Deletion of the LTR enhancer/promoter has no impact on the integration profile of MLV vectors in human hematopoietic progenitors

PLoS One. 2013;8(1):e55721. doi: 10.1371/journal.pone.0055721. Epub 2013 Jan 31.

Abstract

Moloney murine leukemia virus (MLV)-derived gamma-retroviral vectors integrate preferentially near transcriptional regulatory regions in the human genome, and are associated with a significant risk of insertional gene deregulation. Self-inactivating (SIN) vectors carry a deletion of the U3 enhancer and promoter in the long terminal repeat (LTR), and show reduced genotoxicity in pre-clinical assays. We report a high-definition analysis of the integration preferences of a SIN MLV vector compared to a wild-type-LTR MLV vector in the genome of CD34(+) human hematopoietic stem/progenitor cells (HSPCs). We sequenced 13,011 unique SIN-MLV integration sites and compared them to 32,574 previously generated MLV sites in human HSPCs. The SIN-MLV vector recapitulates the integration pattern observed for MLV, with the characteristic clustering of integrations around enhancer and promoter regions associated to H3K4me3 and H3K4me1 histone modifications, specialized chromatin configurations (presence of the H2A.Z histone variant) and binding of RNA Pol II. SIN-MLV and MLV integration clusters and hot spots overlap in most cases and are generated at a comparable frequency, indicating that the reduced genotoxicity of SIN-MLV vectors in hematopoietic cells is not due to a modified integration profile.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Computational Biology / methods
  • Genetic Loci
  • Genetic Vectors*
  • Genome, Human
  • Hematopoietic Stem Cells / metabolism*
  • Hematopoietic Stem Cells / virology
  • Histones
  • Humans
  • Mice
  • Moloney murine leukemia virus / genetics*
  • Mutagenesis, Insertional
  • Promoter Regions, Genetic*
  • Sequence Deletion*
  • Terminal Repeat Sequences*
  • Transduction, Genetic
  • Virus Integration*

Substances

  • Histones

Grant support

This work was supported by grants from the European Commission (PERSIST), the European Research Council (GT-SKIN), and the Italian National Research Council (CNR – EPIGEN). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.