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Circle-seq revealing eccDNA profiling of human bone marrow mesenchymal stem cells

ABSTRACT: Circle-seq revealing eccDNA profiling of human bone marrow mesenchymal stem cells

PROVIDER: PRJNA1089213 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR28380881_1.fastq.gz	Fastqsanger.gz
	SRR28380881_2.fastq.gz	Fastqsanger.gz
	SRR28380882_1.fastq.gz	Fastqsanger.gz
	SRR28380882_2.fastq.gz	Fastqsanger.gz
	SRR28380883_1.fastq.gz	Fastqsanger.gz

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Circle-seq revealing eccDNA profiling of human bone marrow mesenchymal stem cells

Project description:Extrachromosomal circular DNAs (eccDNAs) have been discovered in various species and play a significant role in cancer development However, our understanding of eccDNAs in normal cells is limited. Here, we conducted eccDNA sequencing by Circle-seq in undifferentiated human bone marrow mesenchymal stem cells (uhBMSCs) and their differentiation into osteoblasts (OBs), chondrocytes (CCs), and adipocytes (ACs) to gain knowledge about eccDNAs in cell differentiation,

2025-01-31 | GSE261856 | GEO

The Urinary eccDNA Landscape in Prostate Cancer Reveals Associations with Genome Instability and Vital Roles in Cancer Progression [Circle-Seq]

Project description:Introduction: Extrachromosomal circular DNA (eccDNA) plays significant roles in cancer progression and prognosis. However, it remains unclear whether cell-free eccDNA, considered more stable than linear DNA, possesses cancer-specific genomic features. Furthermore, the biogenesis and function of eccDNAs are not yet fully understood. Objectives: This study aims to characterize the genomic landscape of urinary cell-free eccDNAs in prostate cancer (PCa) and non-cancer (NC) individuals, elucidate their biogenesis and PCa-specific genomic features, and investigate their roles in PCa progression. Methods: We conducted urine Circle-seq for 21 PCa patients and 16 NC individuals, performed integrated analysis with other omics datasets, and finally validated the function of eccDNA by in vitro transfection and RNA-seq. Results: We pioneered the profiling of urinary cell-free eccDNAs landscape in PCa and uncovered a high association between eccDNA generation and active chromatin status as well as gene transcription. Double strand breaks and R-loops, which preferentially occur in active genomic sites and cause genome instability, can promote eccDNA generation. Genome instability frequently results in genomic mutations, and our study further established a link between eccDNA generation and oncogenic mutations. Additionally, genes specifically exhibiting high eccDNA generation frequency (HFGs) in PCa contributed to PCa progression and were associated with poorer survival outcomes in PCa patients. Finally, we demonstrated that eccDNAs derived from PCa-specific HFGs, in contrast to intergenic eccDNAs, could suppress PCa cell proliferation and migration, which was independent of their host gene expression. Conclusion: Our study illustrated the biogenesis of eccDNAs from DSBs in active genes, revealed PCa-specific eccDNA features and suggested new mechanisms underlying eccDNA function.

2025-05-01 | GSE292750 | GEO

Extrachromosomal circular SUZ12 amplicon dictates retinoblastoma progression through reprogramming H3K27 methylation [eccDNA-seq]

Project description:Extrachromosomal circular DNA (eccDNA) is double-stranded circular DNA that is derived from but independent of chromosomal DNA. Owing to its nonchromosomal inheritance, eccDNA facilitates the amplification of oncogenes and expedites the process of genome evolution in tumor. However, the role of eccDNA in RB remains enigmatic. We combined Circle-Seq and RNA-Seq to identified crucial extrachromosomal circular oncogene amplicons. Herein, we revealed that extrachromosomal circular SUZ12 amplicon regulates H3K27me3 modification during the oncogenic progression of retinoblastoma. Conclusively, our study initially delineated an integrated picture of the eccDNA landscape in retinoblastoma and unveiled a novel SUZ12-containing eccDNA/H3K27me3 oncogenic mechanism where eccDNA dictates retinoblastoma progression through regulating transcription levels of linear DNA.

2023-07-02 | GSE235888 | GEO

Circle-seq reveals that eccDNA may be a key blood biomarker for HBV-associated liver cancer (4)

Project description:To explore the expression of eccDNA in patients with liver cirrhosis and liver cancer, focusing on their impact on disease development.

2025-01-29 | GSE271574 | GEO

Circle-seq reveals that eccDNA may be a key blood biomarker for HBV-associated liver cancer (2)

Project description:To explore the expression of eccDNA in patients with chronic hepatitis B and liver cirrhosis, focusing on their impact on disease development.

2025-01-29 | GSE271570 | GEO

Whole-genome sequencing of Extrachromosomal circular DNA (eccDNA) of cerebrospinal fluid of Medulloblastoma

Project description:Background: Medulloblastoma (MB) is one of the malignant tumors of the central nervous system (CNS) with a poor prognosis and lack of effective detection. Extrachromosomal circular DNA (eccDNA) has been reported to be closely related to CNS tumors. However, there is still a gap in eccDNA of MB.Methods: Genomic features of eccDNAs were identified in MB tissues and matched cerebrospinal fluid (CSF) using a circle-map, compared with normal. The nucleotides on both sides of the eccDNAs breakpoint were analyzed to investigate the mechanisms of eccDNAs formation. Bioinformatics analysis combined with the GEO database identified reliable features of eccDNA-related genes in MB. Lasso Cox regression model, univariate and multivariate Cox regression analysis, time-dependent ROC, and Kaplan–Meier curve were used to assess the potential diagnostic and prognostic value of the Hub genes.Results: 35179 eccDNAs were identified, with the majority less than 1000 base pairs (bp). The distribution of eccDNAs on the genome was closely related to gene density. EccDNAs in CSF exhibited phase parallelism with matched MB tissues and were shown differently in tumors and normal. Ten core genes were identified in combination with GEO and showed reliable diagnostic and prognostic value in independent datasets through univariate and multivariate Cox regression. Nomogram included Hub-gene signatures was established and showed clinical benefit.Conclusions: This study described the characteristics and formation mechanism of eccDNAs in MB and CSF. The role of eccDNA in MB was revealed, and eccDNA-associated hub genes in CSF could be used as diagnostic and prognostic biomarkers for MB.

2022-10-20 | GSE205178 | GEO

The Urinary eccDNA Landscape in Prostate Cancer Reveals Associations with Genome Instability and Vital Roles in Cancer Progression [R-loop CUT&Tag]

2025-05-01 | GSE292749 | GEO

Circle-seq reveals that eccDNA may be a key blood biomarker for HBV-associated liver cancer (2)

Project description:Circle-seq reveals that eccDNA may be a key blood biomarker for HBV-associated liver cancer (2)

| PRJNA1132231 | ENA

Circle-seq reveals that eccDNA may be a key blood biomarker for HBV-associated liver cancer (4)

Project description:Circle-seq reveals that eccDNA may be a key blood biomarker for HBV-associated liver cancer (4)

| PRJNA1132236 | ENA

eccDNA in maternal plasma

Project description:We developed a new bioinformatics method for detecting the eccDNA in plasma. We revealed that the biological properties between eccDNA and linear DNA are different. eccDNA could be potentially provided as a new class of circulating biomarker.

| EGAS00001003827 | EGA

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