581, 69120 Heidelberg, Germany
| | - Alessandro Vasciaveo
- Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Center, Im Neuenheimer Feld 581, 69120 Heidelberg, Germany; Department of Control and Computer Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
| | - Alfredo Benso
- Department of Control and Computer Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
| | - Manfred Schmidt
- Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Center, Im Neuenheimer Feld 581, 69120 Heidelberg, Germany
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4
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Isolation of genomic insertion sites of proviruses using Splinkerette-PCR-based procedures. Methods Mol Biol 2011; 687:25-42. [PMID: 20967599 DOI: 10.1007/978-1-60761-944-4_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The availability of whole genomic sequences provides a great framework for biologists to address a broad range of scientific questions. However, functions of most mammalian genes remain obscure. The forward genetics strategy of insertional mutagenesis uses DNA mutagens such as retroviruses and transposable elements; this strategy represents a powerful approach to functional genomics. A variety of methods to uncover insertion sites have been described. This chapter details SplinkTA-PCR and SplinkBlunt-PCR, modified from splinkerette-PCR, for mapping chromosomally the insertion sites of a murine leukemia virus that causes leukemia in the BXH-2 strain of mice. These protocols are easy to use, reliable, and efficient.
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5
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Aster JC, Blacklow SC, Pear WS. Notch signalling in T-cell lymphoblastic leukaemia/lymphoma and other haematological malignancies. J Pathol 2010; 223:262-73. [PMID: 20967796 DOI: 10.1002/path.2789] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2010] [Revised: 09/10/2010] [Accepted: 09/16/2010] [Indexed: 12/21/2022]
Abstract
Notch receptors participate in a highly conserved signalling pathway that regulates normal development and tissue homeostasis in a context- and dose-dependent manner. Deregulated Notch signalling has been implicated in many diseases, but the clearest example of a pathogenic role is found in T-cell lymphoblastic leukaemia/lymphoma (T-LL), in which the majority of human and murine tumours have acquired mutations that lead to aberrant increases in Notch1 signalling. Remarkably, it appears that the selective pressure for Notch mutations is virtually unique among cancers to T-LL, presumably reflecting a special context-dependent role for Notch in normal T-cell progenitors. Nevertheless, there are some recent reports suggesting that Notch signalling has subtle, yet important roles in other forms of haematological malignancy as well. Here, we review the role of Notch signalling in various blood cancers, focusing on T-LL with an eye towards targeted therapeutics.
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Affiliation(s)
- Jon C Aster
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA.
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6
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Abstract
During the past several years, retroviral insertional mutagenesis has been fruitfully applied to search for genes/pathways involved in tumorigenesis. Techniques used to identify proviral insertion sites are critical for fulfilling these projects. Although a variety of approaches have been described, an improvement over existing methods is required to recover every possible insertion site for cancer gene discovery, so-called saturation analysis. Here, we have described the development of two ligation-mediated PCR variants, SplinkTA-PCR (STA-PCR) and SplinkBlunt-PCR, for efficient isolation of insertion sites in retrovirus-induced leukemia. Our results demonstrated that these two protocols are complementary to each other and that they are better employed in combination for maximal cloning efficiency. These protocols are easy-to-use, reliable and efficient, and are readily applicable to large-scale cloning of insertion sites of provirus and other integrated DNA elements, as well as for detection and cloning of differential insertions unique to drug-resistant cells.
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Affiliation(s)
- Bin Yin
- University of Minnesota, Minneapolis, MN, USA.
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7
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Tsang S, Sun Z, Luke B, Stewart C, Lum N, Gregory M, Wu X, Subleski M, Jenkins NA, Copeland NG, Munroe DJ. A comprehensive SNP-based genetic analysis of inbred mouse strains. Mamm Genome 2006; 16:476-80. [PMID: 16151692 DOI: 10.1007/s00335-005-0001-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2005] [Accepted: 04/06/2005] [Indexed: 12/21/2022]
Abstract
Dense genetic maps of mammalian genomes facilitate a variety of biological studies including the mapping of polygenic traits, positional cloning of monogenic traits, mapping of quantitative or qualitative trait loci, marker association, allelic imbalance, speed congenic construction, and evolutionary or phylogenetic comparison. In particular, single nucleotide polymorphisms (SNPs) have proved useful because of their abundance and compatibility with multiple high-throughput technology platforms. SNP genotyping is especially suited for the genetic analysis of model organisms such as the mouse because biallelic markers remain fully informative when used to characterize crosses between inbred strains. Here we report the mapping and genotyping of 673 SNPs (including 519 novel SNPs) in 55 of the most commonly used mouse strains. These data have allowed us to construct a phylogenetic tree that correlates and expands known genealogical relationships and clarifies the origin of strains previously having an uncertain ancestry. All 55 inbred strains are distinguishable genetically using this SNP panel. Our data reveal an uneven SNP distribution consistent with a mosaic pattern of inheritance and provide some insight into the changing dynamics of the physical architecture of the genome. Furthermore, these data represent a valuable resource for the selection of markers and the design of experiments that require the genetic distinction of any pair of mouse inbred strains such as the generation of congenic mice, positional cloning, and the mapping of quantitative or qualitative trait loci.
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Affiliation(s)
- Shirley Tsang
- Laboratory of Molecular Technology, SAIC-Frederick, Inc., National Cancer Institute at Frederick, 915 Tollhouse Avenue, Suite 211, Frederick, Maryland 21701, USA
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8
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Okanoue T, Minami M. Update of research and management of hepatitis B. J Gastroenterol 2006; 41:107-18. [PMID: 16568369 DOI: 10.1007/s00535-006-1774-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2006] [Accepted: 01/13/2006] [Indexed: 02/04/2023]
Affiliation(s)
- Takeshi Okanoue
- Molecular Gastroenterology and Hepatology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Hirokoji, Kawaramachi, Kamigyo-ku, Kyoto 602-8566, Japan
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9
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Minami M, Daimon Y, Mori K, Takashima H, Nakajima T, Itoh Y, Okanoue T. Hepatitis B virus-related insertional mutagenesis in chronic hepatitis B patients as an early drastic genetic change leading to hepatocarcinogenesis. Oncogene 2005; 24:4340-8. [PMID: 15806150 DOI: 10.1038/sj.onc.1208628] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Growing evidence demonstrates that hepatitis B virus (HBV) integration and resulting insertional mutagenesis play an important role in cell growth or maintenance in hepatocellular carcinomas (HCCs). To determine if HBV integration occurs and affects cellular genes at such a stage of infection, we analysed viral-host junctions in chronic hepatitis tissues without HCC using PCR amplification with primers specific to human Alu-repeat and HBV. We obtained 42 independent viral-host junctions from six patients examined and identified chromosomal locations for 20 of the 42 junctions. In six clones, each integration apparently affected a single gene. These six candidate genes included one known tumor suppressor gene, three human homologs of drosophila genes that are critical for organ development, one putative oncogene and one recently found chemokine. Our data, together with previously reported HBV integrants in HCCs, suggested preferential HBV integration into chromosome 3 (P = 0.022). Our virus-tagging approach provided (a) firm evidence of HBV integration in hepatocytes at an early stage of chronic infection and (b) revealed cellular genes possibly affected by HBV integration and potentially involved in early steps of the process leading to carcinogenesis.
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Affiliation(s)
- Masahito Minami
- Molecular Gastroenterology and Hepatology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Hirokoji, Kawaramachi, Kamigyo-ku, Kyoto 602-8566, Japan.
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10
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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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