Clonality, latency and integration of HTLV-1 in vivo

Abstract

Background The HTLV-1 proviral load set point is the strongest correlate of the inflammatory and malignant diseases associated with HTLV-1. This set point appears to be determined by an equilibrium between virus-driven proliferation and CTL-mediated killing of HTLV-1-infected T cells. However, we do not know what determines the number, the abundance or the pathogenic potential of HTLV-1-infected T cell clones. In addition, the contribution of de novo infection to HTLV-1 persistence in the host remains uncertain. We hypothesize that the genomic integration site (IS) of the HTLV-1 provirus determines the pattern and intensity of spontaneous proviral expression; the viral gene products in turn determine the rate of proliferation of the infected cells, and the rate of CTL-mediated killing. We aim to identify the factors that determine the integration site targeting, expression and abundance of the HTLV-1 provirus in natural infection. Materials and methods We developed a novel protocol [1,2] for high-throughput mapping and accurate quantification of proviral integration sites in the host genome in fresh uncultured peripheral blood mononuclear cells from individuals with different clinical manifestations of HTLV-1 infection. Results Each infected individual carries about 25,000 distinct clones of HTLV-1-infected T cells - between 100 and 1000 times more than previously believed. HTLV-1 preferentially integrates into host DNA within 10 to 100 bases of binding sites for specific DNA-binding factors, notably P53 and STAT1. Spontaneous expression of HTLV-1 Tax is associated with antisense orientation of the provirus in the host gene and with specific transcription factor binding sites upstream or downstream of the provirus. Genomic hotspots of HTLV-1 integration are observed in cases of adult T-cell leukaemia/lymphoma (ATLL). HTLV-1 preferentially survives in vivo when integrated in an acrocentric chromosome. Conclusions The results suggest that transcriptional interference and chromatin remodelling are critical determinants of proviral latency in natural HTLV-1 infection. These results open the way to tests of the molecular mechanisms of targeting, expression and clone proliferation in vivo.