Defining early drivers of virus-associated leukaemia at the clonal level

Cancer is derived from a single cell that carries mutations that drive an uncontrolled increase in cell number. Recent research has revealed that a surprisingly high number of mutations also accumulate in healthy tissues as we age. For example, by the age of 50, the genetic material of the average white blood cell has accumulated between 800-1,600 mutations. It is thought that mutations that cause cancer have a more profound impact on cell behaviour than mutations found in healthy tissue; however, research is ongoing, and many open questions remain.

Viruses cause around 10% of cancers. Therefore, it is vital to investigate how viral infection impacts the burden of mutations in healthy tissue and virus-related cancer. This has been technically challenging to do in humans, as it requires obtaining samples at different stages of infection and cancer development.

In this project, I will investigate the consequences of persistent infection with of a cancer-causing virus, Human T cell leukaemia virus type-1 (HTLV-1), on the genetic material of human blood cells. Because HTLV-1 infects cells that circulate in the blood, they can be easily collected and grown in the lab, enabling us to map the locations where mutations occur in each cell's genes. We will study cells from healthy carriers of the virus and cells from people who are in the process of developing Adult T cell Leukaemia/Lymphoma.

This analysis will reveal whether the virus changes the type of mutations and the rate at which mutations occur within infected cells, identify if certain mutations are associated with changes in cell behaviour, and can indicate which cellular processes caused the mutations. This research will allow us for the first time to gain direct insight into how HTLV-1 disrupts the genetic material of otherwise healthy cells which it infects, and is key to understanding how HTLV-1 and other similar viruses cause cancer.

In the last decade, cancer genomes have been characterised in unprecedented depth. Thanks to recent advances in low-input sequencing protocols, we now know that healthy human tissue has a complex clonal structure in which each clone carries a multitude of somatic mutations.
This project will use ex vivo samples to investigate how a cancer-causing virus impacts the mutational burden of healthy and transforming human cells. Human T cell leukaemia virus type 1 (HTLV-1) infects CD4+ T cells causing Adult T cell Leukaemia/Lymphoma (ATL) in ~5% of carriers. On infection, HTLV-1 integrates into the host cell genome, establishing >10,000 infected T cell clones which persist at frequencies below ~0.5% of T cells for decades. In contrast, T cell clones carrying ATL-driver mutations circulate at frequencies >5% of T cells during the premalignant stage of ATL.
We hypothesise that HTLV-1 induces somatic mutations in infected cells and that clonal expansion observed in premalignancy is linked to the occurrence of certain mutations. We will perform whole genome sequencing on an ex vivo panel of infected T cells and compare the genomic landscape of infected T cells with that of T cells from uninfected controls, enabling us to establish whether the rate of somatic mutation is increased in HTLV-1 infected T cells relative to uninfected memory T cells. We will test whether novel or known signatures of particular mutational processes are enriched in infected cells and estimate the time at which each mutation occurred and the time each T cell clonally expanded. Finally, we will also study how the depletion of cells that carry the proviral reservoir impacts the mutational profile of HTLV-1 infected cells.
Together these data will reveal for the first time the effect of HTLV-1 on genome integrity of the cells which it infects, provide insight into the dominant mutational processes active in HTLV-1 infected cells, and identify critical events which initiate the development of ATL.