Introducing Extrachromosomal DNA (ecDNA)

What is the Extrachromosomal DNA (ecDNA)?

Extrachromosomal DNA (ecDNA) is a type of circular DNA element present in the genome of cancer cells. Unlike the chromosomal inheritance mechanism in normal cells, ecDNA typically contains highly expressed enhancers and driver oncogenes. The circular topology of ecDNA leads to open chromatin conformation, generating novel gene regulatory interactions, including interactions with distal enhancers. Due to the lack of centromeres, ecDNA is randomly distributed during cell division and genes are transmitted in a non-Mendelian manner. Additionally, ecDNA can integrate into or exit from chromosomal DNA. Therapies may lead to changes in the specific quantity of ecDNA. In conclusion, ecDNA is a common circular DNA element found in cancer cells, and its presence is closely associated with phenomena such as tumor heterogeneity, cancer genome reshaping, and drug resistance. Based on their sizes, ecDNA can be classified into three categories:

• Small ecDNA: with molecular sizes of several hundred base pairs, also known as microDNA/eccDNA/spcDNA (small polydisperse circular DNA);
• Large ecDNA: with molecular sizes ranging from several hundred kilobases to megabases, also known as ecDNA/DM;
• Intermediate-sized molecules between small ecDNA and large ecDNA, also known as ring/neo chromosomes.

The fate of ecDNA. (Lauren, T. P.; et al, 2022)

* Related services from BOC RNA.

Formation and Distribution of ecDNA

ecDNA is formed primarily through the following four mechanisms:

• Breakage-Fusion-Bridge (BFB) Cycle: The BFB cycle starts with telomere loss, leading to chromosomal breakage and fusion. This occurs during the pre-mitotic DNA replication phase, resulting in two chromatid chromosomes.
• Chromosomal Translocation-Deletion-Amplification: Gene rearrangements occur near chromosomal translocation breakpoints, where segments close to the translocation breakpoints are amplified, deleted, and looped, leading to the formation of ecDNA.
• Extrachromosomal Elements: Extrachromosomal elements originate from excised small circular DNA. They can gradually expand to form ecDNA through over-replication or recombination.
• Chromosomal Fragmentation: Chromosomal fragmentation can produce multiple DNA fragments lacking centromeres, some of which can self-ligate into circular DNA structures. Due to the lack of centromeres, ecDNA is randomly and unevenly distributed to daughter cells during mitosis.

These mechanisms contribute to the formation and distribution of ecDNA, which plays a significant role in genomic instability and cancer progression.

Characteristics of ecDNA

Main Carrier of Oncogene Amplification

In tumor cells, ecDNA is considered one of the main carriers of oncogene amplification. Compared to conventional chromosomes, the presence of ecDNA provides additional opportunities for the amplification of oncogenes. This extra gene copy can lead to the overexpression of oncogenes, thereby promoting the growth and proliferation of tumor cells. Furthermore, the circular structure of ecDNA makes it easier to replicate and pass on to the cell's offspring, which helps maintain the stability of oncogene amplification.

High Transcriptional Activity

Oncogenes on ecDNA typically exhibit higher transcriptional activity compared to those on chromosomes. This may be due to the unique structure and organization of ecDNA, which allows regulatory elements associated with oncogenes to be more accessible, thereby facilitating transcription. Additionally, there may be central structures within ecDNA that form transcriptional interaction networks, further enhancing the transcriptional activity of oncogenes.

Remodeling of Regulatory Networks

The presence of ecDNA can remodel the gene regulatory networks within cells. It may establish new regulatory pathways by forming physical contacts with DNA on chromosomes, enabling previously suppressed enhancers to more effectively regulate oncogenes. This remodeling of regulatory networks may be an important mechanism for tumor cells to rapidly adapt to environmental changes and develop drug resistance.

Promotion of Transcription by ecDNA Hubs

In certain cases, ecDNA may aggregate to form hub-like structures containing numerous ecDNA molecules. These hub structures exhibit higher transcriptional activity, possibly due to close interactions among multiple ecDNA molecules within them. This interaction may contribute to enhanced transcription of oncogenes, further driving the growth and development of tumors.

Function as Mobile Enhancers

As a freely moving circular molecule, ecDNA may have a broader range of mobility compared to DNA on chromosomes, making it easier to physically interact with genes on other chromosomes. This mobility allows ecDNA to function as mobile enhancers, influencing the regulation of genes located on different chromosomes. This characteristic may assist tumor cells in adapting to diverse microenvironments and adjusting gene expression to promote their survival and proliferation.

The Role of ecDNA in Cancer

ecDNA plays a significant role in cancer pathogenesis, contributing to adverse outcomes across various cancer types. Unlike chromosomal inheritance, ecDNA operates through non-chromosomal mechanisms, facilitating high oncogene copy numbers and rapid tumor evolution. This distinct genetic mechanism allows ecDNA to regulate its copy number within cancer cell nuclei, resulting in treatment resistance and reduced patient survival. The swift evolution of ecDNA-driven tumors cannot be solely explained by chromosomal inheritance principles. Random ecDNA inheritance during cell division leads to extensive heterogeneity in ecDNA copy numbers within tumors, enabling cancer cells to adapt rapidly to metabolic stress and targeted therapy by adjusting copy numbers. These traits explain why tumor cells harboring ecDNA can resist targeted therapy or metabolic stress. Mechanisms of ecDNA formation in cancer are complex, including excision models originating from chromosomal breaks and circularization of excised fragments, as well as chromosomal aberrations. Although the direct link between processes like BFB cycles and translocation bridge amplification and ecDNA formation remains unclear, ecDNA persists through active replication, positive selection for adaptive traits, and association with mitotic chromosomes during division. It can also reintegrate into chromosomes, forming homogeneously staining regions (HSRs), or be eliminated via cellular clearance or micronucleus formation.

ecDNA Drives Amplification of Oncogenes

In human tumor cells, ecDNA can drive the amplification of oncogenes, resulting in high levels of oncogene products. ecDNA effectively enhances the amplification efficiency and expression levels of genes, and ecDNA is randomly distributed during mitosis, allowing oncogenes to flow between tumor cells. Additionally, the quantity of ecDNA can change with alterations in environmental conditions.

ecDNA is Associated with Tumor Drug Resistance

ecDNA is associated with drug resistance. The role and mechanism of ecDNA depend on the gene content and structure of the elements it contains. ecDNA provides genetic plasticity and heterogeneity driven by additional chromosomes. For example, in glioblastomas, particularly oncogenes and drug resistance genes such as EGFR, the quantity of ecDNA changes dynamically at different stages of cell division. This continuous amplification of drug-resistant genes by ecDNA is closely related to tumor resistance.

ecDNA Promotes Cellular Malignancy

Previous studies have shown that ecDNA structures are widespread in human cancers, especially in advanced tumors, but are rarely found in healthy cells. However, recent research has discovered that ecDNA can even appear in pre-cancerous cells, where their presence initiates cellular malignancy. ecDNA can promote cancer development through several mechanisms, elucidating how ecDNA appears before cancer fully develops, indicating that ecDNA is not just a late manifestation of genomic instability. This suggests that tumors may exhibit varying degrees of ecDNA heterogeneity in the early stages. This heterogeneity helps pre-cancerous cells or tumor cells adapt to constantly changing survival conditions, promoting the branching out of tumors during evolution.

Reference

1. Lauren, T. P.; et al. Extrachromosomal DNA (ecDNA): An Origin of Tumor Heterogeneity, Genomic Remodeling, and Drug Resistance. Biochemical Society Transactions. 2022, 50(6): 1911-1920.

Introducing Extrachromosomal DNA (ecDNA)

- mg g kg ton

We recommend you to leave us your work email address so that we can serve you better. Please leave your organization information here if you don't have a work email address.

SUBMIT