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Retroviruses

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Retroviruses and retrotransposons both insert copies of their genetic elements into the genome of the host cell. Thus, the viral genes are passed on when the host genome is replicated or translated. A typical retroviral DNA sequence contains 3-4 genes that encode the different proteins required for its structural assembly and function as a molecular parasite. This DNA is transcribed into a single mRNA, which is very similar in structure to conventional mRNAs, i.e., it is capped at the 5’...
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A mutation is a change in the sequence of bases of DNA or RNA in a genome. Some mutations occur during replication of the genome due to errors made by the polymerase enzymes that replicate DNA or RNA. Unlike DNA polymerase, RNA polymerase is prone to errors because it is not capable of “proofreading” its work. Viruses with RNA-based genomes, like HIV, therefore accrue mutations faster than viruses with DNA-based genomes. Because mutation and recombination provide the raw material...
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LTR retrotransposons are class I transposable elements with long terminal repeats flanking an internal coding region. These elements are less abundant in mammals compared to other class I transposable elements. About 8 percent of human genomic DNA comprises LTR retrotransposons. Some of the common examples of LTR retrotransposons are Ty elements in yeast and Copia elements in Drosophila.
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Viral genomes exhibit remarkable diversity in size, structure, and composition, influencing their replication strategies and interactions with host cells. These genomes consist of either DNA or RNA and may be linear or circular. Additionally, they can be single-stranded or double-stranded, with each configuration affecting how the virus propagates within a host. RNA viruses, for instance, generally have smaller genomes than DNA viruses, a factor that contributes to their high mutation rates and...
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Production of Lentiviral Vectors for Transducing Cells from the Central Nervous System
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HIV-based lentiviral vectors: origin and sequence differences.

Nathan M Johnson1, Anna Francesca Alvarado2, Trey N Moffatt2

  • 1Division of Immunology, Tulane National Primate Research Center, Tulane University School of Medicine, Covington, LA 70433, USA.

Molecular Therapy. Methods & Clinical Development
|May 13, 2021
PubMed
Summary
This summary is machine-generated.

Gene therapy vectors derived from human immunodeficiency virus (HIV-1) are FDA-approved. Analysis reveals sequence variations in key elements like LTR and RRE, impacting lentiviral vector development.

Keywords:
3rd generatation LV vectorsHIV-based lentiviral vectorsLTR and Ψ domainRREcPPT/CTSgene therapy clinical trialsphylogenetic originΔLTR

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Area of Science:

  • Molecular Biology
  • Virology
  • Gene Therapy

Background:

  • Three gene therapy strategies have received FDA approval, with one utilizing human immunodeficiency virus type 1 (HIV-1)-based lentiviral vectors.
  • These lentiviral vectors are engineered for long-term gene transfer and expression, with deleted viral protein-coding regions and retained cis-acting regulatory elements to ensure safety and efficacy.
  • Key vector components include the 5' long terminal repeat (LTR) to Ψ packaging signal, central polypurine tract/chain termination sequence (cPPT/CTS), Rev responsive element (RRE), and 3' LTR with a poly(A) signal.

Purpose of the Study:

  • To compare the vector backbone sequences of representative clinical/commercial lentiviral vectors to their original HIV-1 sources.
  • To examine the functional significance of each region within a lentiviral vector.
  • To identify molecular differences between vectors and potential areas for optimization in lentiviral delivery system development.

Main Methods:

  • Sequence comparison of vector backbones from clinical/commercial applications against HIV-1 reference genomes (HXB2 and NL4-3).
  • Analysis of sequence similarity and divergence in key lentiviral vector elements: Ψ packaging signal, cPPT/CTS, RRE, and LTRs.
  • Phylogenetic analysis of the cPPT/CTS region to infer its evolutionary history within lentiviral vector systems.

Main Results:

  • The Ψ signaling sequence exhibited the highest similarity across all analyzed vectors with minimal alterations.
  • The 3' LTR demonstrated the most significant divergence, characterized by a range of deletions.
  • Variations in RRE length were observed, and phylogenetic analysis of cPPT/CTS suggested multiple origins, potentially due to its later integration into vector design.

Conclusions:

  • Sequence analysis reveals critical differences in essential lentiviral vector components, particularly the 3' LTR and RRE.
  • Understanding these molecular variations is crucial for enhancing the safety and efficiency of lentiviral vector-based gene therapies.
  • Further optimization based on these findings can guide the development of next-generation lentiviral delivery systems.