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Expression changes of ecDNA in colorectal epithelium-adenoma-adenocarcinoma evolution (eccDNA)

ABSTRACT: Expression changes of ecDNA in colorectal epithelium-adenoma-adenocarcinoma evolution (eccDNA)

PROVIDER: PRJNA941311 | ENA |

REPOSITORIES: ENA

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Expression changes of ecDNA in colorectal epithelium-adenoma-adenocarcinoma evolution (eccDNA)

Project description:We collected 5 normal colon tissues, 5 colorectal adenomas, and 5 colorectal cancer tissues for high-throughput sequencing， Identify differential expression changes in ecDNA during disease progression

2024-11-27 | GSE226738 | GEO

Expression changes of ecDNA in colorectal epithelium-adenoma-adenocarcinoma evolution

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Expression changes of ecDNA in colorectal epithelium-adenoma-adenocarcinoma evolution

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-11-27 | GSE226741 | GEO

Expression changes of ecDNA in colorectal epithelium-adenoma-adenocarcinoma evolution (mRNA)

Project description:We collected 5 normal colon tissues, 5 colorectal adenomas, and 5 colorectal cancer tissues for high-throughput sequencing. Identify differential expression changes in mRNA during disease progression

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Proteome profiling of normal epithelium, tubular adenoma, tubulovillous adenoma, high-grade neoplasia, cancer tissues in colorectum

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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.

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ecDNA

Project description:ecDNA Kelly and plasmid samples

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ecDNA hubs drive cooperative intermolecular oncogene expression [HiChIP]

Project description:Extrachromosomal DNA (ecDNA) is prevalent in human cancers and mediates high oncogene expression through gene amplification and altered gene regulation. Gene induction typically involves cis regulatory elements that contact and activate genes on the same chromosome. Here we show that ecDNA hubs, clusters of ~10-100 ecDNAs within the nucleus, enable intermolecular enhancer-gene interactions to promote oncogene overexpression in trans. ecDNAs encoding multiple distinct oncogenes form hubs in diverse cancer cell types and primary tumors. Each ecDNA is more likely to transcribe the oncogene when spatially clustered with additional ecDNAs. ecDNA hubs are tethered by the BET protein BRD4 in a MYC-amplified colorectal cancer cell line. BET inhibitor JQ1 disperses ecDNA hubs and preferentially inhibits ecDNA-based oncogene transcription. A BRD4-bound promoter in PVT1 is ectopically fused to MYC and duplicated in ecDNA, receiving promiscuous enhancer input to drive potent MYC expression. PVT1 promoter on a heterologous episome suffices to mediate gene activation in trans by ecDNA hubs in a JQ1-sensitive manner. Systematic CRISPRi silencing of ecDNA enhancers reveal intermolecular enhancer-gene activation among multiple oncogene loci amplified on distinct ecDNAs. Together, these results demonstrate that ecDNA hubs are protein-tethered clusters of ecDNAs which enable intermolecular transcriptional regulation. ecDNA hubs may act as units of oncogene function, cooperative evolution, and potential targets for cancer therapy.

2020-11-25 | GSE159985 | GEO

ecDNA hubs drive cooperative intermolecular oncogene expression [ChIP]

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