Genetic drivers define transcriptomic characteristics and clonal hierarchy within intratumoral heterogeneity in adult T-cell leukemia-lymphoma

Subclonal genetic heterogeneity and their diverse characteristics are common features of cancer, associating as a pathogenic driver and therapeutic responsiveness. Here, we developed a capture-based sequencing panel, which covers host hotspot genes and the full-length genome of human T-cell leukemia virus type-1 (HTLV-1), to investigate the clonal architecture of adult T-cell leukemia-lymphoma (ATL). Using this platform, we demonstrated the genetic heterogeneity and complex clonal characteristics in ATL patients and HTLV-1-infected individuals. The dynamic change of clonality during the disease development and clinical course was significantly correlated with variant frequencies of driver genes. Chronological single-cell resolution RNA sequencing combined with clonotyping revealed specific traits and differential use of multiple signaling pathways such as the T-cell receptor/NFAT, NOTCH, and JAK-STAT3 pathways, depending on genotype. Although the genetic landscape was highly-diverse, clonal evolution driven by somatic mutations was critical for malignant transformation from the polyclonal population. Early detection and characterization of the malignant clones are useful for precise therapeutic intervention and risk stratification to manage intractable malignancies.