RNA-seq reveals cis-perturbation of key host genes by the HTLV-1/BLV proviruses

An estimated 10 to 20 million humans and 50 million dairy cattle are infected with the closely-related Human T-cell leukemia virus type-1 (HTLV-1) and Bovine Leukemia Virus (BLV) respectively. These retroviruses infect T (HTLV-1) and B (BLV) lymphocytes, provoking an asymptomatic polyclonal expansion that will evolve into an aggressive lethal monoclonal leukemia in ~5% of individuals following decades of latency. It is generally assumed that early oncogenic changes are largely dependent on virus-encoded products and especially the trans-activating effects of the Tax and HTLV-1 bZIP HBZ oncoproteins, while progression to acute leukemia/lymphoma involves somatic mutations in cancer drivers, yet that both are independent of proviral integration site that has been found to be very variable between tumors. Using RNA-seq we demonstrate that HTLV-1/BLV proviruses are integrated in the vicinity of cancer drivers which they perturb either by provirus-dependent transcription termination or as a result of viral antisense RNA-dependent cis-perturbation. RNA-seq of ATLs (HTLV-1) and B-cell tumors (BLV) revealed in all tumors (i) the complete absence of viral 5’LTR-dependent sense transcripts (corresponding to the gag, pol, env structural genes and the regulatory genes including tax) and (ii) abundant 3’LTR-dependent antisense transcripts (3’AS) corresponding to HTLV-1 Hbz and BLV As1/2 RNAs. Additionally, mapping the RNA reads to the proviral and host reference genomes uncovered 5’LTR-dependent transcriptional termination of the interrupted gene in ~23 % of the tumors. In the remaining ~77 % of the tumors, this revealed the systematic interactions between the viral antisense transcripts (3’AS) and host genes located upstream of the provirus.