HIV-1 sequences in lentiviral vector genomes can be substantially reduced without compromising transduction efficiency

Abstract Many lentiviral vectors used for gene therapy are derived from HIV-1. An optimal vector genome would include only the viral sequences required for transduction efficiency and gene expression to minimize the amount of foreign sequence inserted into a patient’s genome. However, it remains unc...

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Autores principales:	Helin Sertkaya, Mattia Ficarelli, Nathan P. Sweeney, Hannah Parker, Conrad A. Vink, Chad M. Swanson
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/9e4cd1425eb842c698f1446a5655b4b4
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spelling	oai:doaj.org-article:9e4cd1425eb842c698f1446a5655b4b42021-12-02T17:52:12ZHIV-1 sequences in lentiviral vector genomes can be substantially reduced without compromising transduction efficiency10.1038/s41598-021-91309-w2045-2322https://doaj.org/article/9e4cd1425eb842c698f1446a5655b4b42021-06-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-91309-whttps://doaj.org/toc/2045-2322Abstract Many lentiviral vectors used for gene therapy are derived from HIV-1. An optimal vector genome would include only the viral sequences required for transduction efficiency and gene expression to minimize the amount of foreign sequence inserted into a patient’s genome. However, it remains unclear whether all of the HIV-1 sequence in vector genomes is essential. To determine which viral sequences are required, we performed a systematic deletion analysis, which showed that most of the gag region and over 50% of the env region could be deleted. Because the splicing profile for lentiviral vectors is poorly characterized, we used long-read sequencing to determine canonical and cryptic splice site usage. Deleting specific regions of env sequence reduced the number of splicing events per transcript and increased the proportion of unspliced genomes. Finally, combining a large deletion in gag with repositioning the Rev-response element downstream of the 3’ R to prevent its reverse transcription showed that 1201 nucleotides of HIV-1 sequence can be removed from the integrated vector genome without substantially compromising transduction efficiency. Overall, this allows the creation of lentiviral vector genomes that contain minimal HIV-1 sequence, which could improve safety and transfer less viral sequence into a patient’s DNA.Helin SertkayaMattia FicarelliNathan P. SweeneyHannah ParkerConrad A. VinkChad M. SwansonNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-15 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Helin Sertkaya Mattia Ficarelli Nathan P. Sweeney Hannah Parker Conrad A. Vink Chad M. Swanson HIV-1 sequences in lentiviral vector genomes can be substantially reduced without compromising transduction efficiency
description	Abstract Many lentiviral vectors used for gene therapy are derived from HIV-1. An optimal vector genome would include only the viral sequences required for transduction efficiency and gene expression to minimize the amount of foreign sequence inserted into a patient’s genome. However, it remains unclear whether all of the HIV-1 sequence in vector genomes is essential. To determine which viral sequences are required, we performed a systematic deletion analysis, which showed that most of the gag region and over 50% of the env region could be deleted. Because the splicing profile for lentiviral vectors is poorly characterized, we used long-read sequencing to determine canonical and cryptic splice site usage. Deleting specific regions of env sequence reduced the number of splicing events per transcript and increased the proportion of unspliced genomes. Finally, combining a large deletion in gag with repositioning the Rev-response element downstream of the 3’ R to prevent its reverse transcription showed that 1201 nucleotides of HIV-1 sequence can be removed from the integrated vector genome without substantially compromising transduction efficiency. Overall, this allows the creation of lentiviral vector genomes that contain minimal HIV-1 sequence, which could improve safety and transfer less viral sequence into a patient’s DNA.
format	article
author	Helin Sertkaya Mattia Ficarelli Nathan P. Sweeney Hannah Parker Conrad A. Vink Chad M. Swanson
author_facet	Helin Sertkaya Mattia Ficarelli Nathan P. Sweeney Hannah Parker Conrad A. Vink Chad M. Swanson
author_sort	Helin Sertkaya
title	HIV-1 sequences in lentiviral vector genomes can be substantially reduced without compromising transduction efficiency
title_short	HIV-1 sequences in lentiviral vector genomes can be substantially reduced without compromising transduction efficiency
title_full	HIV-1 sequences in lentiviral vector genomes can be substantially reduced without compromising transduction efficiency
title_fullStr	HIV-1 sequences in lentiviral vector genomes can be substantially reduced without compromising transduction efficiency
title_full_unstemmed	HIV-1 sequences in lentiviral vector genomes can be substantially reduced without compromising transduction efficiency
title_sort	hiv-1 sequences in lentiviral vector genomes can be substantially reduced without compromising transduction efficiency
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/9e4cd1425eb842c698f1446a5655b4b4
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HIV-1 sequences in lentiviral vector genomes can be substantially reduced without compromising transduction efficiency

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