scholarly journals 50. Novel Bioinformatic Framework for Quantification of Retroviral Integration Sites From Genomic DNA Sonication-Based PCR Data

2014 ◽  
Vol 22 ◽  
pp. S20
2002 ◽  
Vol 76 (11) ◽  
pp. 5540-5547 ◽  
Author(s):  
Yi Feng Jin ◽  
Toshio Ishibashi ◽  
Akio Nomoto ◽  
Michiaki Masuda

ABSTRACT Upon retroviral infection, the genomic RNA is reverse transcribed to make proviral DNA, which is then integrated into the host chromosome. Although the viral elements required for successful integration have been extensively characterized, little is known about the host DNA structure constituting preferred targets for proviral integration. In order to elucidate the mechanism for the target selection, comparison of host DNA sequences at proviral integration sites may be useful. To achieve simultaneous analysis of the upstream and downstream host DNA sequences flanking each proviral integration site, a Moloney murine leukemia virus-based retroviral vector was designed so that its integrated provirus could be removed by Cre-loxP homologous recombination, leaving a solo long terminal repeat (LTR). Taking advantage of the solo LTR, inverse PCR was carried out to amplify both the upstream and downstream cellular flanking DNA. The method called solo LTR inverse PCR, or SLIP, proved useful for simultaneously cloning the upstream and downstream flanking sequences of individual proviral integration sites from the polyclonal population of cells harboring provirus at different chromosomal sites. By the SLIP method, nucleotide sequences corresponding to 38 independent proviral integration targets were determined and, interestingly, atypical virus-host DNA junction structures were found in more than 20% of the cases. Characterization of retroviral integration sites using the SLIP method may provide useful insights into the mechanism for proviral integration and its target selection.


2009 ◽  
Vol 71 (1) ◽  
pp. 1-11 ◽  
Author(s):  
Cherry Ee Lin Ng ◽  
Yoshiaki Ito ◽  
Motomi Osato

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 1744-1744
Author(s):  
Frank A. Giordano ◽  
Stephanie Laufs ◽  
Katalin Z. Nagy ◽  
Boris Fehse ◽  
Agnes Hotz-Wagenblatt ◽  
...  

Abstract Retroviral vectors encoding the herpes simplex thymidine kinase gene (HSV-Tk) have been employed to render T-lymphocytes (TLCs) sensitive to the prodrug ganciclovir. Such genetically modified T cells have been used for adoptive immunotherapy in the context of allogeneic hematopoietic stem cell transplantation (SCT). Infused T cells have been shown to be susceptible to elimination through exposure to ganciclovir in the event of graft-versus-host disease (GvHD). Recent reports on insertional “genotoxicity” in a mouse gene marking study and a clinical gene therapy trial for X-chromosomal severe combined immunodeficiency (X-SCID) reminded us the actual risk of insertional oncogene activation and subsequent leukemia development. Here we investigated retroviral integration sites in donor TLCs transduced with the MoLV-based TK/neoR vector Mo3TIN of four donors in a clinical HSV-Tk study. A total of 114 retroviral integration sites were detected using highly sensitive and specific ligation-mediated PCR (LM-PCR). 41.2% of all integrations appeared near the transcription start regions (+/−10kb) of genes. Further analysis showed that 57 (50%) of all integrations targeted RefSeq genes. 24 of those appeared in intron 1 (42% of all integrations into genes) while 18% (10/57) of all integrations into genes landed in exon sequences whereas 6 hit the first exon. 18 of the targeted genes (15.8% of all integrations) could be at last assigned to signal transduction pathways, whereas the transcription factor family was afflicted 13 times (11.4% of all integrations). The zinc ion binding group makes up 4 (resp. 6, minding that GTF2HII contains a C2H2 type and KIAA0427 a C-x8-C-x5-C-x3-H-type zinc finger) of them. Among the targeted genes we found integrations into the CD8, CD100, CD44, CX3CR1, HLA-DMP and IL10-receptor genes. Within at a range of 5kb up- and 5kb downstream of vector integrations 15 genes were located that were not hit. 5 are known as transcription factors, whereas two of those are involved in leukemia, namely the homo sapiens myeloid/lymphoid or mixed-lineage leukemia 5 gene (MLL5) and the homo sapiens ALL1 fused gene from 5q31 (AF5Q31). Hit genes are currently examined more systematically in terms of function, e.g. involvement in signal transduction and transcription promoting processes. RISC (Retroviral Insertion estimate of Chromosomal Integration) scores and integration specific data will be submitted to a data warehouse, the collaborative RISC score database (CRSD). Such a systematic data collection similar to the IBMTR or EBMT databases will allow to recognize factors contributing to the safety, optimal transgene expression and persistence of transduced cells in the setting of allogenic matched donor transplantation.


Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 820-820
Author(s):  
Claudia Cattoglio ◽  
Barbara Felice ◽  
Davide Cittaro ◽  
Annarita Miccio ◽  
Giuliana Ferrari ◽  
...  

Abstract Gamma-retroviruses and lentiviruses integrate non-randomly in mammalian genomes, with specific preferences for active chromatin, promoters and regulatory regions. Gamma-retroviral gene transfer vectors show a high frequency of insertional gene activation, and may induce neoplastic or pre-neoplastic clonal expansions in patients treated with genetically modified cells. An analysis of >10,000 integration sites of a Moloney leukemia virus (MLV)-derived vector in human CD34+ hematopoietic progenitors showed that genes involved the control of growth, differentiation and development of the hematopoietic and immune system are targeted at high frequency and enriched in integration hot spots, suggesting that the cell gene expression program is instrumental in directing MLV integration. To investigate the role of transcriptional regulatory networks in retroviral target site selection, we analyzed the distribution of transcription factor binding sites (TFBSs) flanking >4,000 MLV- and HIV-derived proviruses in human hematopoietic and non-hematopoietic cells. We show that MLV vectors integrate in genomic regions enriched in cell-type specific subsets of TFBSs, independently from their relative position with respect to genes and transcription start sites. Conversely, HIV vectors appear to avoid TFBS-rich genomic regions. Hierarchical clustering and a principal component analysis of TFBSs flanking retroviral integration sites in CD34+ and HeLa cells showed that TFBS subsets are vector- and cell type-specific. Analysis of sequences flanking the integration sites of vectors carrying mutations in their long terminal repeats (LTRs), and of HIV vectors packaged with a MLV integrase, indicates that the MLV integrase and LTR enhancer are the viral determinants of the selection of TFBS-rich regions in the genome. Chromatin immunoprecipitation analysis shows that transcription factors bind the LTR enhancers in the cell nucleus before integration, and may therefore synergize with the integrase in tethering retroviral pre-integration complexes to transcriptionally active regulatory regions. This study identifies TFBSs as differential genomic determinants of retroviral target site selection in the human genome, and indicates that gamma-retroviruses and lentiviruses have evolved dramatically different strategies to interact with the host cell chromatin. These differences predict a higher risk in using gamma-retroviral vs. lentiviral vectors for human gene therapy applications, independently from the design of the vector and the transgene expression cassette.


Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 3452-3452
Author(s):  
Salemiz Sandoval ◽  
Michelle Cho ◽  
Christina Kraus ◽  
Er-Chieh Cho ◽  
Linda Wolff ◽  
...  

Abstract Abstract 3452 The cAMP Response Element Binding Protein, CREB, is a transcription factor that is critical for cell proliferation and survival in neuronal and hematopoietic cells. We previously reported that CREB is overexpressed in leukemic blasts from patients with AML. CREB overexpression is also associated with an increased risk of relapse and decreased event-free survival in AML patients. We generated transgenic mice in which CREB is expressed under the control of the myeloid specific promoter, hMRP8. In vitro, bone marrow progenitors from CREB transgenic mice have increased proliferative potential and replating ability and these mice develop myeloproliferative disease, but not AML. Therefore, CREB is not sufficient to fully transform hematopoietic cells. To identify genes that cooperate with CREB, we performed retroviral insertional mutagenesis with CREB or wildtype C57/Blk6 mice. Newborn mice were infected with the MOL4070LTR retrovirus. Leukemia was observed in both CREB transgenic and wild type mice, however, latency for disease was significantly shortened in CREB transgenic mice at 9 months vs. 14 months for wild type mice (p<0.001). Infected mice developed hepatosplenomegaly (weighing up to 10-fold more than spleens from uninfected wild type mice). The leukemic phenotype by FACs analysis showed that 75% (24/32 mice analyzed) had AML with blast cells expressing Gr-1/Mac-1. Therefore, wild type MOL4070LTR infected mice had decreased penetrance for myeloid disease (45% or 5/11 mice analyzed). To identify potential cooperating oncogenes, genomic DNA was subjected to long-mediated PCR analysis to amplify genomic sequences upstream of the virus. Viral integration sites were identified by Southern blot analysis with genomic DNA from spleens from mice with leukemia. These sequences were mapped to the mouse genome to identify the chromosomal location. Blast analysis of retroviral integration sites (RIS) was performed on the publicly available Ensembl database and compared to known common integration sites on the Retroviral Tagged Cancer Gene Database (RTCGD http://rtcgd.ncifcrf.gov/). Sequencing of integration sites identified previously known oncogenes, such as Evi1/Mds, Evi5/Gfi1, Myb/Ahi, and Ras. Common integration sites identified in multiple mice include, sox4, Evi5/Gfi1, Myb/Ahi, Cbfa2t3. The highest incidence of integration in the mutagenesis screen was in the sox4 gene. Sox4 is a transcription factor that regulates embryonic development and cell fate. Transduction of CREB transgenic mouse bone marrow progenitor cells with a sox4 retrovirus increased survival and self-renewal by 2-fold (p<0.01) in serial replating and methylcellulose colony assays compared to wild type bone marrow progenitors. CREB overexpressing bone marrow progenitor cells stained with Brdu had a 10% increase in cycling cells compared to wild type bone marrow progenitor cells transduced with sox4 retrovirus (p<0.0001). Consistent with this observation is that sox4 retroviral transduction of CREB transgenic bone marrow cells led to increased CREB and cyclin D expression (p<0.01 and p<0.001, respectively). CREB transgenic mouse bone marrow transduced with sox4 retrovirus and stained with Annexin/7AAD also showed decreased apoptosis when cultured in low serum and absence of growth factor (p<0.05). Furthermore, the expression of the sox4 gene was increased in bone marrow cells from AML patients that also overexpressed CREB. Our results indicate that sox4 and CREB cooperate and contribute to transformation of hematopoietic progenitor cells. Disclosures: No relevant conflicts of interest to declare.


2004 ◽  
Vol 279 (44) ◽  
pp. 45810-45814 ◽  
Author(s):  
René Daniel ◽  
Joseph Ramcharan ◽  
Emmy Rogakou ◽  
Konstantin D. Taganov ◽  
James G. Greger ◽  
...  

The histone variant H2AX is rapidly phosphorylated (denoted γH2AX) in large chromatin domains (foci) flanking double strand DNA (dsDNA) breaks that are produced by ionizing radiation or genotoxic agents and during V(D)J recombination. H2AX-deficient cells and mice demonstrate increased sensitivity to dsDNA break damage, indicating an active role for γH2AX in DNA repair; however, γH2AX formation is not required for V(D)J recombination. The latter finding has suggested a greater dependence on γH2AX for anchoring free broken endsversusends that are held together during programmed breakage-joining reactions. Retroviral DNA integration produces a unique intermediate in which a dsDNA break in host DNA is held together by the intervening viral DNA, and such a reaction provides a useful model to distinguish γH2AX functions. We found that integration promotes transient formation of γH2AX at retroviral integration sites as detected by both immunocytological and chromatin immunoprecipitation methods. These results provide the first direct evidence for the association of newly integrated viral DNA with a protein species that is an established marker for the onset of a DNA damage response. We also show that H2AX is not required for repair of the retroviral integration intermediate as determined by stable transduction. These observations provide independent support for an anchoring model for the function of γH2AX in chromatin repair.


2018 ◽  
Author(s):  
D. Michieletto ◽  
M. Lusic ◽  
D. Marenduzzo ◽  
E. Orlandini

Certain retroviruses, including HIV, insert their DNA in a non-random fraction of the host genome via poorly understood selection mechanisms. Here, we develop a biophysical model for retroviral integrations as stochastic and quasi-equilibrium topological reconnections between polymers. We discover that physical effects, such as DNA accessibility and elasticity, play important and universal roles in this process. Our simulations predict that integration is favoured within nucleosomal and flexible DNA, in line with experiments, and that these biases arise due to competing energy barriers associated with DNA deformations. By considering a long chromosomal region in human T-cells during interphase, we discover that at these larger scales integration sites are predominantly determined by chromatin accessibility. Finally, we propose and solve a reaction-diffusion problem that recapitulates the distribution of HIV hot-spots within T-cells. With few generic assumptions, our model can rationalise experimental observations and identifies previously unappreciated physical contributions to retroviral integration site selection.


2002 ◽  
Vol 83 (4) ◽  
pp. 819-827 ◽  
Author(s):  
Peter Haviernik ◽  
Stephen M. Festin ◽  
Rene Opavsky ◽  
Richard P. Koller ◽  
Nighean I. Barr ◽  
...  

Mml loci have been identified as provirus integration sites among a subset of monocytic tumours induced by murine leukaemia virus (MuLV) infection of BALB/c and DBA/2 mice. These myeloid leukaemias contain a retrovirus integrated on chromosome 10 in proximity to the c-myb locus; however, c-myb expression was not altered. Detailed physical mapping enabled placement of the retroviral integration sites ∼25 kb (Mml1), ∼51 kb (Mml2), and ∼70 kb (Mml3) upstream of the c-myb locus. Furthermore, the Fti1 (fit-1) locus, a common integration site in feline leukaemia virus-induced T cell lymphomas, was mapped upstream of Mml3. Sequence analysis of Mml1, Mml2 and Mml3 loci (39·6, 16·4 and 5·9 kb, respectively) in conjunction with the BLAST (basic local alignment search tool) homology searches against the expressed sequence tag (EST) database and the use of gene/exon prediction programs revealed potential coding sequences that were not confirmed by Northern analysis or RT–PCR. The sequences between c-myb and Fti1, which were shown to include two potential scaffold/matrix attachment regions (S/MARs), are most likely regulatory in nature. An extended search for transcribed sequences far upstream of Mml3 revealed five genes, four of which were expressed in multiple tissues in mice. These genes could not be linked to tumour formation by the virus but their homologous sequences were found on human chromosome 6, thus allowing extension of the syntenic region on mouse chromosome 10 to approximately 250 kb.


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