Extrachromosomal circular DNA: Current status and future prospects

  1. Yiheng Zhao
  2. Linchan Yu
  3. Shuchen Zhang
  4. Xiangyu Su
  5. Xiang Zhou  Is a corresponding author
  1. Department of Cardiology, The Second Affiliated Hospital of Soochow University, China
3 figures and 1 table

Figures

Models and pathways of extrachromosomal circular DNA (eccDNA) biogenesis.

(A) Chromothripsis model. Chromothripsis causes DNA fragmentation through catastrophic chromosomal breakage. A portion of the fragments is reassembled randomly through DNA repair mechanisms, including homologous recombination and nonhomologous end-joining (NHEJ). During the repair process, eccDNAs are generated and their chromosomal segments are lost. (B) Mild DNA damage. Only one arm of a chromosome generates DNA fragment via DNA double-strand breakage, from which the putative eccDNA fragment is produced and also results in a scarred chromosome. The ligation of these DNA fragment contributes to eccDNA formation. (C) Episome model. A drop in the replication bubble can cause episome formation when errors occur in DNA replication. Episome replication or recombination leads to the formation of eccDNA. (D) Breakage–fusion–bridge (BFB) cycle. The loss of telomeres in the chromosome is the earliest event of the BFB cycle. After being replicated, the telomere-free chromosomes can fuse and form a dicentric anaphase bridge. The above cycle was repeated to prolong the telomere-free bridge, ultimately falling off and circularizing into eccDNA. (E) Translocation–excision–deletion–amplification model. When gene translocation occurs, the fragments adjacent to translocation positions can be amplified or deleted. Then eccDNA forms after the circularization of DNA fragments. (F) Fork stalling and template switching mechanism. When a DNA lesion exists following DNA bidirectional replication, the lagging strand anneals to the template strand of the adjacent replication fork through the microhomology mechanism to continue DNA synthesis. The process abovementioned may be repeated many times until the lagging strand returns to the original template.

Extrachromosomal circular DNAs (eccDNAs) are associated with multiple human systems.

Several eccDNAs have been identified in multiple human systems such as nervous system, circulatory system, digestive system, immune system, musculoskeletal system, and genitourinary system.

Future research prospects for eccDNAs.

In basic research, the biogenesis of eccDNAs remains unclear, although numerous mechanistic models have been proposed. Further studies are required to investigate the regulatory mechanisms of eccDNAs in the occurrence and development of various diseases. Because of the limited tools currently available for analyzing eccDNAs, the development of new research methods is imperative. In clinical application, eccDNAs can be used as diagnostic and prognostic biomarkers because of their stable presence in human plasma. Moreover, eccDNAs are expected to serve as therapeutic targets for treating various diseases.

Tables

Table 1
Summary of extrachromosomal circular DNAs (eccDNAs) identified in various diseases.
NameDiseaseFunctionReference
eccDNA (EGFR)GlioblastomaEndogenous enhancer elementsShiras and Mondal, 2021
ecDNA (ecEGFRx1, ecCCAT1, ecEGFR, and ecCCDC26)GlioblastomaUneven segregation of ecDNA during mitosisYi et al., 2022
eccDNA (PDGFRA, CDK4)Radiation-induced high-grade gliomaeccDNA-mediated amplification of oncogenesDeSisto et al., 2021
eccDNA (TRPS1)Breast cancerTRPS1-driven genome deletionsYang et al., 2021b
ecDNA (ecMYC)Prostate cancerMobile transcriptional enhancersZhu et al., 2021
ecDNA/eccDNA (cyclin-E1, ERBB2, CDK12, EGFR, MYC)Gastric cardia adenocarcinomaFocal amplifications of oncogene prognostic molecular markersZhao et al., 2021
eccDNA (RAB3B)Hypopharyngeal squamous cell carcinomaPromote cisplatin resistanceLin et al., 2022
eccDNA (MYCN, CDK4, MDM2)NeuroblastomaSeismic amplification modelRosswog et al., 2021
eccDNA (entire genome)Immune systemTrigger immune responseWang et al., 2021
TTNcircleMusculoskeletal systemFunction of transcriptionMøller et al., 2018
MI-related eccDNA (MIRECD)Myocardial infarction (MI)MI prognosis prediction and risk stratificationNot yet published

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  1. Yiheng Zhao
  2. Linchan Yu
  3. Shuchen Zhang
  4. Xiangyu Su
  5. Xiang Zhou
(2022)
Extrachromosomal circular DNA: Current status and future prospects
eLife 11:e81412.
https://doi.org/10.7554/eLife.81412