Characterising the tumour evolution and genetic heterogeneity underlying follicular lymphoma and its progression.

Abstract

Follicular lymphoma (FL) is an incurable indolent non-Hodgkin’s lymphoma (NHL) that behaves heterogeneously. Although epitomised by the t(14;18), the full spectrum of genetic lesions and the clonal hierarchy that contribute to the malignancy had been incomplete. Thereby, the goal of this thesis was to enumerate, using next generation sequencing (NGS) approaches, the genomic landscape of FL, modes of clonal evolution and intra-tumour heterogeneity by undertaking multi-site (spatial) and multi-time point (temporal) genetic profiling. Discovery exome or genome sequencing followed by targeted sequencing in over 130 FL patients demonstrated that epigenetic deregulation is critical for this malignancy with almost every tumour carrying at least one mutation in genes involved in epigenetic control (‘epimutations’). Other biological pathways were also frequently altered including genes involved in B-cell development, chromatin remodelling, immune modulation, JAK-STAT and NF-ĸB signalling, overlapping with the genomic landscape of closely-related diffuse large B cell lymphoma. Previously unreported mutations in components of the amino-acid sensing arm of the mTOR pathway (RRAGC, ATP6V1B2 and ATP6AP1) were identified in >25% of FL patients indicating a role for mTOR-driven metabolic and signalling processes in lymphomagenesis. Tumour evolution was not linear, but rather arose divergently through an ancestral population referred to as the common progenitor cell (CPC) that acts as a reservoir that repopulates the tumour during successive disease events. Additionally, clonality assessment together with temporal profiling of both transformed and untransformed FL cohorts revealed mutations in epigenetic regulators, CREBBP and KMT2D, as early initiating events whilst genes involved in cell cycle regulation and NF-ĸB signalling were predominantly late relapse- or transformation-specific events. Spatial and temporal profiling demonstrate diverse intra-tumour heterogeneity cautioning against an over-reliance on a patient’s single diagnostic biopsy to capture the entire genetic landscape of an individual’s FL tumour. Collectively these data provide new insights into the genetic basis of FL that could be used to spur the development of precision or stratified-based therapeutic approaches.