Extrachromosomal DNA: An Emerging Hallmark in Human Cancer

Abstract

Human genes are arranged on 23 pairs of chromosomes, but in cancer, tumor-promoting genes and regulatory elements can free themselves from chromosomes and relocate to circular, extrachromosomal pieces of DNA (ecDNA). ecDNA, because of its nonchromosomal inheritance, drives high-copy-number oncogene amplification and enables tumors to evolve their genomes rapidly. Furthermore, the circular ecDNA architecture fundamentally alters gene regulation and transcription, and the higher-order organization of ecDNA contributes to tumor pathogenesis. Consequently, patients whose cancers harbor ecDNA have significantly shorter survival. Although ecDNA was first observed more than 50 years ago, its critical importance has only recently come to light. In this review, we discuss the current state of understanding of how ecDNAs form and function as well as how they contribute to drug resistance and accelerated cancer evolution.

Keywords: cancer genomics; ecDNA; extrachromosomal DNA; gene amplification; non-Mendelian inheritance; tumor evolution.

Conflict of interest statement

DISCLOSURE STATEMENT

V.B. is a cofounder, consultant, and Scientific Advisory Board member of and has equity interest in Boundless Bio, Inc. (BB) and Abterra Bio, Inc. The terms of this arrangement have been reviewed and approved by the University of California, San Diego, in accordance with its conflict-of-interest policies. H.Y.C. is a cofounder of Accent Therapeutics and BB and an advisor for 10× Genomics, Arsenal Biosciences, and Spring Discovery. P.S.M. is a cofounder of BB. He has equity in the company and serves as the chair of its Scientific Advisory Board, for which he is compensated.

Figures

Figure 1

A circular map of circular extrachromosomal DNA (ecDNA). Current evidence unequivocally shows that ecDNA is circular. However, traditional genome browsers still use linear maps, which cannot show the true nature of ecDNA. (a) For ecDNA with a simple structure (e.g., EGFR ecDNA in GBM39 cells), a linear map may still be useful. (b) However, ecDNA with complicated rearrangements (e.g., MYC ecDNA in COLO320DM cells) is difficult to visualize with a linear map, while a circular map helps disambiguate the orders and orientations of rearranged genomic segments, including material that is duplicated within an ecDNA. Abbreviation: FISH, fluorescence in situ hybridization. Linear and circular maps were created on the basis of publicly deposited whole-genome sequencing data (27).

Figure 2

Extrachromosomal DNA (ecDNA) acts in cis and in trans. (a) ecDNA is a vector of enhancer hijacking. By incorporating an enhancer from an adjacent topologically associating domain into a circle, or from a distal region such as a different chromosome by chimeric circularization, the oncogene encoded on ecDNA can access a variety of enhancers through cis-interactions that are not possible in chromosomes. (b) ecDNA can act in trans with other DNA, including ecDNA–chromosomal DNA interaction and ecDNA–ecDNA interaction.

Figure 3

Unequal segregation of extrachromosomal DNA (ecDNA) drives rapid tumor evolution. Acentric ecDNA segregates unequally to two daughter cells during cell division. Therefore, each cell division generates genetic heterogeneity in the cancer population, allowing a portion of cancer cells to gain oncogene copy number rapidly. Furthermore, this process creates a pool of genetically heterogeneous cancer cells for microenvironmental selection, increasing cancer fitness and promoting rapid cancer evolution.

Figure 4

Potential pathogenesis pathways of extrachromosomal DNA (ecDNA). (a) Religation of shattered DNA segments from chromothripsis can form ecDNA. (b) Two DNA double-strand breaks in one arm of a chromosome can create ecDNA by religation of the excised segment, leaving a scarred chromosome. (c) If mild DNA damage occurs between two replication foci, the chromosome may be repaired through a homologous recombination mechanism while generating an ecDNA particle. (d) Speculative model for ecDNA generation through fork stalling and template switching. In this model, a DNA lesion occurs in the template strand, stalling the lagging strand in DNA replication. The lagging strand can disengage from the current template and invade the adjacent replication fork through microhomology to continue DNA synthesis. Strand disengagement and invasion can occur over multiple rounds until the strand returns to the original template. Although the mechanism is unclear, this process may generate ecDNA through DNA repair.