Extrachromosomal oncogene amplification in tumour pathogenesis and evolution

Abstract

Recent reports have demonstrated that oncogene amplification on extrachromosomal DNA (ecDNA) is a frequent event in cancer, providing new momentum to explore a phenomenon first discovered several decades ago. The direct consequence of ecDNA gains in these cases is an increase in DNA copy number of the oncogenes residing on the extrachromosomal element. A secondary effect, perhaps even more important, is that the unequal segregation of ecDNA from a parental tumour cell to offspring cells rapidly increases tumour heterogeneity, thus providing the tumour with an additional array of responses to microenvironment-induced and therapy-induced stress factors and perhaps providing an evolutionary advantage. This Perspectives article discusses the current knowledge and potential implications of oncogene amplification on ecDNA in cancer.

Figure 1.. Reconstructing the Architecture of ecDNA using short-read sequencing data.

Directed assembly techniques have been developed to reconstruct the architecture of ecDNA. Short-read sequences acquired from ecDNA containing samples are mapped back to a reference genome. The copy number of the reads mapping to ecDNA segments (colored boxes) is proportional to the average number of ecDNA copies per cell, and reveals itself as copy number amplification in the mappings. Reads that span junctions of adjoining segments map back to the reference in a split fashion, revealing breakpoints. These mapping signatures of ecDNA derived complex rearrangements cannot be easily distinguished from chromosomal structural variants, posibly leading to an undercounting of ecDNA. ecDNA reconstruction algorithms explore amplicon graphs where nodes correspond to amplified segments, and edges correspond to breakpoints. Cyclic paths reconstructed by traversing the graph are indicative of ecDNA (Deshpande). Note also that if ecDNA contains large, repeated segments, long reads may be required for unambiguous reconstruction. Improvements in genomic and computational technologies will enhance ecDNA discovery.

Figure 2.. Inheritance of chromosomal versus extrachromosomal DNA.

(Left panel) During mitosis, chromosomal DNA is evenly split between two daughter cells. (Right panel) Extrachromosomal DNA lacks centromeres and possibly segregates unevenly. As a result, the number of options for distribution of ecDNA between daughter cells equals n+1, where n is the number of ecDNA elements in the parental cell.

Figure 3.. Sequence of ecDNA formation and propagation in tumors.

1. Genomic instability causes chromosomal breakage; 2. DNA segments form circular DNA structures through non-homologous recombination. 3. ecDNA elements, lacking centromeres, inherit unevenly from parental to daughter cells. 4. Following the formation of an ecDNA element, cells harboring the ecDNA element (marked in red) are afforded a competitive advantage through the expression of the oncogene contained on the ecDNA. This selection coefficient correlates proportionally with the number of ecDNA elements., resulting in rapid selection of ecDNA-positive cancer cells through increased proliferation rates.