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Expression data from early and macroscopic HCC lesions isolated from the Rb family Triple Knock Out model (Bulk RNA-Seq)

ABSTRACT: we report the expression profiles of various liver progenitor subpopulations upon inactivation of the Rb family of genes

ORGANISM(S): Mus musculus

PROVIDER: GSE173949 | GEO | 2024/05/05

REPOSITORIES: GEO

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Expression data from early and macroscopic HCC lesions isolated from the Rb family Triple Knock Out model (scRNA-Seq)

Project description:we report the mRNA expression of single cells at two different time points of HCC development upon inactivation of Rb family. The first time point corresponds to lesions appearing in the portal triad area 9 weeks after Rb family inactivation. The second time point corresponds to macroscopic tumors, typically visible at the 20-25 weeks time point.

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Expression data from early and macroscopic HCC lesions isolated from the Rb family Triple Knock Out model (ATAC-Seq)

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Expression data from early and macroscopic HCC lesions isolated from the Rb family Triple Knock Out model

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

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Expression data from early and macroscopic HCC lesions isolated from the Rb family Triple Knock Out model

Project description:Expression data from early and macroscopic HCC lesions isolated from the Rb family Triple Knock Out model

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Rb family triple knock out liver progenitor cells

Project description:This serie was performed on liver progenitor isolated based on their expression of the Sca1 surface marker. It contains two independent samples from Rb family deficient liver and three independent samples from control liver, all isolated 2 weeks after Tamoxifen-induced Rb family ablation. Hematopoietic (CD45, Ter119) and endothelial (CD31) markers were used as negative selection markers to exclude blood or endothelial cells from the isolated fraction.

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Expression data from early and macroscopic HCC lesions isolated from the Rb family Triple Knock Out model (scRNA-Seq)

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Expression data from early and macroscopic HCC lesions isolated from the Rb family Triple Knock Out model (ATAC-Seq)

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Expression data from early and macroscopic HCC lesions isolated from the Rb family Triple Knock Out model (Bulk RNA-Seq)

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Transcription profiling of mouse Rb family triple knock-out (TKO) embryonic stem cells as they differentiate in vivo

Project description:The retinoblastoma cell cycle regulator pRb and the two related proteins p107 and p130 are thought to suppress cancer development both by inhibiting the G1/S transition of the cell cycle in response to growth-arrest signals and by promoting cellular differentiation. Here, we investigated the phenotype of Rb family triple knock-out (TKO) embryonic stem cells as they differentiate in vivo and in culture. Confirming the central role of the Rb gene family in cell cycle progression, TKO mouse embryos did not survive past mid-gestation and differentiating TKO cells displayed increased proliferation and cell death. However, patterning and cell fate determination were largely unaffected in these TKO embryos. Furthermore, a number of TKO cells, including in the neural lineage, were able to exit the cell cycle in G1 and terminally differentiate. This ability of Rb family TKO cells to undergo cell cycle arrest was associated with the repression of target genes for the E2F6 transcription factor, uncovering a pRb-independent control of the G1/S transition of the cell cycle. These results show that the Rb gene family is required for proper embryonic development but is not absolutely essential to induce G1 arrest and differentiation in certain lineages. Experiment Overall Design: Genome-wide gene expression was analyzed for wild-type and TKO ESC and EB cells. Three biological replicates were isolated for wild-type ESCs, TKO ESCs, and wild-type EBs, while five biological replicates were isolated for TKO EBs.

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TRANSCRIPTIONAL ACTIVATION BY E2F4 INDEPENDENT OF THE RB FAMILY

Project description:E2F transcription factors are central regulators of cell cycle progression and cell fate decisions in mammalian cells. E2F4 is a transcriptional repressor implicated in cell cycle arrest and whose repressive activity depends on its interaction with members of the RB family. E2F4 often represents the predominant E2F activity in cells. Here we show that E2F4 is important for the proliferation and the survival of mouse embryonic stem cells. In these cells, E2F4 acts in part as a transcriptional activator that promotes the expression of cell cycle genes. Importantly, this role for E2F4 is completely independent of the RB family. Accordingly, an unbiased analysis of the E2F4 interactome shows that E2F4 functionally interacts with chromatin regulators associated with gene activation in RB family-mutant cells. Taken together, our findings uncover a non-canonical role for E2F4 that reveal novel insights into the biology of rapidly dividing cell types.

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