Lentiviral vector integration in the human genome induces alternative splicing and generates aberrant transcripts

Arianna Moiani, Ylenia Paleari, Daniela Sartori, Riccardo Mezzadra, Annarita Miccio, Claudia Cattoglio, Fabienne Cocchiarella, Maria Rosa Lidonnici, Giuliana Ferrari, Fulvio Mavilio

Research output: Contribution to journalArticle

Abstract

Retroviral vectors integrate in genes and regulatory elements and may cause transcriptional deregulation of gene expression in target cells. Integration into transcribed genes also has the potential to deregulate gene expression at the posttranscriptional level by interfering with splicing and polyadenylation of primary transcripts. To examine the impact of retroviral vector integration on transcript splicing, we transduced primary human cells or cultured cells with HIV-derived vectors carrying a reporter gene or a human β-globin gene under the control of a reduced-size locus-control region (LCR). Cells were randomly cloned and integration sites were determined in individual clones. We identified aberrantly spliced, chimeric transcripts in more than half of the targeted genes in all cell types. Chimeric transcripts were generated through the use of constitutive and cryptic splice sites in the HIV 5′ long terminal repeat and gag gene as well as in the β-globin gene and LCR. Compared with constitutively spliced transcripts, most aberrant transcripts accumulated at a low level, at least in part as a consequence of nonsense-mediated mRNA degradation. A limited set of cryptic splice sites caused the majority of aberrant splicing events, providing a strategy for recoding lentiviral vector backbones and transgenes to reduce their potential posttranscriptional genotoxicity.

Original languageEnglish
Pages (from-to)1653-1666
Number of pages14
JournalJournal of Clinical Investigation
Volume122
Issue number5
DOIs
Publication statusPublished - May 1 2012

Fingerprint

Alternative Splicing
Human Genome
Locus Control Region
RNA Splice Sites
Globins
Genes
HIV Long Terminal Repeat
gag Genes
Gene Expression
Polyadenylation
RNA Stability
Regulator Genes
Transgenes
Reporter Genes
Cultured Cells
Clone Cells
HIV

ASJC Scopus subject areas

  • Medicine(all)

Cite this

Moiani, A., Paleari, Y., Sartori, D., Mezzadra, R., Miccio, A., Cattoglio, C., ... Mavilio, F. (2012). Lentiviral vector integration in the human genome induces alternative splicing and generates aberrant transcripts. Journal of Clinical Investigation, 122(5), 1653-1666. https://doi.org/10.1172/JCI61852

Lentiviral vector integration in the human genome induces alternative splicing and generates aberrant transcripts. / Moiani, Arianna; Paleari, Ylenia; Sartori, Daniela; Mezzadra, Riccardo; Miccio, Annarita; Cattoglio, Claudia; Cocchiarella, Fabienne; Lidonnici, Maria Rosa; Ferrari, Giuliana; Mavilio, Fulvio.

In: Journal of Clinical Investigation, Vol. 122, No. 5, 01.05.2012, p. 1653-1666.

Research output: Contribution to journalArticle

Moiani, A, Paleari, Y, Sartori, D, Mezzadra, R, Miccio, A, Cattoglio, C, Cocchiarella, F, Lidonnici, MR, Ferrari, G & Mavilio, F 2012, 'Lentiviral vector integration in the human genome induces alternative splicing and generates aberrant transcripts', Journal of Clinical Investigation, vol. 122, no. 5, pp. 1653-1666. https://doi.org/10.1172/JCI61852
Moiani, Arianna ; Paleari, Ylenia ; Sartori, Daniela ; Mezzadra, Riccardo ; Miccio, Annarita ; Cattoglio, Claudia ; Cocchiarella, Fabienne ; Lidonnici, Maria Rosa ; Ferrari, Giuliana ; Mavilio, Fulvio. / Lentiviral vector integration in the human genome induces alternative splicing and generates aberrant transcripts. In: Journal of Clinical Investigation. 2012 ; Vol. 122, No. 5. pp. 1653-1666.
@article{1fdc1e5cd6c4453f89a74e1334e8cd72,
title = "Lentiviral vector integration in the human genome induces alternative splicing and generates aberrant transcripts",
abstract = "Retroviral vectors integrate in genes and regulatory elements and may cause transcriptional deregulation of gene expression in target cells. Integration into transcribed genes also has the potential to deregulate gene expression at the posttranscriptional level by interfering with splicing and polyadenylation of primary transcripts. To examine the impact of retroviral vector integration on transcript splicing, we transduced primary human cells or cultured cells with HIV-derived vectors carrying a reporter gene or a human β-globin gene under the control of a reduced-size locus-control region (LCR). Cells were randomly cloned and integration sites were determined in individual clones. We identified aberrantly spliced, chimeric transcripts in more than half of the targeted genes in all cell types. Chimeric transcripts were generated through the use of constitutive and cryptic splice sites in the HIV 5′ long terminal repeat and gag gene as well as in the β-globin gene and LCR. Compared with constitutively spliced transcripts, most aberrant transcripts accumulated at a low level, at least in part as a consequence of nonsense-mediated mRNA degradation. A limited set of cryptic splice sites caused the majority of aberrant splicing events, providing a strategy for recoding lentiviral vector backbones and transgenes to reduce their potential posttranscriptional genotoxicity.",
author = "Arianna Moiani and Ylenia Paleari and Daniela Sartori and Riccardo Mezzadra and Annarita Miccio and Claudia Cattoglio and Fabienne Cocchiarella and Lidonnici, {Maria Rosa} and Giuliana Ferrari and Fulvio Mavilio",
year = "2012",
month = "5",
day = "1",
doi = "10.1172/JCI61852",
language = "English",
volume = "122",
pages = "1653--1666",
journal = "Journal of Clinical Investigation",
issn = "0021-9738",
publisher = "The American Society for Clinical Investigation",
number = "5",

}

TY - JOUR

T1 - Lentiviral vector integration in the human genome induces alternative splicing and generates aberrant transcripts

AU - Moiani, Arianna

AU - Paleari, Ylenia

AU - Sartori, Daniela

AU - Mezzadra, Riccardo

AU - Miccio, Annarita

AU - Cattoglio, Claudia

AU - Cocchiarella, Fabienne

AU - Lidonnici, Maria Rosa

AU - Ferrari, Giuliana

AU - Mavilio, Fulvio

PY - 2012/5/1

Y1 - 2012/5/1

N2 - Retroviral vectors integrate in genes and regulatory elements and may cause transcriptional deregulation of gene expression in target cells. Integration into transcribed genes also has the potential to deregulate gene expression at the posttranscriptional level by interfering with splicing and polyadenylation of primary transcripts. To examine the impact of retroviral vector integration on transcript splicing, we transduced primary human cells or cultured cells with HIV-derived vectors carrying a reporter gene or a human β-globin gene under the control of a reduced-size locus-control region (LCR). Cells were randomly cloned and integration sites were determined in individual clones. We identified aberrantly spliced, chimeric transcripts in more than half of the targeted genes in all cell types. Chimeric transcripts were generated through the use of constitutive and cryptic splice sites in the HIV 5′ long terminal repeat and gag gene as well as in the β-globin gene and LCR. Compared with constitutively spliced transcripts, most aberrant transcripts accumulated at a low level, at least in part as a consequence of nonsense-mediated mRNA degradation. A limited set of cryptic splice sites caused the majority of aberrant splicing events, providing a strategy for recoding lentiviral vector backbones and transgenes to reduce their potential posttranscriptional genotoxicity.

AB - Retroviral vectors integrate in genes and regulatory elements and may cause transcriptional deregulation of gene expression in target cells. Integration into transcribed genes also has the potential to deregulate gene expression at the posttranscriptional level by interfering with splicing and polyadenylation of primary transcripts. To examine the impact of retroviral vector integration on transcript splicing, we transduced primary human cells or cultured cells with HIV-derived vectors carrying a reporter gene or a human β-globin gene under the control of a reduced-size locus-control region (LCR). Cells were randomly cloned and integration sites were determined in individual clones. We identified aberrantly spliced, chimeric transcripts in more than half of the targeted genes in all cell types. Chimeric transcripts were generated through the use of constitutive and cryptic splice sites in the HIV 5′ long terminal repeat and gag gene as well as in the β-globin gene and LCR. Compared with constitutively spliced transcripts, most aberrant transcripts accumulated at a low level, at least in part as a consequence of nonsense-mediated mRNA degradation. A limited set of cryptic splice sites caused the majority of aberrant splicing events, providing a strategy for recoding lentiviral vector backbones and transgenes to reduce their potential posttranscriptional genotoxicity.

UR - http://www.scopus.com/inward/record.url?scp=84860594261&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84860594261&partnerID=8YFLogxK

U2 - 10.1172/JCI61852

DO - 10.1172/JCI61852

M3 - Article

C2 - 22523069

AN - SCOPUS:84860594261

VL - 122

SP - 1653

EP - 1666

JO - Journal of Clinical Investigation

JF - Journal of Clinical Investigation

SN - 0021-9738

IS - 5

ER -