Sites of retroviral DNA integration: From basic research to clinical applications

Abstract

One of the most crucial steps in the life cycle of a retrovirus is the integration of the viral DNA (vDNA) copy of the RNA genome into the genome of an infected host cell. Integration provides for efficient viral gene expression as well as for the segregation of the viral genomes to daughter cells upon cell division. Some integrated viruses are not well expressed, and cells latently infected with HIV-1 can resist the action of potent antiretroviral drugs and remain dormant for decades. Intensive research has been dedicated to understanding the catalytic mechanism of integration, as well as the viral and cellular determinants that influence integration site distribution throughout the host genome. In this review we summarize the evolution of techniques that have been used to recover and map retroviral integration sites, from the early days that first indicated that integration could occur in multiple cellular DNA locations, to current technologies that map upwards of millions of unique integration sites from single in vitro integration reactions or cell culture infections. We further review important insights gained from the use of such mapping techniques, including the monitoring of cell clonal expansion in patients treated with retrovirus-based gene therapy vectors, or AIDS patients on suppressive antiretroviral therapy (ART). These insights span from integrase (IN) enzyme sequence preferences within target DNA (tDNA) at the sites of integration, to the roles of host cellular proteins in mediating global integration distribution, to the potential relationship between genomic location of vDNA integration site and retroviral latency.

What Integration Sites Tell Us about HIV Persistence

“…Those who would like additional background information can consult recent reviews (Demeulemeester et al, 2015; Serrao and Engelman, 2016). …”

Maedi-visna virus as a model for HIV

“…However, integration into undesirable sites has hampered their development; for example Moloney-murine leukaemia virus (Mo-MLV)-based vectors have integrated into unintended genomic sites that led to oncogene activation in a number of cases (reviewed in Serrao & Engelman 2016).…”

“…One of the determinants of integration targeting of lentiviruses is a host factor termed LEDGF/ p75, which is a lentiviral integrase-binding protein that tethers viral DNA integration to transcriptionally active regions of the host genome (Cherepanov 2007, Hare et al 2009). However, there is evidence to suggest that LEDGF/p75 is not the only host factor directing lentiviral integrase to actively transcribed sites in the genome, and the viral capsid and CAbinding host proteins seem also to play a role (rewieved by Serrao & Engelman 2016).…”

Connecting HIV‐1 integration and transcription: a step toward new treatments

“…However, recent evidence point to the presence of viral capsid (CA) protein in the nucleus, suggesting that uncoating might as well be finalized in the nucleus . After reverse transcription is completed both viral and cellular proteins associate with the double‐stranded viral DNA in the so‐called pre integration complex (PIC) (see reviews by ). Different viral determinants were implicated in the process of PIC nuclear entry, the most significant being CA (see recent review by on HIV CA) and Integrase (IN), which also catalyzes integration into the cellular genome.…”

“…Upon infection of the permissive cell, viral DNA (vDNA) is synthesized by reverse transcription in the cytoplasm. The viral protein IN which is introduced with the new virions, then associates with vDNA and other viral and cellular protein components into a large nucleoprotein complex termed the preintegration complex (PIC); this complex is transferred into the nucleus where IN catalyzes the integration reaction into the cellular chromatin .…”