Follicular lymphoma (FL) is an incurable malignancy1, with transformation to an aggressive subtype being a critical event during disease progression. Here we performed whole genome or exome sequencing on 10 FL-transformed FL pairs, followed by deep sequencing of 28 genes in an extension cohort and report the key events and evolutionary processes governing initiation and transformation. Tumor evolution occurred through either a ‘rich’ or ‘sparse’ ancestral common progenitor clone (CPC). We identified recurrent mutations in linker histones, JAK-STAT signaling, NF-κB signaling and B-cell development genes. Longitudinal analyses revealed chromatin regulators (CREBBP, EZH2 and MLL2) as early driver genes, whilst mutations in EBF1 and regulators of NF-κB signaling (MYD88 and TNFAIP3) were gained at transformation. Collectively, this study provides novel insights into the genetic basis of follicular lymphoma, the clonal dynamics of transformation and suggests that personalizing therapies to target key genetic alterations within the CPC represents an attractive therapeutic strategy.

The DNA damage response (DDR) arrests cell-cycle progression until damage is removed. DNA damage-induced cellular senescence is associated with persistent DDR. The molecular bases that distinguish transient from persistent DDR are unknown. Here we show that a large fraction of exogenously-induced persistent DDR markers are associated with telomeric DNA in cultured cells and mammalian tissues. In yeast, a chromosomal DNA double-strand break (DSB) next to telomeric sequences resists repair and impairs DNA ligase 4 recruitment. In mammalian cells, ectopic localization of telomeric factor TRF2 next to a DSB induces persistent DNA damage and DDR. Linear telomeric DNA, but not circular or scrambled DNA, induces a prolonged checkpoint in normal cells. In terminally-differentiated tissues of old primates, DDR markers accumulate at telomeres which are not critically short. We propose that linear genomes are not uniformly reparable and telomeric DNA tracts, if damaged, are irreparable and trigger persistent DDR and cellular senescence.

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