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DNA Methylome Analysis of Human Cancer Cells with Depleted or Overexpressed STELLA Proteins [Array]

ABSTRACT: DNA Methylome Analysis of Human Cancer Cells with Depleted or Overexpressed STELLA Proteins [Array]

PROVIDER: PRJNA1073492 | ENA |

REPOSITORIES: ENA

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DNA Methylome Analysis of Human Cancer Cells with Depleted or Overexpressed STELLA Proteins [Array]

Project description:Genome-wide DNA methylation profiling of the human STELLA (hSTELLA) knockout cell clones derived from TGCT cell lines (BeWo and NCCIT). The DNA methylome profiles are also studied on the CRC cells lines (HCT116 and RKO) stably expressing hSTELLA and mouse STELLA (mSTELLA), as well as on the HCT116 cells treated by LNP-delivered mRNA encoding mSTELLA. The Infinium MethylationEPIC 850k array was used to obtain DNA methylation profiles across more than 850,000 CpGs in 26 samples. Samples included 6 cell clones derived from BeWo cells with hSTELLA knockout or sgRNA control, 5 cell clones derived from NCCIT cells with hSTELLA knockout or sgRNA control, 6 stable CRC cells expressing STELLA orthologs, and 9 LNP-mRNA treated HCT116 cells.

2024-10-25 | GSE255083 | GEO

Transcriptome Analysis of Human Cancer Cells with Depleted or Overexpressed STELLA Proteins [RNA-seq]

Project description:Transcriptome Analysis of Human Cancer Cells with Depleted or Overexpressed STELLA Proteins [RNA-seq]

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Transcriptome Analysis of Human Cancer Cells with Depleted or Overexpressed STELLA Proteins [RNA-seq]

Project description:UHRF1 maintains DNA methylation by recruiting DNA methyltransferases (DNMT’s) to chromatin. These dynamics are well defined for mouse STELLA (mSTELLA) but poorly characterized for human STELLA (hSTELLA). Herein, we demonstrate that hSTELLA is defective, while mSTELLA is fully proficient in associating with UHRF1 and inhibiting the abnormal DNA methylation and oncogenic functions of UHRF1 in human cancer cells. We illustrate, in structural studies a region of low sequence homology between the above STELLA orthologs, allows mSTELLA but not hSTELLA to bind tightly to the essential histone binding domains of UHRF1, thus mediating their above functional differences. The ortholog-specific binding modes of STELLA proteins with UHRF1 prompt us to explore a rationale for designing UHRF1 inhibitors for cancer therapy. For this, we use a lipid nanoparticle (LNP)-mediated mRNA delivery approach demonstrating the short mSTELLA, but not hSTELLA regions are required to reverse cancer-specific DNA methylation abnormalities and impair CRC tumor growth.

2024-10-25 | GSE255105 | GEO

Expression data from cell lines forced expressed PGC7/Stella

Project description:Global DNA hypomethylation and DNA hypermethylation of promoter regionsâincluding tumor suppressor genesâare frequently detected in human cancers. Although many studies have suggested a contribution to carcinogenesis, it is still unclear whether the aberrant DNA hypomethylation observed in tumors is a consequence or a cause of cancer. We found that overexpression of Stella (also known as PGC7, Dppa3), a maternal factor required for the maintenance of DNA methylation in early embryos, induced global DNA hypomethylation and transformation in NIH3T3 cells. This hypomethylation was due to the binding of Stella to Np95 (also known as Uhrf1, ICBP90) and the subsequent impairment of Dnmt1 localization. In addition, enforced expression of Stella enhanced the metastatic ability of B16 melanoma cells through the induction of metastasis-related genes by inducing DNA hypomethylation of their promoter regions. Such DNA hypomethylation itself causes cellular transformation and metastatic ability. These data provide new insight into the function of global DNA hypomethylation in carcinogenesis. We used microarrays to detail the global programme of gene expression by PGC7/Stella overexpression. RNA was extracted from NIH3T3 or B16F10 murine cell lines overexpressed PGC7/Stella and was hybridized on Affymetrix microarrays. We compared gene expression levels between control and PGC7/Stella-overexpressed cells. Microarray analysis was performed in NIH3T3 cells including two independent Stella-expressing NIH3T3 clones and a mixture of Stella-expressing NIH3T3 clones and in B16-F10 cells including three independent Stella-expressing B16-F10 clones.

2016-05-13 | E-GEOD-68837 | biostudies-arrayexpress

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Project description:Analysis of m6A methylome in CHAPIR overexpressed heart [MeRIP]

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Project description:Genome sequencing of genus Stella bacteria.

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Deep transcriptome analysis of mouse embryonic fibroblast following simultaneous overexpression of Stella, Oct4 and Nanos2 (SON)

Project description:We constructed a polycistronic lentiviral vector to overexpress 3 germ cell specific genes (Stella, Oct4 and Nanos2) in mouse embryonic fibroblast (MEFs) and evaluated the transcriptome portrait in partially reprogrammed cells.We sequenced RNA samples from bulk cell population of two biological duplicates of MEF-GFP (control) and MEF-SON (overexpressed) 21 days post infection. Differential expression analysis of 50 M pair-end read per samples showed overexpression of neurogenesis, blood vessel and proliferation related genes and downregulation of chondroitin sulphate metabolic process, nitric oxide production and innate immune response genes. Examination of whole transcriptome following concurrent overexpression of Stella, Oct4 and Nanos2 in MEFs.

2016-07-30 | E-GEOD-77351 | biostudies-arrayexpress

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Project description:Nonionella stella Raw sequence reads

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Stella prevents excessive de novo DNA methylation during mouse oogenesis

Project description:Oocyte acquires developmental competence during its maturation. This stage is accompanied with large-scale alteration in transcription, and series of genome-wide epigenetic reprogramming, including de novo establishment of DNA methylation. However, our understanding of mechanisms regulating this process is limited. To investigate the role of Stella (Dppa3) in de novo methylation during mouse oogenesis, here we measured DNA methylation by RRBS and expression profiles by RNA-seq in PGCs and oocytes at serveral development stages, including genotypes of both Stella (Dppa3) +/- and Stella -/-.

2018-09-24 | GSE78149 | GEO

Aspergillus stella-maris

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