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Retroviruses and Retroviral, Lentiviral Vectors in Modern Biology
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Retroviruses and Retroviral, Lentiviral Vectors in Modern Biology

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Microbiology".

Deadline for manuscript submissions: closed (30 November 2022) | Viewed by 15721

Special Issue Editor

Prof. Dr. Vladimir S. Prassolov

E-Mail Website
Guest Editor
Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova str. 32, 199991 Moscow, Russia
Interests: molecular biology of cancer cells; signaling pathways; anticancer drugs; retroviruses; retroviral and lentiviral vectors; transfer and expression of genes in animal and human cells; natural and synthetic inhibitors of replication of lentiviruses

Special Issue Information

Dear Colleagues, 

The Special Issue “Retroviruses and Retroviral, Lentiviral Vectors in Modern Biology” is devoted to the latest research advances in this area of ​​research.

Although retroviruses were one of the first viruses to be isolated from animals over a hundred years ago, their molecular nature remained unclear for a long time. A breakthrough in their research was the discovery by David Baltimore and Howard Temin, showing that reverse transcription is a key step in the retrovirus life cycle. Prior to this, the synthesis of double-stranded genomic viral DNA (provirus) on a single-stranded RNA template was not known. Soon after this, Harold E. Varmus and J. Michael Bishop showed that transforming retroviruses arise as a result of the inclusion of cellular proto-oncogenes in their genome, which in this case are out of the control of cellular control elements and become activated oncogenes. When normal cells are infected with such a transforming virus, the activated oncogene contributes to its malignant transformation.

These discoveries have become a powerful stimulus for the development of research on retro- and lentiviruses. The establishment of the retroviral nature of AIDS and human T-cell leukemia and the search for effective methods to combat them has greatly stimulated the study of simple and complex retroviruses.

Many areas of modern fundamental biology and biomedicine are based on the use of reverse transcription for gene cloning, and retro- and lentiviral vectors are widely used for the transfer and expression of target and marker genes and genetic constructs in a variety of studies, including genome editing and gene therapy.

Of particular interest is the study of endogenous viruses of animals and humans, which can be used in the design of vector particles with the targeted delivery of therapeutic genes.

Original investigations as well as concise review manuscripts from experts in the relevant research fields will be considered for publication.

Prof. Dr. Vladimir S. Prassolov
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • nature of retroviruses
  • retrovirus and lentivirus
  • lentiviral system for transfer and expression of genes in mammalian cells in vitro and in vivo
  • retroviruses in gene therapy
  • genome editing
  • endogenous retroviruses

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Published Papers (5 papers)

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13 pages, 2508 KiB  
Article
Both ATM and DNA-PK Are the Main Regulators of HIV-1 Post-Integrational DNA Repair
by Andrey Anisenko, Anastasiia Nefedova, Yulia Agapkina and Marina Gottikh
Int. J. Mol. Sci. 2023, 24(3), 2797; https://doi.org/10.3390/ijms24032797 - 1 Feb 2023
Cited by 6 | Viewed by 2118
Abstract
The integration of a DNA copy of an HIV-1 RNA genome into the host genome, carried out by the viral enzyme integrase, results in the formation of single-stranded gaps in cellular DNA that must be repaired. Here, we have analyzed the involvement of [...] Read more.
The integration of a DNA copy of an HIV-1 RNA genome into the host genome, carried out by the viral enzyme integrase, results in the formation of single-stranded gaps in cellular DNA that must be repaired. Here, we have analyzed the involvement of the PI3K kinases, ATM, ATR, and DNA-PKcs, which are important players in the DNA damage response (DDR) in HIV-1 post-integrational DNA repair (PIR). The participation of the DNA-PK complex in HIV-1 PIR has been previously shown, and the formation of a complex between the viral integrase and the DNA-PK subunit, Ku70, has been found to be crucial for efficient PIR. Now, we have shown that the inhibition of both DNA-PKcs and ATM, but not ATR, significantly reduces PIR efficiency. The activation of both kinases is a sequential process, where one kinase, being activated, activates the other, and it occurs simultaneously with the integration of viral DNA. This fact suggests that the activation of both kinases triggers PIR. Most interestingly, the activation of not only DNA-PKcs, but also ATM depends on the complex formation between integrase and Ku70. The elucidation of the interactions between viruses and DDR is important both for understanding the modulation of host cell functions by these pathogens and for developing new approaches to combat viral infections. Full article
(This article belongs to the Special Issue Retroviruses and Retroviral, Lentiviral Vectors in Modern Biology)
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19 pages, 3194 KiB  
Article
Efficient Selection of Enhancers and Promoters from MIA PaCa-2 Pancreatic Cancer Cells by ChIP-lentiMPRA
by Kirill Nikitich Kashkin, Elena Sergeevna Kotova, Irina Vasilievna Alekseenko, Svetlana Sergeevna Bulanenkova, Sergey Borisovich Akopov, Eugene Pavlovich Kopantzev, Lev Grigorievich Nikolaev, Igor Pavlovich Chernov and Dmitry Alexandrovich Didych
Int. J. Mol. Sci. 2022, 23(23), 15011; https://doi.org/10.3390/ijms232315011 - 30 Nov 2022
Viewed by 2048
Abstract
A library of active genome regulatory elements (putative promoters and enhancers) from MIA PaCa-2 pancreatic adenocarcinoma cells was constructed using a specially designed lentiviral vector and a massive parallel reporter assay (ChIP-lentiMPRA). Chromatin immunoprecipitation of the cell genomic DNA by H3K27ac antibodies was [...] Read more.
A library of active genome regulatory elements (putative promoters and enhancers) from MIA PaCa-2 pancreatic adenocarcinoma cells was constructed using a specially designed lentiviral vector and a massive parallel reporter assay (ChIP-lentiMPRA). Chromatin immunoprecipitation of the cell genomic DNA by H3K27ac antibodies was used for primary enrichment of the library for regulatory elements. Totally, 11,264 unique genome regions, many of which are capable of enhancing the expression of the CopGFP reporter gene from the minimal CMV promoter, were identified. The regions tend to be located near promoters. Based on the proximity assay, we found an enrichment of highly expressed genes among those associated with three or more mapped distal regions (2 kb distant from the 5′-ends of genes). It was shown significant enrichment of genes related to carcinogenesis or Mia PaCa-2 cell identity genes in this group. In contrast, genes associated with 1–2 distal regions or only with proximal regions (within 2 kbp of the 5′-ends of genes) are more often related to housekeeping functions. Thus, ChIP-lentiMPRA is a useful strategy for creating libraries of regulatory elements for the study of tumor-specific gene transcription. Full article
(This article belongs to the Special Issue Retroviruses and Retroviral, Lentiviral Vectors in Modern Biology)
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17 pages, 2324 KiB  
Article
Subtype of Neuroblastoma Cells with High KIT Expression Are Dependent on KIT and Its Knockdown Induces Compensatory Activation of Pro-Survival Signaling
by Timofey Lebedev, Anton Buzdin, Elmira Khabusheva, Pavel Spirin, Maria Suntsova, Maxim Sorokin, Vladimir Popenko, Petr Rubtsov and Vladimir Prassolov
Int. J. Mol. Sci. 2022, 23(14), 7724; https://doi.org/10.3390/ijms23147724 - 13 Jul 2022
Cited by 7 | Viewed by 1909
Abstract
Neuroblastoma (NB) is a pediatric cancer with high clinical and molecular heterogeneity, and patients with high-risk tumors have limited treatment options. Receptor tyrosine kinase KIT has been identified as a potential marker of high-risk NB and a promising target for NB treatment. We [...] Read more.
Neuroblastoma (NB) is a pediatric cancer with high clinical and molecular heterogeneity, and patients with high-risk tumors have limited treatment options. Receptor tyrosine kinase KIT has been identified as a potential marker of high-risk NB and a promising target for NB treatment. We investigated 19,145 tumor RNA expression and molecular pathway activation profiles for 20 cancer types and detected relatively high levels of KIT expression in NB. Increased KIT expression was associated with activation of cell survival pathways, downregulated apoptosis induction, and cell cycle checkpoint control pathways. KIT knockdown with shRNA encoded by lentiviral vectors in SH-SY5Y cells led to reduced cell proliferation and apoptosis induction up to 50%. Our data suggest that apoptosis induction was caused by mitotic catastrophe, and there was a 2-fold decrease in percentage of G2-M cell cycle phase after KIT knockdown. We found that KIT knockdown in NB cells leads to strong upregulation of other pro-survival growth factor signaling cascades such as EPO, NGF, IL-6, and IGF-1 pathways. NGF, IGF-1 and EPO were able to increase cell proliferation in KIT-depleted cells in an ERK1/2-dependent manner. Overall, we show that KIT is a promising therapeutic target in NB, although such therapy efficiency could be impeded by growth factor signaling activation. Full article
(This article belongs to the Special Issue Retroviruses and Retroviral, Lentiviral Vectors in Modern Biology)
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20 pages, 1948 KiB  
Article
The TZM-bl Reporter Cell Line Expresses Kynureninase That Can Neutralize 2F5-like Antibodies in the HIV-1 Neutralization Assay
by Vladimir Morozov, Sylvie Lagaye and Alexey Morozov
Int. J. Mol. Sci. 2022, 23(2), 641; https://doi.org/10.3390/ijms23020641 - 7 Jan 2022
Cited by 1 | Viewed by 5093
Abstract
Induction of broadly neutralizing antibodies targeting ectodomain of the transmembrane (TM) glycoprotein gp41 HIV-1 provides a basis for the development of a universal anti-viral vaccine. The HeLa cell-derived TZM-bl reporter cell line is widely used for the estimation of lentiviruses neutralization by immune [...] Read more.
Induction of broadly neutralizing antibodies targeting ectodomain of the transmembrane (TM) glycoprotein gp41 HIV-1 provides a basis for the development of a universal anti-viral vaccine. The HeLa cell-derived TZM-bl reporter cell line is widely used for the estimation of lentiviruses neutralization by immune sera. The cell line is highly permissive to infection by most strains of HIV, SIV, and SHIV. Here we demonstrated that TZM-bl cells express a 48 kDa non-glycosylated protein (p48) recognized by broadly neutralizing monoclonal antibody (mAb) 2F5 targeting the ELDKWA (aa 669–674) epitope of gp41TM of HIV-1. A significant amount of p48 was found in the cell supernatant. The protein was identified as human kynureninase (KYNU), which has the ELDKWA epitope. The protein is further called “p48 KYNU”. The HIV-1 neutralization by mAb 2F5 and 4E10 in the presence of p48KYNU was tested on Jurkat and TZM-bl cells. It was demonstrated that p48KYNU reduces neutralization by 2F5-like antibodies, but it has almost no effect on mAb 4E10. Therefore, p48KYNU can attenuate HIV-1 neutralization by 2F5-like antibodies and hence create false-negative results. Thus, previously tested immune sera that recognized the ELDKWA-epitope and demonstrated a “weak neutralization” of HIV-1 in TZM-bl assay should be reevaluated. Full article
(This article belongs to the Special Issue Retroviruses and Retroviral, Lentiviral Vectors in Modern Biology)
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23 pages, 3272 KiB  
Article
A Comprehensive Analysis of Human Endogenous Retroviruses HERV-K (HML.2) from Teratocarcinoma Cell Lines and Detection of Viral Cargo in Microvesicles
by Vladimir A. Morozov and Alexey V. Morozov
Int. J. Mol. Sci. 2021, 22(22), 12398; https://doi.org/10.3390/ijms222212398 - 17 Nov 2021
Cited by 4 | Viewed by 3742
Abstract
About 8% of our genome is composed of sequences from Human Endogenous Retroviruses (HERVs). The HERV-K (HML.2) family, here abbreviated HML.2, is able to produce virus particles that were detected in cell lines, malignant tumors and in autoimmune diseases. Parameters and properties of [...] Read more.
About 8% of our genome is composed of sequences from Human Endogenous Retroviruses (HERVs). The HERV-K (HML.2) family, here abbreviated HML.2, is able to produce virus particles that were detected in cell lines, malignant tumors and in autoimmune diseases. Parameters and properties of HML.2 released from teratocarcinoma cell lines GH and Tera-1 were investigated in detail. In most experiments, analyzed viruses were purified by density gradient centrifugation. HML.2 structural proteins, reverse transcriptase (RT) activity, viral RNA (vRNA) and particle morphology were analyzed. The HML.2 markers were predominantly detected in fractions with a buoyant density of 1.16 g/cm3. Deglycosylation of TM revealed truncated forms of transmembrane (TM) protein. Free virions and extracellular vesicles (presumably microvesicles—MVs) with HML.2 elements, including budding intermediates, were detected by electron microscopy. Viral elements and assembled virions captured and exported by MVs can boost specific immune responses and trigger immunomodulation in recipient cells. Sequencing of cDNA clones demonstrated exclusive presence of HERV-K108 env in HML.2 from Tera-1 cells. Not counting two recombinant variants, four known env sequences were found in HML.2 from GH cells. Obtained results shed light on parameters and morphology of HML.2. A possible mechanism of HML.2-induced diseases is discussed. Full article
(This article belongs to the Special Issue Retroviruses and Retroviral, Lentiviral Vectors in Modern Biology)
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