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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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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

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

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

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

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

Bone Marrow Transplantation in Treating Patients With Hematologic Cancer

Project description:RATIONALE: Radiation therapy uses high-energy x-rays to damage cancer cells. Drugs used in chemotherapy use different ways to stop cancer cells from dividing so they stop growing or die. Combining chemotherapy with bone marrow transplantation may allow the doctor to give higher doses of chemotherapy drugs and kill more tumor cells. PURPOSE: Phase II trial to study the effectiveness of bone marrow transplantation in treating patients who have hematologic cancer.

| 2004880 | ecrin-mdr-crc

CIRCLE-seq analyais for -175 site

Project description:Adenosine base editing to recreate the HPFH mutations is a promising approach to induce HbF. We used CIRCLE-seq to identify 682 potential off-target sites in purified DNA treated with Cas9 nuclease complexed to sgRNA targeting -globin -175 .

2023-04-28 | GSE228569 | GEO

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