Combining HTLV-1 and BLV genomic studies towards a better understanding of leukemia progression

Adult T-cell leukemia (ATL) is an aggressive CD4+ T-cell malignancy caused by the oncogenic retrovirus Human T-cell leukemia virus-1 (HTLV-1). Bovine Leukemia Virus (BLV), a close relative of HTLV-1, induces a similar disease in cattle with tumors affecting the B-cell lineage. Both viruses produce a chronic infection in their respective host that evolves into full-blown leukemia/lymphoma in ~5% of infected individuals after several decades of latency. While not a natural host, it is possible to infect sheep with BLV. In contrast to cattle, all infected sheep develop tumors at an accelerated rate (~20 months), providing a unique model for studying early asymptomatic stages. Historically, research into both viruses has primarily focused on their transcripts/proteins. However, increasing evidence suggests that both the proviral integration site and somatic alterations within the host genome play a critical role, as only a subset of infected individuals, following a long period of asymptomatic infection, develop a tumor.
To address the role of genomic alterations and proviral integration site at early stages, we carried out a longitudinal follow-up of BLV-infected sheep that developed aggressive leukemia, tracking back the timing of their occurrence during asymptomatic stages. As expected, this revealed frequent aneuploidy, recurrent SVs and SNVs in tumors, both within and outside known cancer genes. Interestingly, many alterations were present prior to leukemia development. High throughput sequencing analysis of proviral integration sites (HTS clonality) at polyclonal time points allowed us to identify hotspots of proviral integration and monitor the evolution of clonal architecture over time, providing novel insights into tumor evolution.
Identifying high-risk HTLV-1 carriers among the community of HTLV-1 infected individuals is a critical issue. The application of a sensitive HTS method to measure HTLV-1 integration sites genome-wide may address the urgent need of molecular tools to reliably detect future progressors. Our team recently focused on improving previously available HTS clonality methods. We will describe how technical and bioinformatic concerns have been addressed and will discuss potential applications of our optimized protocol.