Viral clonality sequencing and TCR beta clonotype sequencing of HTLV-1 carriers

Adult T-cell leukemia (ATL) is a treatment refractory aggressive T-cell malignancy affecting ~5% of Human T-cell Leukemia Virus-1 (HTLV-1) carriers after decades of asymptomatic infection. Asymptomatic carriers (ACs) generally carry multiple T-cell clones, each characterized by a unique proviral integration site (IS) in the host genome, whereas ATLs harbour a single dominant clone. Only ~20% of “high-risk ACs”, identified based on high proviral load (PVL, = 4 HTLV-1 copies/100 PBMCs), the prognostic marker in place, will progress to ATL. Hence, a molecular tool that can better risk-stratify ACs is urgently needed. Our group has developed a NGS method (“clonality”) for quantifying the clonal distribution of ISs, which has proven useful to diagnose ATLs. We hypothesized that clonality can be used to identify the premalignant stage of ATL by detecting the dominant tumor precursor clone prior to the onset of symptoms. We applied our method to longitudinal samples of a unique cohort of HTLV-1-ACs (JSPFAD, Japan), to examine the clonal landscape of high PVL ACs who subsequently developed ATL and compared these with high and low PVL ACs who did not develop malignancy, followed over an equivalent period. We established a metric for quantification of clonality and explored the association between our clonality score and the patients' clinical outcome many years later. We found that – i) clonality outperforms PVL in identifying ACs at high risk of progression, with zero false positives, resulting in better risk-stratification, ii) clonality better discriminates ACs from patients with indolent smoldering ATL, iii) clonality prognostic performance is unaffected by low PVL or multiple ISs within a predominant T-cell clone as determined by TCRB NGS in >30% of progressors. Monitoring clonality signatures in ACs will allay unwarranted anxiety in 80% high-risk ACs who will not progress to ATL and allow individuals with increased risk to be better managed presumptively. Here we provide the NGS viral clonality sequencing data from longitudinal samples of 15 progressors, 18 high risk and 21 low risk carriers who did not develop malignancy. Additionally we provide TCR beta clonotype sequencing data of select samples, corroborating presence of a single T-cell clone corresponding to a single or multiple proviral insertional clones depending on the case.