HTLV-1 Integration into Transcriptionally Active Genomic Regions Is Associated with Proviral Expression and with HAM/TSP

Kiran N Meekings,Jeremy Leipzig,Frederic D Bushman,Graham P Taylor,Charles R M Bangham,Michael H Malim

doi:10.1371/journal.ppat.1000027

Abstract

Human T-lymphotropic virus type 1 (HTLV-1) causes leukaemia or chronic inflammatory disease in ∼5% of infected hosts. The level of proviral expression of HTLV-1 differs significantly among infected people, even at the same proviral load (proportion of infected mononuclear cells in the circulation). A high level of expression of the HTLV-1 provirus is associated with a high proviral load and a high risk of the inflammatory disease of the central nervous system known as HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). But the factors that control the rate of HTLV-1 proviral expression remain unknown. Here we show that proviral integration sites of HTLV-1 in vivo are not randomly distributed within the human genome but are associated with transcriptionally active regions. Comparison of proviral integration sites between individuals with high and low levels of proviral expression, and between provirus-expressing and provirus non-expressing cells from within an individual, demonstrated that frequent integration into transcription units was associated with an increased rate of proviral expression. An increased frequency of integration sites in transcription units in individuals with high proviral expression was also associated with the inflammatory disease HAM/TSP. By comparing the distribution of integration sites in human lymphocytes infected in short-term cell culture with those from persistent infection in vivo, we infer the action of two selective forces that shape the distribution of integration sites in vivo: positive selection for cells containing proviral integration sites in transcriptionally active regions of the genome, and negative selection against cells with proviral integration sites within transcription units.

Highlights

The completion of the human genome sequence has made genome-wide studies of retroviral integration possible
The human leukaemia virus Human T-lymphotropic virus type 1 (HTLV-1) causes a lifelong infection that cannot be cleared by the immune system
The virus is reactivated much faster than in others, and such people are more likely to develop HTLV-1associated inflammatory diseases such as HTLV-1associated myelopathy/tropical spastic paraparesis (HAM/TSP), which results in paralysis of the legs

Summary

Introduction

The completion of the human genome sequence has made genome-wide studies of retroviral integration possible. Such studies have led to a good understanding of the targeting preferences of retroviruses for integration. The genomic distribution of integration sites has not been widely studied in the context of persistent infection, where infected cells are subjected to additional selection forces such as the immune response. We tested the hypothesis that in vivo selection influences the genomic distribution of proviral integration sites in persistent HTLV-1 infection. Genome-wide studies have revealed that proviral integration is not random, but that each retrovirus has distinct target site preferences [1,2,3,4]. The different targeting preferences of the individual retroviruses are determined by several known factors, including the properties of the viral integrase [12], DNA binding proteins [13,14], cellular targeting proteins [15,16,17,18,19] and the chromatin structure at the point of integration [20,21]

Methods

Results

Discussion

Conclusion