Innovative insights into extrachromosomal circular DNAs in gynecologic tumors and reproduction

Originating but free from chromosomal DNA, extrachromosomal circular DNAs (eccDNAs) are organized in circular form and have long been found in unicellular and multicellular eukaryotes. Their biogenesis and function are poorly understood as they are characterized by sequence homology with linear DNA, for which few detection methods are available. Recent advances in high-throughput sequencing technologies have revealed that eccDNAs play crucial roles in tumor formation, evolution, and drug resistance as well as aging, genomic diversity, and other biological processes, bringing it back to the research hotspot. Several mechanisms of eccDNA formation have been proposed, including the breakage-fusion-bridge (BFB) and translocation-deletion-amplification models. Gynecologic tumors and disorders of embryonic and fetal development are major threats to human reproductive health. The roles of eccDNAs in these pathological processes have been partially elucidated since the first discovery of eccDNA in pig sperm and the double minutes in ovarian cancer ascites. The present review summarized the research history, biogenesis, and currently available detection and analytical methods for eccDNAs and clarified their functions in gynecologic tumors and reproduction. We also proposed the application of eccDNAs as drug targets and liquid biopsy markers for prenatal diagnosis and the early detection, prognosis, and treatment of gynecologic tumors. This review lays theoretical foundations for future investigations into the complex regulatory networks of eccDNAs in vital physiological and pathological processes.

Origin of Extrachromosomal DNA and its Influence on Tumor Development / 中国生物化学与分子生物学报

Extrachromosomal DNA (ecDNA) is a class of circular DNA that is found off the chromosomes, either inside or outside the nucleus. ecDNA is abundant in cancer, and plays an important role during the tumor development. ecDNA contains multiple complete genes and regulatory elements that regulate transcription, including promoters and enhancers. It can replicate independently. However, the origin and mechanism of ecDNA is still unknown. Most scholars believe that DNA damage can elicit ecDNA production. The chromosomal fragments produced by DNA double-strand breaks are rearranged and circularized to form ecDNA via the non-homologous end-joining repair way. The chromatin on ecDNA is highly accessible and active. It works with oncogenes and co-amplify with enhancers to promote the transcription of oncogenes. Additionally, there are ultra-long-range chromatin contacts on ecDNA, which increases distant interaction. These features amplify the transcription of oncogenes and promote the development of tumors. Due to lack of centromeres, ecDNA has a non-equal segregation to daughter cells. Daughter cells, containing different copy numbers of ecDNA, can rapidly increase oncogene copy numbers, which drives the genome heterogeneity of the tumors. ecDNA-driven copy number regulation leads drug resistance and enables tumors to adapt quickly to the environment. Here we review the classification, origin of ecDNA and its role in tumorigenesis and development. We discuss the mechanisms of ecDNA promoting the transcription of oncogenes and leading to heterogeneity and drug resistance, aiming to provide new ideas on the diagnosis, treatment, and prognosis of tumors.

Amplification of Extrachromosomal Oncogene and Tumorigenesis and Development / 中国肺癌杂志

Extrachromosomal DNA (ecDNA) is a small segment of circular DNA located outside the chromosome, which has the function of self-replication. Recently, amplification of oncogenes on ecDNA has been proved to be a common phenomenon in tumor cells, and has some characteristics worth studying, such as correlation with patients' poor prognosis. Multiple chromosomal events are involved in the formation of ecDNA, and its amplification can directly increase the number of DNA copies of extra-chromosomal oncogenes and accelerate the generation and development of tumors. Moreover, the segregation pattern of unequal transmission of parental ecDNA cells to offspring not only increases tumor heterogeneity, but also enhances tumor adaptation to environment and response to therapy. This article reviews the current status and potential significance of ecDNA in tumor cells.
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DNA sequences homologous to hepatitis C virus (HCV) in the extrachromosomal circular DNA in peripheral blood mononuclear cells of HCV-negative subjects / 浙江大学学报（英文版）（B辑：生物医学和生物技术）

OBJECTIVE@#This study aimed to investigate DNA sequences that are substantially homologous to the corresponding RNA sequence sections of the hepatitis C virus (HCV). These DNA sequences are present in the whole DNA extracted from peripheral blood mononuclear cells (PBMCs) of HCV-negative subjects. We presumed that these experimentally proven 5'-noncoding region (5'-NCR) homologous DNA sequences could be contained in the extrachromosomal circular DNA (eccDNA) fraction as part of the whole cellular DNA.@*METHODS@#Home-made polymerase chain reaction (PCR) with whole cellular and isolated eccDNA, nucleotide basic local alignment search tool (BLASTn) alignments, and tests for patterns of methylation in selected sequence sections were performed.@*RESULTS@#The PCR tests revealed DNA sequences of up to 320 bp that broadly matched the corresponding sequence sections of known HCV genotypes. In contrast, BLASTn alignment searches of published HCV 5'-NCR sequences with human genome databases revealed only sequence segments of up to 36 bp of the 5'-NCR. The composition of these sequences shows missing base pairs, base pair mismatches as well as complete homology with HCV reference sequences. These short sequence sections are present in numerous copies on both the same and different chromosomes. The selected sequence region within the DNA sequences of the 5'-NCR revealed a broad diversity of individual patterns of methylation.@*CONCLUSIONS@#The experimental results confirm our assumption that parts of the HCV 5'-NCR genomic RNA sequences are present at the DNA level in the eccDNA fraction of PBMCs. The tests for methylation patterns therein revealed individual methylomes which could represent an epigenetic feature. The respective sequence section might be subject to genetic regulation.

DNA sequences homologous to hepatitis C virus (HCV) in the extrachromosomal circular DNA in peripheral blood mononuclear cells of HCV-negative subjects / 浙江大学学报（英文版）（B辑：生物医学和生物技术）

Objective: This study aimed to investigate DNA sequences that are substantially homologous to the corresponding RNA sequence sections of the hepatitis C virus (HCV). These DNA sequences are present in the whole DNA extracted from peripheral blood mononuclear cells (PBMCs) of HCV-negative subjects. We presumed that these experimentally proven 5′-noncoding region (5′-NCR) homologous DNA sequences could be contained in the extrachromosomal circular DNA (eccDNA) fraction as part of the whole cellular DNA. Methods: Home-made polymerase chain reaction (PCR) with whole cellular and isolated eccDNA, nucleotide basic local alignment search tool (BLASTn) alignments, and tests for patterns of methylation in selected sequence sections were performed. Results: The PCR tests revealed DNA sequences of up to 320 bp that broadly matched the corresponding sequence sections of known HCV genotypes. In contrast, BLASTn alignment searches of published HCV 5′-NCR sequences with human genome databases revealed only sequence segments of up to 36 bp of the 5′-NCR. The composition of these sequences shows missing base pairs, base pair mismatches as well as complete homology with HCV reference sequences. These short sequence sections are present in numerous copies on both the same and different chromosomes. The selected sequence region within the DNA sequences of the 5′-NCR revealed a broad diversity of individual patterns of methylation. Conclusions: The experimental results confirm our assumption that parts of the HCV 5′-NCR genomic RNA sequences are present at the DNA level in the eccDNA fraction of PBMCs. The tests for methylation patterns therein revealed individual methylomes which could represent an epigenetic feature. The respective sequence section might be subject to genetic regulation.

Overlooked: Extrachromosomal DNA and Their Possible Impact on Whole Genome Sequencing

Extrachromosomal (ec) DNA in eukaryotic cells has been known for decades. Thestructures described range from linear double stranded (ds) DNA to circular dsDNA, distinct frommitochondrial (mt) DNA. The sizes of circular forms are described from some hundred base pairs(bp) up to more than 150 kbp. The number of molecules per cell ranges from several hundred to athousand. Semi-quantitative determinations of circular dsDNA show proportions as high as severalpercentages of the total DNA per cell. These ecDNA fractions harbor sequences that are known tobe present in chromosomal DNA (chrDNA) too. Sequencing projects on, for example the humangenome, have to take into account the ecDNA sequences which are simultaneously ascertained;corrections cannot be performed retrospectively. Concerning the results of sequencings derivedfrom extracted whole DNA: if the ecDNA fractions contained therein are not taken into account,erroneous conclusions at the chromosomal level may result.

Characterization of a small endogenous plasmid from the Cyanobacterium Plectonema boryanum.

The nonheterocystous filamentous Cyanobacterium Plectonema boryanum strain UTEX 594 contains at least two plasmids. A small 1·45 kb plasmid was cloned in pBR322. It has no homology with the bigger resident plasmid or with chromosomal DNA. A small fraction of the plasmid is present in the form of multimers or concatemers. Copy number and hybridization patterns of the plasmid were similar under dinitrogen-fixing and nonfixing conditions. Restriction site mapping of the plasmid was done to enable its use in the development of cyanobacterial cloning vectors. It is among the smallest natural plasmids reported from bacteria.