A Distinct Mode of Chromosome-End Genome Instability Revealed by Circulome Characterization and Analyses

Abstract

Genome instability is a central hallmark of cancer and it is characterized largely from sequence: mutation, copy-number change and rearrangement scored against a linear reference. The genome has additional degrees of freedom, such as the physical form (topology) of the DNA itself. A specific mode of localized genome dynamics changes both dimensions (sequence and topology) at once: defined chromosomal regions are also represented as extrachromosomal circular DNA (eccDNA). The biogenesis of eccDNA is a feature of many cancers, supplying the tumor with genetic elements that can participate in phenotypic selection, and supplying the observer with a window into the genomic instability landscape. Genome-wide maps of where these circles arise have not been available at scale or at high resolution. Building such maps requires physical selection of circular species, because most sequenced reads from unselected DNA derive from unrearranged sequence, conflating the signal from dynamic rearrangements with that from bulk chromosomal DNA. Here we combine biophysical and biochemical isolation of circular DNA with next-generation sequencing, applying it to a panel of cancer cell lines and to patient tumors, with non-cancerous cells and adjacent normal tissues as controls. The resulting genome-wide maps of the circular-element repertoire, the Circulome, reveal a consistent and previously unreported enrichment of these elements at particular chromosome ends. The circles map to regions extending well past the telomeres, reaching varying distances up to tens of megabases inward. This activity is accompanied by corroborating rearrangements within the linear genome, consistent with regions of chromosomal instability. Together these features define a spatially localized mode of instability in cancer, which we term Erosion at Distal Genomic Ends (EDGE). We formulate a classification problem to discriminate bladder tumor from matched normal tissue, finding that the EDGE signal outperforms the mean of all interior chromosomal regions, for each chromosome. These findings define a distinct spatial signature of cancer chromosome instability detectable through Circulome analysis, and connect early models of region-specific instability to the human cancer genome.