scholarly journals An Improved Sequencing-Based Bioinformatics Pipeline to Track the Distribution and Clonal Architecture of Proviral Integration Sites

2020 ◽  
Vol 11 ◽  
Author(s):  
Nicolas Rosewick ◽  
Vincent Hahaut ◽  
Keith Durkin ◽  
Maria Artesi ◽  
Snehal Karpe ◽  
...  
Keyword(s):  
Proviral Integration ◽  
Bioinformatics Pipeline ◽  
Clonal Architecture ◽  
Integration Sites

scholarly journals Isolation and Analysis of Retroviral Integration Targets by Solo Long Terminal Repeat Inverse PCR

2002 ◽  
Vol 76 (11) ◽  
pp. 5540-5547 ◽  
Author(s):  
Yi Feng Jin ◽  
Toshio Ishibashi ◽  
Akio Nomoto ◽  
Michiaki Masuda
Keyword(s):  
Long Terminal Repeat ◽  
Dna Sequences ◽  
Target Selection ◽  
Terminal Repeat ◽  
Inverse Pcr ◽  
Proviral Integration ◽  
Host Chromosome ◽  
Retroviral Integration ◽  
Integration Sites ◽  
Slip Method

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.

scholarly journals HTLV-1 proviral integration sites differ between asymptomatic carriers and patients with HAM/TSP

2014 ◽  
Vol 11 (1) ◽  
pp. 172 ◽  
Author(s):  
Heather A Niederer ◽  
Daniel J Laydon ◽  
Anat Melamed ◽  
Marjet Elemans ◽  
Becca Asquith ◽  
...  
Keyword(s):  
Proviral Integration ◽  
Asymptomatic Carriers ◽  
Integration Sites

scholarly journals TheMETGene Is a Common Integration Target in Avian Leukosis Virus Subgroup J-Induced Chicken Hemangiomas

2015 ◽  
Vol 89 (9) ◽  
pp. 4712-4719 ◽  
Author(s):  
James Justice ◽  
Sanandan Malhotra ◽  
Miguel Ruano ◽  
Yingying Li ◽  
Guillermo Zavala ◽  
...  
Keyword(s):  
High Throughput ◽  
Insertional Mutagenesis ◽  
High Throughput Sequencing ◽  
Avian Leukosis Virus ◽  
Economic Problem ◽  
Proviral Integration ◽  
Integration Sites ◽  
Myeloid Leukosis ◽  
Subgroup J ◽  
Avian Leukosis Virus Subgroup

ABSTRACTAvian leukosis virus subgroup J (ALV-J) is a simple retrovirus that can cause hemangiomas and myeloid tumors in chickens and is currently a major economic problem in Asia. Here we characterize ALV-J strain PDRC-59831, a newly studied U.S. isolate of ALV-J. Five-day-old chicken embryos were infected with this virus, and the chickens developed myeloid leukosis and hemangiomas within 2 months after hatching. To investigate the mechanism of pathogenesis, we employed high-throughput sequencing to analyze proviral integration sites in these tumors. We found expanded clones with integrations in theMETgene in two of the five hemangiomas studied. This integration locus was not seen in previous work characterizing ALV-J-induced myeloid leukosis.METis a known proto-oncogene that acts through a diverse set of signaling pathways and is involved in many neoplasms. We show that tumors harboringMETintegrations exhibit strong overexpression ofMETmRNA.IMPORTANCEThese data suggest that ALV-J induces oncogenesis by insertional mutagenesis, and integrations in theMEToncogene can drive the overexpression ofMETand contribute to the development of hemangiomas.

scholarly journals Analysis of HIV quasispecies and virological outcome of an HIV D+/R+ kidney–liver transplantation

2022 ◽  
Vol 19 (1) ◽  
Author(s):  
Gabriella Rozera ◽  
Ubaldo Visco-Comandini ◽  
Emanuela Giombini ◽  
Francesco Santini ◽  
Federica Forbici ◽  
...  
Keyword(s):  
Liver Transplantation ◽  
Drug Resistance ◽  
Immunosuppressive Treatment ◽  
Proviral Integration ◽  
Infected Woman ◽  
Cell Counts ◽  
Integration Sites ◽  
Kidney Liver ◽  
Hiv 1

Abstract Introduction Transplantation among HIV positive patients may be a valuable therapeutic intervention. This study involves an HIV D+/R+ kidney–liver transplantation, where PBMC-associated HIV quasispecies were analyzed in donor and transplant recipients (TR) prior to transplantation and thereafter, together with standard viral monitoring. Methods The donor was a 54 year of age HIV infected woman: kidney and liver recipients were two HIV infected men, aged 49 and 61. HIV quasispecies in PBMC was analyzed by ultra-deep sequencing of V3 env region. During TR follow-up, plasma HIV-1 RNA, HIV-1 DNA in PBMC, analysis of proviral integration sites and drug-resistance genotyping were performed. Other virological and immunological monitoring included CMV and EBV DNA quantification in blood and CD4 T cell counts. Results Donor and TR were all ART-HIV suppressed at transplantation. Thereafter, TR maintained a nearly suppressed HIV-1 viremia, but HIV-1 RNA blips and the increase of proviral integration sites in PBMC attested some residual HIV replication. A transient peak in HIV-1 DNA occurred in the liver recipient. No major changes of drug-resistance genotype were detected after transplantation. CMV and EBV transient reactivations were observed only in the kidney recipient, but did not require specific treatment. CD4 counts remained stable. No intermixed quasispecies between donor and TR was observed at transplantation or thereafter. Despite signs of viral evolution in TR, HIV genetic heterogeneity did not increase over the course of the months of follow up. Conclusions No evidence of HIV superinfection was observed in the donor nor in the recipients. The immunosuppressive treatment administrated to TR did not result in clinical relevant viral reactivations.

Chromosomal localization of acquired MMTV proviral integration sites in T-cell lymphomas

1998 ◽  
Vol 9 (1) ◽  
pp. 84-85 ◽  
Author(s):  
Lakshmi Rajan ◽  
Christine A. Kozak ◽  
Jaquelin P. Dudley
Keyword(s):  
T Cell ◽  
Chromosomal Localization ◽  
Proviral Integration ◽  
T Cell Lymphomas ◽  
Integration Sites

Pinpointing recurrent proviral integration sites in new models for latent HIV-1 infection

2018 ◽  
Vol 249 ◽  
pp. 69-75 ◽  
Author(s):  
Ulrike C. Lange ◽  
Julia K. Bialek ◽  
Thomas Walther ◽  
Joachim Hauber
Keyword(s):  
Proviral Integration ◽  
New Models ◽  
Integration Sites ◽  
Latent Hiv ◽  
Hiv 1
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